SBML Discussion Lists RDF feed

Re: Removing reactions from SBML file

Lucian Smith — 2013-06-13T18:22:33-00:00

Yup, libsbml it totally suited to doing that. The most relevant classes here are Model (which contains the list of reactions), and Reaction itself. The URLs for the documentation for those classes are: <a href="http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_model.html" target="_blank">http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_model.html</a> and <a href="http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_reaction.html" target="_blank">http://sbml.org/Special/Software/libSBML/docs/python-api/classlibsbml_1_1_reaction.html</a> You'll probably want the 'getNumReactions' and 'getReaction' functions from Model to find the Reactions you need, then the 'removeReaction' function to remove them. My guess is you'll want to do this by SId, since the number of the reactions will change once you start removing them. (If you decide you want to keep the Reactions in there for some reason, you could also use the 'setKineticLaw' function on the Reaction itself to set it to zero, which effectively stops the reaction from happening.) Do let us know if that's not enough to work from; I can definitely say that what you want to do is totally doable with libsbml-python. -Lucian * rubbertjes <<a href="mailto:robterhorst88@gmail.com" target="_blank">robterhorst88@gmail.com</a>> [2013-06-13 18:31] writes: > > hello everyone, > > I would appreciate any help on the following problem: > I have created a tissue specific model using a published algorithm. The result of this method is a list of reactions that should still be able to potentially carry flux. I also have an SBML file of the original model, containing all other information (stoichiometric matrix, upper and lower bounds, etc.). > > I would like to load my SBML file into python and remove all the reactions that are not in my tissue specific model, and write this new model to an SBML file. If this is not possible, another option is to set the upper and lower bounds of all these reactions to 0. > so basically I have to read in my SBML file (this I managed to do), remove some specific reactions and next write out the new SBML file. the second step of removing those specific reactions is what I'm struggling with. > > I'm still pretty new to LibSBML, so I'm not even sure if this is even possible. > > Thanks in advance! > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Removing reactions from SBML file

rubbertjes — 2013-06-13T15:07:18-00:00

hello everyone, I would appreciate any help on the following problem: I have created a tissue specific model using a published algorithm. The result of this method is a list of reactions that should still be able to potentially carry flux. I also have an SBML file of the original model, containing all other information (stoichiometric matrix, upper and lower bounds, etc.). I would like to load my SBML file into python and remove all the reactions that are not in my tissue specific model, and write this new model to an SBML file. If this is not possible, another option is to set the upper and lower bounds of all these reactions to 0. so basically I have to read in my SBML file (this I managed to do), remove some specific reactions and next write out the new SBML file. the second step of removing those specific reactions is what I'm struggling with. I'm still pretty new to LibSBML, so I'm not even sure if this is even possible. Thanks in advance!

Re: libSBML user survey & prize drawing-- AND THE WINNER IS

Vrushali Inamdar — 2013-06-10T08:40:51-00:00

Hi Sarah and SBML team, Thank you so much! Regards, Vrushali Vrushali Inamdar| Team Lead <a href="mailto:vrushali_inamdar@persistent.co.in" target="_blank">vrushali_inamdar@persistent.co.in</a>| Cell: 9890509149 Persistent Systems Ltd. | Partners in Innovation | www.persistentsys.com<<a href="http://www.persistentsys.com/" target="_blank">http://www.persistentsys.com/</a>> Date: Fri, 07 Jun 2013 19:11:55 +0100 From: Sarah Keating <<a href="mailto:skeating@caltech.edu" target="_blank">skeating@caltech.edu</a>> Subject: Re: [libsbml-development] libSBML user survey & prize drawing -- AND THE WINNER IS To: LibSBML Development List <<a href="mailto:libsbml-development@caltech.edu" target="_blank">libsbml-development@caltech.edu</a>> Cc: SBML Discussion List <<a href="mailto:sbml-discuss@caltech.edu" target="_blank">sbml-discuss@caltech.edu</a>> Message-ID: <<a href="mailto:51B2226B.8020409@caltech.edu" target="_blank">51B2226B.8020409@caltech.edu</a>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Vrushali Deshpande Inamdar Congratulations ! Linda Taddeo from the SBML Team will contact you shortly to arrange the best means to get the prize to you. Thanks to everyone who took time to fill in the survey. We got some very useful feedback which we will incorporate in future releases of libSBML. Sarah and the SBML Team DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML user survey & prize drawing -- AND THE WINNER IS

Sarah Keating — 2013-06-07T18:08:27-00:00

Vrushali Deshpande Inamdar Congratulations ! Linda Taddeo from the SBML Team will contact you shortly to arrange the best means to get the prize to you. Thanks to everyone who took time to fill in the survey. We got some very useful feedback which we will incorporate in future releases of libSBML. Sarah and the SBML Team ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML user survey & prize drawing

Sarah Keating — 2013-05-28T14:41:34-00:00

Don't miss out on the prize draw for a $20 Amazon voucher !! If you have already filled in the survey, Thank you ! and you need read no further :-) If you have not, and you are a libSBML user we encourage you to do so. <a href="http://www.surveymonkey.com/s/RZ85DGR" target="_blank">http://www.surveymonkey.com/s/RZ85DGR</a> It's easy to skip bits that are not relevant to you. Even if all you fill in are the questions related to your general usage of libSBML this provides us with valuable information. This enables us to plan our time effectively for the most benefit to our users. The survey will remain open until Sunday 2nd June. Thanks again The SBML Team ================ On 13/05/2013 12:18, Sarah Keating wrote: > To libSBML-users > > We would like to gather opinions on some questions related to libSBML, > ranging from 'how we organize the code' to 'specific functionality of > certain functions'. We would be very grateful if you could spend a > couple of minutes answering some questions. Everyone who fills out the > survey will be entered into a drawing for a $20 Amazon voucher. > > We appreciate that some questions are very specific to a particular > aspect of libSBML that you may not use or be familiar with, so the > survey is designed to allow you to skip entire sections that you may not > wish or feel able to answer. > > You can answer anonymously, but to be entered into the prize drawing, we > will need your name and contact email. > > <a href="http://www.surveymonkey.com/s/RZ85DGR" target="_blank">http://www.surveymonkey.com/s/RZ85DGR</a> > > We would be grateful for any answers you feel able to give :-) . > > Thank you, > The SBML Team > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: R Bindings for libsbml

Colin Gillespie — 2013-05-16T13:34:41-00:00

Hi Frank, That works. Thanks. I'm running $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 12.04.2 LTS Release: 12.04 Codename: precise However, we use the latest version of R via: <a href="http://cran.r-project.org/bin/linux/ubuntu/" target="_blank">http://cran.r-project.org/bin/linux/ubuntu/</a> Thanks Colin On 14 May 2013 16:23, Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> wrote: > Hello Colin, > > I had to upgrade all the way to saucy (or 13.10), in order to have Ubuntu > come with R 3.0.0 by default. Is that the system you were running? On that > system it worked just fine compiling with CMake just using: > > mkdir build > cd build > cmake -DWITH_R=ON > cd src/bindings/r > make > sudo R CMD INSTALL libSBML_5.8.0_R_x86_64-pc-linux-gnu.tar.gz > > I have file online here: > > <a href="https://www.dropbox.com/s/bhgkbwruxwdjlg3/libSBML_5.8.0_R_x86_64-pc-linux-gn" target="_blank">https://www.dropbox.com/s/bhgkbwruxwdjlg3/libSBML_5.8.0_R_x86_64-pc-linux-gn</a> > u.tar.gz > > For the future we plan to have a source package as well, but we are not > there yet. > > All the best > Frank > >> -----Original Message----- >> From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- >> <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Frank T. Bergmann >> Sent: Tuesday, May 14, 2013 11:13 AM >> To: LibSBML Development List >> Subject: Re: [libsbml-development] R Bindings for libsbml >> >> Hello Colin, >> >> correct, that version was compiled against 2.15. I will upgrade my ubuntu > and >> investigate. I have no experience with the changes from 2.15 to 3.0 but > will >> let you know and hopefully be able to provide you with a binary. >> >> best >> Frank >> >> On May 13, 2013, at 3:42 PM, Colin Gillespie <<a href="mailto:colin.gillespie@ncl.ac.uk" target="_blank">colin.gillespie@ncl.ac.uk</a>> >> wrote: >> >> > Hi, >> > >> > I've recently been using the R bindings for libsbml >> > >> > <a href="http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/" target="_blank">http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/</a> >> > 64-bit/R%20interface/ >> > >> > However since upgrading R to version 3.0.0, it's no longer possible to >> > install the bindings. >> > >> > In the last few weeks, R has changed from version 2.15 to 3.0. The >> > changes were fairly minor, however all packages need to be rebuilt. So >> > I suspect to fix the binding, it just needs to be rebuilt using the >> > current version of R. >> > >> > Thanks >> > >> > Colin >> > >> > Platform: 64 bit Ubuntu >> > >> > _______________________________ >> >> 2:41pm clyde: ~/Downloads > >> > >> > $ R CMD INSTALL libSBML_5.8.0_R_x86_64-pc-linux-gnu.tar.gz >> > * installing to library '/data/ncsg3/Rpackages' >> > * installing *binary* package 'libSBML' ... >> > * DONE (libSBML) >> >> 2:41pm clyde: ~/Downloads > R >> > R> library(libSBML) >> > Error: package 'libSBML' was built before R 3.0.0: please re-install >> > it >> __________________________________________________________ >> __ >> > To manage your libsbml-development list subscription, visit >> > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> > >> > For a web interface to the libsbml-development mailing list, visit >> > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> > >> > For questions or feedback about the libsbml-development list, contact >> > <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> >> > >> >> __________________________________________________________ >> __ >> To manage your libsbml-development list subscription, visit >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> >> For a web interface to the libsbml-development mailing list, visit >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> >> For questions or feedback about the libsbml-development list, contact > sbml- >> <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: R Bindings for libsbml

fbergman — 2013-05-14T15:23:42-00:00

Hello Colin, I had to upgrade all the way to saucy (or 13.10), in order to have Ubuntu come with R 3.0.0 by default. Is that the system you were running? On that system it worked just fine compiling with CMake just using: mkdir build cd build cmake -DWITH_R=ON cd src/bindings/r make sudo R CMD INSTALL libSBML_5.8.0_R_x86_64-pc-linux-gnu.tar.gz I have file online here: <a href="https://www.dropbox.com/s/bhgkbwruxwdjlg3/libSBML_5.8.0_R_x86_64-pc-linux-gn" target="_blank">https://www.dropbox.com/s/bhgkbwruxwdjlg3/libSBML_5.8.0_R_x86_64-pc-linux-gn</a> u.tar.gz For the future we plan to have a source package as well, but we are not there yet. All the best Frank > -----Original Message----- > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Frank T. Bergmann > Sent: Tuesday, May 14, 2013 11:13 AM > To: LibSBML Development List > Subject: Re: [libsbml-development] R Bindings for libsbml > > Hello Colin, > > correct, that version was compiled against 2.15. I will upgrade my ubuntu and > investigate. I have no experience with the changes from 2.15 to 3.0 but will > let you know and hopefully be able to provide you with a binary. > > best > Frank > > On May 13, 2013, at 3:42 PM, Colin Gillespie <<a href="mailto:colin.gillespie@ncl.ac.uk" target="_blank">colin.gillespie@ncl.ac.uk</a>> > wrote: > > > Hi, > > > > I've recently been using the R bindings for libsbml > > > > <a href="http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/" target="_blank">http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/</a> > > 64-bit/R%20interface/ > > > > However since upgrading R to version 3.0.0, it's no longer possible to > > install the bindings. > > > > In the last few weeks, R has changed from version 2.15 to 3.0. The > > changes were fairly minor, however all packages need to be rebuilt. So > > I suspect to fix the binding, it just needs to be rebuilt using the > > current version of R. > > > > Thanks > > > > Colin > > > > Platform: 64 bit Ubuntu > > > > _______________________________ > >> 2:41pm clyde: ~/Downloads > > > > > $ R CMD INSTALL libSBML_5.8.0_R_x86_64-pc-linux-gnu.tar.gz > > * installing to library '/data/ncsg3/Rpackages' > > * installing *binary* package 'libSBML' ... > > * DONE (libSBML) > >> 2:41pm clyde: ~/Downloads > R > > R> library(libSBML) > > Error: package 'libSBML' was built before R 3.0.0: please re-install > > it > __________________________________________________________ > __ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, contact > > <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > > > __________________________________________________________ > __ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, contact sbml- > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: R Bindings for libsbml

fbergman — 2013-05-14T09:12:54-00:00

Hello Colin, correct, that version was compiled against 2.15. I will upgrade my ubuntu and investigate. I have no experience with the changes from 2.15 to 3.0 but will let you know and hopefully be able to provide you with a binary. best Frank On May 13, 2013, at 3:42 PM, Colin Gillespie <<a href="mailto:colin.gillespie@ncl.ac.uk" target="_blank">colin.gillespie@ncl.ac.uk</a>> wrote: > Hi, > > I've recently been using the R bindings for libsbml > > <a href="http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/64-bit/R%20interface/" target="_blank">http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/64-bit/R%20interface/</a> > > However since upgrading R to version 3.0.0, it's no longer possible to > install the bindings. > > In the last few weeks, R has changed from version 2.15 to 3.0. The > changes were fairly minor, however all packages need to be rebuilt. So > I suspect to fix the binding, it just needs to be rebuilt using the > current version of R. > > Thanks > > Colin > > Platform: 64 bit Ubuntu > > _______________________________ >> 2:41pm clyde: ~/Downloads > > > $ R CMD INSTALL libSBML_5.8.0_R_x86_64-pc-linux-gnu.tar.gz > * installing to library '/data/ncsg3/Rpackages' > * installing *binary* package 'libSBML' ... > * DONE (libSBML) >> 2:41pm clyde: ~/Downloads > R > R> library(libSBML) > Error: package 'libSBML' was built before R 3.0.0: please re-install it > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

R Bindings for libsbml

Colin Gillespie — 2013-05-13T13:42:43-00:00

Hi, I've recently been using the R bindings for libsbml <a href="http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/64-bit/R%20interface/" target="_blank">http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Linux/64-bit/R%20interface/</a> However since upgrading R to version 3.0.0, it's no longer possible to install the bindings. In the last few weeks, R has changed from version 2.15 to 3.0. The changes were fairly minor, however all packages need to be rebuilt. So I suspect to fix the binding, it just needs to be rebuilt using the current version of R. Thanks Colin Platform: 64 bit Ubuntu _______________________________ > 2:41pm clyde: ~/Downloads > $ R CMD INSTALL libSBML_5.8.0_R_x86_64-pc-linux-gnu.tar.gz * installing to library '/data/ncsg3/Rpackages' * installing *binary* package 'libSBML' ... * DONE (libSBML) > 2:41pm clyde: ~/Downloads > R R> library(libSBML) Error: package 'libSBML' was built before R 3.0.0: please re-install it ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

libSBML user survey & prize drawing

Sarah Keating — 2013-05-13T11:16:00-00:00

To libSBML-users We would like to gather opinions on some questions related to libSBML, ranging from 'how we organize the code' to 'specific functionality of certain functions'. We would be very grateful if you could spend a couple of minutes answering some questions. Everyone who fills out the survey will be entered into a drawing for a $20 Amazon voucher. We appreciate that some questions are very specific to a particular aspect of libSBML that you may not use or be familiar with, so the survey is designed to allow you to skip entire sections that you may not wish or feel able to answer. You can answer anonymously, but to be entered into the prize drawing, we will need your name and contact email. <a href="http://www.surveymonkey.com/s/RZ85DGR" target="_blank">http://www.surveymonkey.com/s/RZ85DGR</a> We would be grateful for any answers you feel able to give :-) . Thank you, The SBML Team ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML and web2py

Sebastian Thieme — 2013-04-19T13:06:19-00:00

Many many many thanks =) it works Best, Basti 2013/4/19 Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> > Indeed there is a trick to it, and the hint is given in this line: > > > ld: symbol(s) not found for architecture x86_64 > > If you look at the library: > > file > > /packages/web2py/web2py.app/Contents/Frameworks/Python.framework/Versions/2. > 5/Python > > it will show you that web2py comes only with i386 and ppc archictectures. > Since by default cmake will link only with the native architecture this has > to change. On my system I don't have an SDK installed with PPC architecture > (would have to be 10.5 I believe) I set it to i386 only. So please add: > > CMAKE_OSX_ARCHITECTURES=i386 > > In your cmake line. > > Best > Frank > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML and web2py

fbergman — 2013-04-19T11:38:06-00:00

Indeed there is a trick to it, and the hint is given in this line: > ld: symbol(s) not found for architecture x86_64 If you look at the library: file /packages/web2py/web2py.app/Contents/Frameworks/Python.framework/Versions/2. 5/Python it will show you that web2py comes only with i386 and ppc archictectures. Since by default cmake will link only with the native architecture this has to change. On my system I don't have an SDK installed with PPC architecture (would have to be 10.5 I believe) I set it to i386 only. So please add: CMAKE_OSX_ARCHITECTURES=i386 In your cmake line. Best Frank ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML and web2py

Sebastian Thieme — 2013-04-19T09:00:01-00:00

Hi =) I still run in trouble with this issue =( I did the following. 1) download of libsbml 5.6.0 2) extract everything 3) change in the libsbml folder and create a build folder 4) start cmake-gui and create a unix makefile 5) change the python path with (I use swig 2.0.2) cmake -DWITH_PYTHON=ON -DPYTHON_EXECUTABLE=/usr/bin/python2.5 -DDPYTHON_INCLUDE_DIR=/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -DPYTHON_LIBRARY=/packages/web2py/web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python ./build 6) after that I switch in the build folder and starte compilation with make everything works well Linking CXX static library libsbml-static.a [100%] Built target sbml-static Scanning dependencies of target binding_python_swig [100%] Swig Python source [100%] Built target binding_python_swig Scanning dependencies of target binding_python_lib [100%] Building CXX object src/bindings/python/CMakeFiles/binding_python_lib.dir/libsbml_wrap.cpp.o but than I get the following error ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [src/bindings/python/_libsbml.so] Error 1 make[1]: *** [src/bindings/python/CMakeFiles/binding_python_lib.dir/all] Error 2 make: *** [all] Error 2 which looks like a compatibility problem what did I wrong? Thank you very very much for your help Best, Basti 2013/4/18 Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> > Hello Sebastian, > > In order to link against it, I manually set the cmake python variables to: > > PYTHON_EXECUTABLE=/usr/bin/python2.5 > > PYTHON_INCLUDE_DIR=/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 > > PYTHON_LIBRARY=web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python > > then simply configure & compile. > > Best > Frank > > > On Apr 18, 2013, at 4:28 PM, Sebastian Thieme <<a href="mailto:thieme.sebastian@gmail.com" target="_blank">thieme.sebastian@gmail.com</a>> > wrote: > > > Thanks a lot Frank your pre-compiled version works very well =) but I > have > > some trouble by reproducing it. The first step is clear. I installed > > libsbml with bindings to python2.5 but the second step is not clear for > me. > > How do you link the binding against the Python library in > > web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python ? > > > > Thank you for your help > > > > Best Basti > > > > > > 2013/4/16 Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> > > > >> Hello Sebastian, > >> > >> it is actually be a bit tougher on OSX. Mainly for the reason, that > web2py > >> is coming with its own python version, which is not compatible with the > one > >> from the OS. So the trick is to create the bindings with python 2.5 (I > also > >> needed to use an older version of swig (i used 2.0.2) as I had issues > with > >> the wrapper linking) and linking it against the Python library in > >> web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python. > Once > >> that is done I just copied the bindings into the > >> web2py.app/Contents/Resources/site-packages/ directory, and then a view > >> like: > >> > >> {{extend 'layout.html'}} > >> {{ > >> import libsbml; > >> version = libsbml.getLibSBMLDottedVersion(); > >> }} > >>

Welcome to the LibSBML Test page</h1> > >>
You are running libSBML version: {{=version}} > >> > >> > >> worked just fine. If you like here the compiled version that I've > created > >> to test this: > >> > >> > >> > <a href="https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip" target="_blank">https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip</a> > >> > >> Please let us know whether that works for you, > >> > >> Cheers > >> Frank > >> > >> > >> > >> On Apr 16, 2013, at 2:42 PM, Sebastian Thieme < > <a href="mailto:thieme.sebastian@gmail.com" target="_blank">thieme.sebastian@gmail.com</a>> > >> wrote: > >> > >>> Hi, > >>> > >>> I am new on this list and hope that you can help me with a problem I > >> have. > >>> I work with web2py for developing a software tool which needs libSBML. > >> Now > >>> I get everything running under Linux but run in trouble if I want use > >>> Windows or OSX. The main problem I see is that web2py provide his own > >>> python version and I am not sure if this works with libSBML. I got it > >>> running under Windows by installing libSBML and copying the installed > >>> site-package into the site-package folder of web2py but this does not > >> work > >>> for OSX. Has anybody a solution for this problem? So that I can use > >> web2py > >>> with libSBML under Windows and OSX. > >>> > >>> Thanks a lot for your help. > >>> > >>> Best, > >>> > >>> Basti > >>> ____________________________________________________________ > >>> To manage your libsbml-development list subscription, visit > >>> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > >>> > >>> For a web interface to the libsbml-development mailing list, visit > >>> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > >>> > >>> For questions or feedback about the libsbml-development list, > >>> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > >>> > >> > >> ____________________________________________________________ > >> To manage your libsbml-development list subscription, visit > >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > >> > >> For a web interface to the libsbml-development mailing list, visit > >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > >> > >> For questions or feedback about the libsbml-development list, > >> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > >> > >> > > ____________________________________________________________ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, > > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML and web2py

fbergman — 2013-04-18T14:55:46-00:00

Hello Sebastian, In order to link against it, I manually set the cmake python variables to: PYTHON_EXECUTABLE=/usr/bin/python2.5 PYTHON_INCLUDE_DIR=/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 PYTHON_LIBRARY=web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python then simply configure & compile. Best Frank On Apr 18, 2013, at 4:28 PM, Sebastian Thieme <<a href="mailto:thieme.sebastian@gmail.com" target="_blank">thieme.sebastian@gmail.com</a>> wrote: > Thanks a lot Frank your pre-compiled version works very well =) but I have > some trouble by reproducing it. The first step is clear. I installed > libsbml with bindings to python2.5 but the second step is not clear for me. > How do you link the binding against the Python library in > web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python ? > > Thank you for your help > > Best Basti > > > 2013/4/16 Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> > >> Hello Sebastian, >> >> it is actually be a bit tougher on OSX. Mainly for the reason, that web2py >> is coming with its own python version, which is not compatible with the one >> from the OS. So the trick is to create the bindings with python 2.5 (I also >> needed to use an older version of swig (i used 2.0.2) as I had issues with >> the wrapper linking) and linking it against the Python library in >> web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python. Once >> that is done I just copied the bindings into the >> web2py.app/Contents/Resources/site-packages/ directory, and then a view >> like: >> >> {{extend 'layout.html'}} >> {{ >> import libsbml; >> version = libsbml.getLibSBMLDottedVersion(); >> }} >>

Welcome to the LibSBML Test page</h1> >>
You are running libSBML version: {{=version}} >> >> >> worked just fine. If you like here the compiled version that I've created >> to test this: >> >> >> <a href="https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip" target="_blank">https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip</a> >> >> Please let us know whether that works for you, >> >> Cheers >> Frank >> >> >> >> On Apr 16, 2013, at 2:42 PM, Sebastian Thieme <<a href="mailto:thieme.sebastian@gmail.com" target="_blank">thieme.sebastian@gmail.com</a>> >> wrote: >> >>> Hi, >>> >>> I am new on this list and hope that you can help me with a problem I >> have. >>> I work with web2py for developing a software tool which needs libSBML. >> Now >>> I get everything running under Linux but run in trouble if I want use >>> Windows or OSX. The main problem I see is that web2py provide his own >>> python version and I am not sure if this works with libSBML. I got it >>> running under Windows by installing libSBML and copying the installed >>> site-package into the site-package folder of web2py but this does not >> work >>> for OSX. Has anybody a solution for this problem? So that I can use >> web2py >>> with libSBML under Windows and OSX. >>> >>> Thanks a lot for your help. >>> >>> Best, >>> >>> Basti >>> ____________________________________________________________ >>> To manage your libsbml-development list subscription, visit >>> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >>> >>> For a web interface to the libsbml-development mailing list, visit >>> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >>> >>> For questions or feedback about the libsbml-development list, >>> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> >>> >> >> ____________________________________________________________ >> To manage your libsbml-development list subscription, visit >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> >> For a web interface to the libsbml-development mailing list, visit >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> >> For questions or feedback about the libsbml-development list, >> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> >> >> > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML and web2py

Sebastian Thieme — 2013-04-18T14:28:32-00:00

Thanks a lot Frank your pre-compiled version works very well =) but I have some trouble by reproducing it. The first step is clear. I installed libsbml with bindings to python2.5 but the second step is not clear for me. How do you link the binding against the Python library in web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python ? Thank you for your help Best Basti 2013/4/16 Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> > Hello Sebastian, > > it is actually be a bit tougher on OSX. Mainly for the reason, that web2py > is coming with its own python version, which is not compatible with the one > from the OS. So the trick is to create the bindings with python 2.5 (I also > needed to use an older version of swig (i used 2.0.2) as I had issues with > the wrapper linking) and linking it against the Python library in > web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python. Once > that is done I just copied the bindings into the > web2py.app/Contents/Resources/site-packages/ directory, and then a view > like: > > {{extend 'layout.html'}} > {{ > import libsbml; > version = libsbml.getLibSBMLDottedVersion(); > }} >

Welcome to the LibSBML Test page</h1> >
You are running libSBML version: {{=version}} > > > worked just fine. If you like here the compiled version that I've created > to test this: > > > <a href="https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip" target="_blank">https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip</a> > > Please let us know whether that works for you, > > Cheers > Frank > > > > On Apr 16, 2013, at 2:42 PM, Sebastian Thieme <<a href="mailto:thieme.sebastian@gmail.com" target="_blank">thieme.sebastian@gmail.com</a>> > wrote: > > > Hi, > > > > I am new on this list and hope that you can help me with a problem I > have. > > I work with web2py for developing a software tool which needs libSBML. > Now > > I get everything running under Linux but run in trouble if I want use > > Windows or OSX. The main problem I see is that web2py provide his own > > python version and I am not sure if this works with libSBML. I got it > > running under Windows by installing libSBML and copying the installed > > site-package into the site-package folder of web2py but this does not > work > > for OSX. Has anybody a solution for this problem? So that I can use > web2py > > with libSBML under Windows and OSX. > > > > Thanks a lot for your help. > > > > Best, > > > > Basti > > ____________________________________________________________ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, > > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML and web2py

fbergman — 2013-04-16T16:34:39-00:00

Hello Sebastian, it is actually be a bit tougher on OSX. Mainly for the reason, that web2py is coming with its own python version, which is not compatible with the one from the OS. So the trick is to create the bindings with python 2.5 (I also needed to use an older version of swig (i used 2.0.2) as I had issues with the wrapper linking) and linking it against the Python library in web2py.app/Contents/Frameworks/Python.framework/Versions/2.5/Python. Once that is done I just copied the bindings into the web2py.app/Contents/Resources/site-packages/ directory, and then a view like: {{extend 'layout.html'}} {{ import libsbml; version = libsbml.getLibSBMLDottedVersion(); }}

Welcome to the LibSBML Test page</h1> 
You are running libSBML version: {{=version}} worked just fine. If you like here the compiled version that I've created to test this: <a href="https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip" target="_blank">https://www.dropbox.com/s/dpjirog655voygq/2013-04-16_-_web2py_osx_libsbml_site-packages.zip</a> Please let us know whether that works for you, Cheers Frank On Apr 16, 2013, at 2:42 PM, Sebastian Thieme <<a href="mailto:thieme.sebastian@gmail.com" target="_blank">thieme.sebastian@gmail.com</a>> wrote: > Hi, > > I am new on this list and hope that you can help me with a problem I have. > I work with web2py for developing a software tool which needs libSBML. Now > I get everything running under Linux but run in trouble if I want use > Windows or OSX. The main problem I see is that web2py provide his own > python version and I am not sure if this works with libSBML. I got it > running under Windows by installing libSBML and copying the installed > site-package into the site-package folder of web2py but this does not work > for OSX. Has anybody a solution for this problem? So that I can use web2py > with libSBML under Windows and OSX. > > Thanks a lot for your help. > > Best, > > Basti > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

libSBML and web2py

Sebastian Thieme — 2013-04-16T12:42:51-00:00

Hi, I am new on this list and hope that you can help me with a problem I have. I work with web2py for developing a software tool which needs libSBML. Now I get everything running under Linux but run in trouble if I want use Windows or OSX. The main problem I see is that web2py provide his own python version and I am not sure if this works with libSBML. I got it running under Windows by installing libSBML and copying the installed site-package into the site-package folder of web2py but this does not work for OSX. Has anybody a solution for this problem? So that I can use web2py with libSBML under Windows and OSX. Thanks a lot for your help. Best, Basti ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Is libSBML threadsafe?

totte_karlsson — 2013-03-15T04:34:27-00:00

Hi, I am using libSBML in a threaded application and getting some problems. For some compilers, this code (in SBMLReader.cpp) SBMLReader::readSBMLFromString (const std::string& xml) { if (&xml == NULL) return NULL; const static string dummy_xml ("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); is not threadsafe. I heard from some newsgroups that according to C++11 standard, it 'should' be safe, but the compiler I am working with (CodeGear) seem not to handle it gracefully, and many posts on the web points to problems having local statics with most other compilers as well. Browsing trough the libSBML code, local statics are used at many places, causing crashes when using multiple threads. Currently, wrapping libSBML calls in critical sections works, but it decrease the performance significantly unfortunately. -totte

Release of libSBML-5.8.0

fbergman — 2013-02-28T11:56:59-00:00

--------------------- libSBML-5.8.0 --------------------- We are pleased to announce the release of libSBML-5.8.0 which is available for download from <a href="https://sourceforge.net/projects/sbml/files/libsbml/5.8.0/" target="_blank">https://sourceforge.net/projects/sbml/files/libsbml/5.8.0/</a> ==================================================================== Version 5.8.0 (2013-02-28) ==================================================================== STABLE RELEASE * Flux Balance Constraints - The first official version of the specification of Flux Balance Constraints is now available and thus the libSBML code for 'fbc' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'fbc' package code. The src archive containing libSBML core code will continue to be available but there will be additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. * New features - The converter that expands SBML FunctionDefinition constructs has been extended with an additional option that allows the user to specify particular objects that should not be expanded. - We have changed the behavior of the converter that converts between core Levels and Versions of SBML. This converter has a boolean option, 'strict', that determines whether an invalid model can be converted or produced. The code originally assumed that 'strict = false' refers to syntactic validity only, and so even when the flag was set to false, the converter could fail to convert a model if semantic validity was not preserved. This interpretation has been changed because people felt it was not useful; now, setting 'strict' to 'false' will always convert a model, and if there are errors related to altered semantics, the errors will be logged in the usual error log. - Documentation for the 'comp' and 'fbc' C++ API is now available. - 'comp' package updates: - The C API for comp is now available with an example of creating a model using this API. - The majority of 'comp' package validation rules have now been implemented and will be reported. Validation has also been expanded to apply validation from core and other packages (where appropriate) to any ModelDefinitions contained within a comp model. * Bug fixes - LibSBML was still writing out the deprecated, and in some cases removed, attribute 'charge' on a . This is no longer the case. - Some files caused the SBML Level and Version converter to enter an endless loop. This has been fixed. Thanks to the good folks at Persistent Systems Ltd. for reporting this. - Reading an attribute with a value of type 'double' was failing to report when a different type was encountered for the value. This has now been sorted and will be correctly logged as an error by the readSBML functions. - The Level and Version converter was in some cases running unit validation even if the user had specified that they did not require strict unit validation. This was in fact done by libSBML to allow an error to be logged; however, it has become clear that the large computational overhead of running unit validation is unecessary to merely log an error. Thus, if the user has declared that they do not require unit validity, the checks will no longer be applied. - 'layout' package-specific bug fixes: - The extension namespaces were not being correctly set. This has been fixed. - 'comp' package-specific bug fixes: - The function 'renameSIdRefs' now functions properly for SBaseRef-derived classes. * Configuration/build system changes - 'fbc' package-specific build system changes: + The GNUMake build system has not been implemented for packages. Thus, to build from src, it is necessary to use CMake. * Miscellaneous - The structure of the API documentation has been slightly overhauled to provide clearer access to relevant information. EXPERIMENTAL RELEASE * New features - 'qual' package-specific new features: - New functions getInputBySpecies(std::string) and getOutputBySpecies(std::string) have been added to the Tranisition class. These will return the first Input/Output in the relevant list that matches the qualitativeSpecies attribute value supplied as argument. * Bug fixes - 'qual' package-specific bug fixes: - As validation of packages is starting to be introduced the situation whereby a ListOfFunctionTerms can contain no FunctionTerm elements but only a DefaultTerm caused issue with the code that reports an empty ListOf object. This has been fixed. - 'render' package-specific bug fixes: - Conversion between L3 and L2 annotation was not working as expected. This has been fixed. - The interaction between layout GraphicalObjects and the render 'objectRole' attribute was removing the attribute on occasion. This has been fixed and more fully tested. ==================================================================== Please report any problems you encounter using libSBML either to the mailing list <a href="mailto:libsbml-team@caltech.edu" target="_blank">libsbml-team@caltech.edu</a> or using the issue tracker for libSBML at <a href="https://sourceforge.net/tracker/?group_id=71971&atid=942737" target="_blank">https://sourceforge.net/tracker/?group_id=71971&atid=942737</a> Thanks the LibSBMLTeam ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libsbml.parseFormula

myers — 2013-02-21T00:18:28-00:00

One issue though is the parser is only one way. If you want to go from ASTnodes to a String, you need to write your own. I've done this in Java, and I can provide you the code, if you like. Chris On Feb 20, 2013, at 3:50 PM, Lucian Smith <<a href="mailto:lpsmith@spod-central.org" target="_blank">lpsmith@spod-central.org</a>> wrote: > * kieran <<a href="mailto:kieran.smallbone@manchester.ac.uk" target="_blank">kieran.smallbone@manchester.ac.uk</a>> [2013-02-20 22:20] writes: >> Thanks Lucian, >> >> My three examples of when it works were meant to be 1e2 + 3, 1e+2+ 3, >> 1e-2+ 3, so I guess the parser gives up after the first + or -. >> >> Anyway, I'll move over to the L3 parser. Are there any things to watch >> out for that may work differently? > > Yes. "log(x)" is treated as "log10(x)" by default, instead of as a > natural log. When there's an L3 ASTNode-to-infix routine, this will be > fine, but until then, if you want to round-trip your infix to XML, you'll > need to explicitly set it to interpret that as a natural log instead. > > Also, "x + y + z" is translated as a single 'plus' ASTNode with three > children, instead of as two binary 'plus' nodes. The intent here is > eventually to match the XML more closely, and allow parsing to presever > parentheses: have "x + y + z" produce a single XML 'plus' node with three > children, while "x + (y + z)" produce nested ones. This is all in the > planning stages for now; right now, if you manipulate ASTNodes directly, > you may be surprised by the presence of more than two children of plus and > times nodes. > > Other than that, the main difference is that the new parser allows more > constructs, including binary and comparative operators ('&&', '!', '<=', > '==', etc.), and allows you to define the units for numbers ("2 mL"). > > (Oh, and there's one place where spacing counts: "(2/3)" is translated as > a single rational number, while "(2 / 3)" is translated as a 'divide' > node.) > > In general, the documentation can be found at: > > <a href="http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html" target="_blank">http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html</a> > > -Lucian > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libsbml.parseFormula

Lucian Smith — 2013-02-20T22:50:19-00:00

* kieran <<a href="mailto:kieran.smallbone@manchester.ac.uk" target="_blank">kieran.smallbone@manchester.ac.uk</a>> [2013-02-20 22:20] writes: > Thanks Lucian, > > My three examples of when it works were meant to be 1e2 + 3, 1e+2+ 3, > 1e-2+ 3, so I guess the parser gives up after the first + or -. > > Anyway, I'll move over to the L3 parser. Are there any things to watch > out for that may work differently? Yes. "log(x)" is treated as "log10(x)" by default, instead of as a natural log. When there's an L3 ASTNode-to-infix routine, this will be fine, but until then, if you want to round-trip your infix to XML, you'll need to explicitly set it to interpret that as a natural log instead. Also, "x + y + z" is translated as a single 'plus' ASTNode with three children, instead of as two binary 'plus' nodes. The intent here is eventually to match the XML more closely, and allow parsing to presever parentheses: have "x + y + z" produce a single XML 'plus' node with three children, while "x + (y + z)" produce nested ones. This is all in the planning stages for now; right now, if you manipulate ASTNodes directly, you may be surprised by the presence of more than two children of plus and times nodes. Other than that, the main difference is that the new parser allows more constructs, including binary and comparative operators ('&&', '!', '<=', '==', etc.), and allows you to define the units for numbers ("2 mL"). (Oh, and there's one place where spacing counts: "(2/3)" is translated as a single rational number, while "(2 / 3)" is translated as a 'divide' node.) In general, the documentation can be found at: <a href="http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html" target="_blank">http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html</a> -Lucian ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libsbml.parseFormula

kieransmallbone — 2013-02-20T22:18:52-00:00

Thanks Lucian, My three examples of when it works were meant to be 1e2 + 3, 1e+2+ 3, 1e-2+ 3, so I guess the parser gives up after the first + or -. Anyway, I'll move over to the L3 parser. Are there any things to watch out for that may work differently? Cheers, Kieran On 20/02/2013 21:53, Lucian Smith wrote: > * kieran <<a href="mailto:kieran.smallbone@manchester.ac.uk" target="_blank">kieran.smallbone@manchester.ac.uk</a>> [2013-02-20 13:06] writes: >> I think there's something a bit wonky with parseFormula, in python at >> least. It doesn't seem able to cope with the strings >> >> 1e2+ 3 >> 1e2- 3 >> 1E2+ 3 >> 1E2- 3 >> >> but works fine with >> >> 1e2 + 3 >> 1e+2 + 3 >> 1e-2 + 3 >> >> I guess, in general, spacing plays no role in formula parsing? > > In general, yes, but as you have noticed, there is indeed a problem here > (I've confirmed it's present in the base libsbml code, not just the python > bindings). The trailing '+' and '-' on e-formatted numbers is silently > being ignored, probably because there's one routine that lumps digits, > decimals, e's, +'s, and -'s together, and another routine that figures out > what that number's value is. > > The level 3 parser (SBML_parseL3Formula) will indeed parse all of the > above correctly. I will file a bug for the former, but I'm not sure if it > will be able to be fixed; the original parser is old machine-generated > code and I dont' know if that machine can still be found. Hopefully, the > L3 parser will work for you for now if the issue is important. > > -Lucian -- kieran smallbone <a href="mailto:kieran.smallbone@manchester.ac.uk" target="_blank">kieran.smallbone@manchester.ac.uk</a> <a href="http://u003f.com/" target="_blank">http://u003f.com/</a> manchester centre for integrative systems biology manchester interdisciplinary biocentre 131 princess street manchester m1 7dn. uk ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libsbml.parseFormula

Lucian Smith — 2013-02-20T21:53:44-00:00

* kieran <<a href="mailto:kieran.smallbone@manchester.ac.uk" target="_blank">kieran.smallbone@manchester.ac.uk</a>> [2013-02-20 13:06] writes: > I think there's something a bit wonky with parseFormula, in python at > least. It doesn't seem able to cope with the strings > > 1e2+ 3 > 1e2- 3 > 1E2+ 3 > 1E2- 3 > > but works fine with > > 1e2 + 3 > 1e+2 + 3 > 1e-2 + 3 > > I guess, in general, spacing plays no role in formula parsing? In general, yes, but as you have noticed, there is indeed a problem here (I've confirmed it's present in the base libsbml code, not just the python bindings). The trailing '+' and '-' on e-formatted numbers is silently being ignored, probably because there's one routine that lumps digits, decimals, e's, +'s, and -'s together, and another routine that figures out what that number's value is. The level 3 parser (SBML_parseL3Formula) will indeed parse all of the above correctly. I will file a bug for the former, but I'm not sure if it will be able to be fixed; the original parser is old machine-generated code and I dont' know if that machine can still be found. Hopefully, the L3 parser will work for you for now if the issue is important. -Lucian ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

libsbml.parseFormula

kieransmallbone — 2013-02-20T13:05:39-00:00

I think there's something a bit wonky with parseFormula, in python at least. It doesn't seem able to cope with the strings 1e2+ 3 1e2- 3 1E2+ 3 1E2- 3 but works fine with 1e2 + 3 1e+2 + 3 1e-2 + 3 I guess, in general, spacing plays no role in formula parsing? Cheers, Kieran -- kieran smallbone <a href="mailto:kieran.smallbone@manchester.ac.uk" target="_blank">kieran.smallbone@manchester.ac.uk</a> <a href="http://u003f.com/" target="_blank">http://u003f.com/</a> manchester centre for integrative systems biology manchester interdisciplinary biocentre 131 princess street manchester m1 7dn. uk ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Release of libSBML-5.7.0

Sarah Keating — 2013-01-14T10:39:22-00:00

--------------------- libSBML-5.7.0 --------------------- We are pleased to announce the release of libSBML-5.7.0 which is available for download from <a href="https://sourceforge.net/projects/sbml/files/libsbml/5.7.0/" target="_blank">https://sourceforge.net/projects/sbml/files/libsbml/5.7.0/</a> ==================================================================== Version 5.7.0 (2013-01-14) ==================================================================== STABLE RELEASE * Hierarchical Model Composition - The first official version of the specification of Hierarchical Model Composition is now available and thus the libSBML code for 'comp' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'comp' package code. The src archive containing libSBML core code will continue to be available but there will be additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. Known limitations of the 'comp' code: + Documentation has not yet been integrated into the libsbml documentation. + Whilst the majority of validation rules have been implemented, some will report the schema error id rather than the specific comp validation rule id. The more involved rules involving circular dependencies and in-depth referencing have not been implemented. Validation of ModelDefinitions is implemented with respect to comp validation, but not with respect to core validation. + There is no C API for interacting directly with comp objects. However the C API for reading and validation will apply to the 'comp' package and flattening can be accessed via the converter C API to call the CompFlatteningConverter. * New features - Convenience functions have been added to the SBMLExtensionRegistry class to facilitate enabling/disabling packages using just the package name. For example: disablePackage(const std::string& package); enablePackage(const std::string& package); - Previously the setNotes function accepting a string as argument expected the string to contain the appropriate XHTML tags and would not set the value of the element to a string that did not meet this requirement. The functionality of the setNotes(const std::string&) function has been extended to allow a user to add an optional boolean argument addXHTMLMarkup. When the value of this argument is 'true' the function will accept a string; wrap it with the XHTML

tag and set the element to this. - A C API for use with the converters has been added. Examples of using the converter API are available in all supported languages. - 'comp' package - Access to the flattening routines has been restricted to the CompFlatteningConverter. This allows options to be specified by the user regarding ignoring other packages and whether to produce a document with no comp namespace or a document with the comp namespace but the required attribute set to 'false'. - Validation has been implemented (see note above). This is called via the checkConsistency function within core libSBML; which now accesses a checkConsistency function in the comp plugin. There are two categories of validation: LIBSBML_CAT_GENERAL_CONSISTENCY and LIBSBML_CAT_IDENTIFIER_CONSISTENCY which are enables or disable via the setConsistencyChecks() function on the SBMLDocument (in libSBML core). - The API for resolving external models has been updated to use a registry of resolvers. This facilitates the addition of user specific resolvers. * Bug fixes - The number of arguments expected by a piecewise function was incorrectly assumed to be two. However, a piecewise function can have a single argument. This has been corrected. - Validation of SBML Level 3 was issuing a general warning about missing required attributes but failing to identify which attribute had caused the error to be reported. This has been corrected. Thanks to Nicolas Rodriguez for pointing this out. - Validation was failing to report the incorrect use of a function call if the lambda function usesd expected no arguments. This has been fixed. - The L3Parser was not dealing with the sqrt function correctly. This has been sorted. - 'comp' package-specific bug fixes: + SBOTerms were not being correctly dealt with when they occured on a Port element. This has been corrected. Thanks to Chris Myers for reporting this. * Configuration/build system changes - Building the MATLAB binding for libSBML can be problematic due to the need to identify and use the MATLAB mex compiler. When MATLAB is being accessed over a network this can result in misleading error messages. The build system has been improved to halt compilation if the mex compiler is not available and to give a clearer error message as to how to proceed. - The build system has been updated to facilitate use with the Mac OS X 10.8 operating system (Mountain Lion). - 'comp' package-specific build system changes: + The GNUMake build system has not been implemented for packages. Thus, to build from src, it is necessary to use CMake. * Miscellaneous - It was reported that gcc 4.7 found the various definitions of isnan used within some parts of libSBML to be problematic. This problem has been addressed and there are now functions util_isNaN and util_isFinite in the util file that are used throughout libsbml. Thanks to Totte Karlsson for reporting this. - Where test files compare double values the comparisons have been unified to use the util_isEqual(double, double) function and thus avoid inaccurate results that can be machine dependent. - This NEWS.txt file has reduced in size with NEWS dating from prior to libSBML-5 now saved as an OLD_NEWS.txt file. EXPERIMENTAL RELEASE * New features - 'Qual' package: - The package specification redefined whether some attributes or elements were required; the code has been updated appropriately. - 'Fbc' package: - The package specification added some optional attributes and deprecated the use of strict less than or greater than; the code has been updated appropriately. * Bug fixes - 'Render' package: - In some cases the code was failing to add expected attributes to particular elements. This has been corrected. ======================================================= Please report any problems you encounter using libSBML either to the mailing list <a href="mailto:libsbml-team@caltech.edu" target="_blank">libsbml-team@caltech.edu</a> or using the issue tracker for libSBML at <a href="https://sourceforge.net/tracker/?group_id=71971&atid=942737" target="_blank">https://sourceforge.net/tracker/?group_id=71971&atid=942737</a> Thanks LibSBMLTeam ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: SBML to R/Matlab differential equation

rodrigue — 2012-11-07T12:44:08-00:00

On 07/11/12 12:00, Kai Wohlfahrt wrote: > Hi all, > > I would like to know if there is currently support for going from an SBML > document with appropriate kinetic laws to a differential equation function > (in the style of R or matlab) that can then be solved. There seem to be > some references to software doing this, but I can't find it anywhere in the > actual API or bindings. > > If this is not available, I would be very interested in writing such a > package for R, as this would be very useful to me. If anybody could give me > some hints as to which parts of the API and bindings are available for > this, or any previous work that does something similar, that would be very > helpful. > > Regards, > Kai > > > For those unfamiliar with the concept, in R, this function would look like > (where species 2 is produced from 1): > > dy_dt<- function(t, y, p){ > # y stores current concentrations or values, t is the time, and p is a > list of optional parameters. > dt<- rep(NA, length(y)) > > dt[1]<- -p["k_1"] * y[1] > dt[2]<- p["k_1"] * y[1] > > return(list(dt)) > } You could have a look at the existing converter available in SBFC (<a href="http://sbfc.sourceforge.net/" target="_blank">http://sbfc.sourceforge.net/</a>). SBML to Octave/Matlab or SBML to XPP would have most of the needed code to show you what to check and which methods to use. Nico ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML to R/Matlab differential equation

Kai Wohlfahrt — 2012-11-07T12:00:07-00:00

Hi all, I would like to know if there is currently support for going from an SBML document with appropriate kinetic laws to a differential equation function (in the style of R or matlab) that can then be solved. There seem to be some references to software doing this, but I can't find it anywhere in the actual API or bindings. If this is not available, I would be very interested in writing such a package for R, as this would be very useful to me. If anybody could give me some hints as to which parts of the API and bindings are available for this, or any previous work that does something similar, that would be very helpful. Regards, Kai For those unfamiliar with the concept, in R, this function would look like (where species 2 is produced from 1): dy_dt <- function(t, y, p){ # y stores current concentrations or values, t is the time, and p is a list of optional parameters. dt <- rep(NA, length(y)) dt[1] <- -p["k_1"] * y[1] dt[2] <- p["k_1"] * y[1] return(list(dt)) } ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: R bindings + CMake error: missing folder

Kai Wohlfahrt — 2012-11-06T22:16:14-00:00

Well, the attached ebuild should work for any gentoo users out there. I'm missing the relevant use-variables for the experimental package, so it's probably building a whole lot of unnecessary additions (display, render, etc), but I don't have much time to implement it. Let me know if you have any other problems though - as with my last one, only the python and R additions are tested since I do not use any of the other bindings. Kai On Tue, Nov 6, 2012 at 12:51 PM, Kai Wohlfahrt <<a href="mailto:kjw53@cam.ac.uk" target="_blank">kjw53@cam.ac.uk</a>> wrote: > Great, this builds correctly now (sorry for the delay, turns out my > version of R was also too old). I would also like to create a gentoo ebuild > (install script), and it doesn't seem like the generated R files are > installed by "make install", is this expected? What additional steps do I > need to add? > > I'll post the ebuild up here as soon as it's finished :) > > Thanks, > Kai > > > On Mon, Nov 5, 2012 at 5:10 PM, Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>>wrote: > >> Hello Kai, >> >> I'm sorry for this. There was a bundling error that caused the source >> archive to be built with the r examples, but not the swig wrapping code. >> Could you please download the 'experimental' archive. That will include >> them. The only thing experimental in the bundle are support for the Level >> 3 >> packages, which you can enable / disable individually. >> >> Sorry for the inconvenience, the stable source archive will include them >> for >> the next release. >> >> Best >> Frank >> >> > -----Original Message----- >> > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- >> > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Kai Wohlfahrt >> > Sent: Monday, November 5, 2012 6:07 PM >> > To: libSBML Development >> > Subject: [libsbml-development] R bindings + CMake error: missing folder >> > >> > Hi all, >> > >> > I'm trying to build libSBML (5.6.0) on linux with the R bindings. >> Building >> > without them works fine, however as soon as I tick the box for 'WITH_R' >> I >> get >> > the error >> > >> > 'CMake Error at src/bindings/CMakeLists.txt:91 (add_subdirectory): >> > add_subdirectory given source "r" which is not an existing >> directory.' >> > >> > Creating the directory in "src/bindings" suppresses the warning, but >> also >> > doesn't seem to build any of the relevant bindings. Does anybody know >> how >> > to fix this? >> > >> > Thanks, >> > Kai >> > ____________________________________________________________ >> > To manage your libsbml-development list subscription, visit >> > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> > >> > For a web interface to the libsbml-development mailing list, visit >> > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> > >> > For questions or feedback about the libsbml-development list, contact >> sbml- >> > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> >> >> >> ____________________________________________________________ >> To manage your libsbml-development list subscription, visit >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> >> For a web interface to the libsbml-development mailing list, visit >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> >> For questions or feedback about the libsbml-development list, >> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> >> >> >

Re: R bindings + CMake error: missing folder

Kai Wohlfahrt — 2012-11-06T12:51:44-00:00

Great, this builds correctly now (sorry for the delay, turns out my version of R was also too old). I would also like to create a gentoo ebuild (install script), and it doesn't seem like the generated R files are installed by "make install", is this expected? What additional steps do I need to add? I'll post the ebuild up here as soon as it's finished :) Thanks, Kai On Mon, Nov 5, 2012 at 5:10 PM, Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>>wrote: > Hello Kai, > > I'm sorry for this. There was a bundling error that caused the source > archive to be built with the r examples, but not the swig wrapping code. > Could you please download the 'experimental' archive. That will include > them. The only thing experimental in the bundle are support for the Level 3 > packages, which you can enable / disable individually. > > Sorry for the inconvenience, the stable source archive will include them > for > the next release. > > Best > Frank > > > -----Original Message----- > > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Kai Wohlfahrt > > Sent: Monday, November 5, 2012 6:07 PM > > To: libSBML Development > > Subject: [libsbml-development] R bindings + CMake error: missing folder > > > > Hi all, > > > > I'm trying to build libSBML (5.6.0) on linux with the R bindings. > Building > > without them works fine, however as soon as I tick the box for 'WITH_R' I > get > > the error > > > > 'CMake Error at src/bindings/CMakeLists.txt:91 (add_subdirectory): > > add_subdirectory given source "r" which is not an existing > directory.' > > > > Creating the directory in "src/bindings" suppresses the warning, but also > > doesn't seem to build any of the relevant bindings. Does anybody know how > > to fix this? > > > > Thanks, > > Kai > > ____________________________________________________________ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, contact > sbml- > > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: R bindings + CMake error: missing folder

fbergman — 2012-11-05T17:10:40-00:00

Hello Kai, I'm sorry for this. There was a bundling error that caused the source archive to be built with the r examples, but not the swig wrapping code. Could you please download the 'experimental' archive. That will include them. The only thing experimental in the bundle are support for the Level 3 packages, which you can enable / disable individually. Sorry for the inconvenience, the stable source archive will include them for the next release. Best Frank > -----Original Message----- > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Kai Wohlfahrt > Sent: Monday, November 5, 2012 6:07 PM > To: libSBML Development > Subject: [libsbml-development] R bindings + CMake error: missing folder > > Hi all, > > I'm trying to build libSBML (5.6.0) on linux with the R bindings. Building > without them works fine, however as soon as I tick the box for 'WITH_R' I get > the error > > 'CMake Error at src/bindings/CMakeLists.txt:91 (add_subdirectory): > add_subdirectory given source "r" which is not an existing directory.' > > Creating the directory in "src/bindings" suppresses the warning, but also > doesn't seem to build any of the relevant bindings. Does anybody know how > to fix this? > > Thanks, > Kai > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, contact sbml- > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

R bindings + CMake error: missing folder

Kai Wohlfahrt — 2012-11-05T17:06:56-00:00

Hi all, I'm trying to build libSBML (5.6.0) on linux with the R bindings. Building without them works fine, however as soon as I tick the box for 'WITH_R' I get the error 'CMake Error at src/bindings/CMakeLists.txt:91 (add_subdirectory): add_subdirectory given source "r" which is not an existing directory.' Creating the directory in "src/bindings" suppresses the warning, but also doesn't seem to build any of the relevant bindings. Does anybody know how to fix this? Thanks, Kai ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Calling libSBML from a Browser

fbergman — 2012-10-22T14:28:15-00:00

Sorry about that. It started this morning, when I read the suggestion on libsbml-devel, that it would be very difficult to use libsbml with tomcat, and people could simply use JSBML. True enough due to the particularities of java you have to take some things into account when doing this. Then I remembered that we had encountered this issue in the past, when I did those experiments (back in early 2011). Back then I mailed those documents around and we discussed them during a TC. It was then decided that we modify the example and put it into the help file, and (having searched for it now) there people would find it under: <a href="http://sbml.org/Software/libSBML/docs/java-api/libsbml-java-misc.html" target="_blank">http://sbml.org/Software/libSBML/docs/java-api/libsbml-java-misc.html</a> I just wanted a place for the files and did not see the right place to put them on sbml.org. That being said it would be a great place for it to live! Frank > -----Original Message----- > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Michael Hucka > Sent: Montag, 22. Oktober 2012 15:12 > To: LibSBML Development List > Subject: Re: [libsbml-development] Calling libSBML from a Browser > > Frank, this looks great and useful. However, I'm puzzled about why this is not > written and made available as an SBML Team item. It's the sort of thing that > we should make available from sbml.org (perhaps creating a new area for > tutorials). > > MH > > On Mon, 22 Oct 2012 08:37:39 +0200, Frank T. Bergmann wrote: > > I'm sorry that it caused trouble to run libSBML from Tomcat. After > > hearing this issue some time ago, I spend quite some time investigating the > issue. > > I've put together a brief tutorial that should make it easy for you to > > get started. > > > > <a href="http://frank-fbergmann.blogspot.de/2012/10/using-libsbml-from-" target="_blank">http://frank-fbergmann.blogspot.de/2012/10/using-libsbml-from-</a> > tomcat.h > > tml > > > > All the best > > Frank > > > >> -----Original Message----- > >> From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > >> <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Neil Swainston > >> Sent: Sonntag, 21. Oktober 2012 18:47 > >> To: <a href="mailto:libsbml-development@caltech.edu" target="_blank">libsbml-development@caltech.edu</a> > >> Subject: Re: [libsbml-development] Calling libSBML from a Browser > >> > >> > >> Hi Herbert, > >> > >> I've used the Java bindings on Tomcat in the past. Can be a bit of a > >> pain, > > linking > >> to the native libraries but doable. > >> > >> Depending upon what you're doing, could you use JSBML? Pure Java, so > >> one jar in Tomcat and you're done. > >> > >> Cheers, > >> > >> Neil. > >> ____________________________________________________________ > >> To manage your libsbml-development list subscription, visit > >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > >> > >> For a web interface to the libsbml-development mailing list, visit > >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > >> > >> For questions or feedback about the libsbml-development list, contact > > sbml- > >> <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> > > > > > > ____________________________________________________________ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, contact > > <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, contact sbml- > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Calling libSBML from a Browser

Mike Hucka — 2012-10-22T13:12:22-00:00

Frank, this looks great and useful. However, I'm puzzled about why this is not written and made available as an SBML Team item. It's the sort of thing that we should make available from sbml.org (perhaps creating a new area for tutorials). MH On Mon, 22 Oct 2012 08:37:39 +0200, Frank T. Bergmann wrote: > I'm sorry that it caused trouble to run libSBML from Tomcat. After hearing > this issue some time ago, I spend quite some time investigating the issue. > I've put together a brief tutorial that should make it easy for you to get > started. > > <a href="http://frank-fbergmann.blogspot.de/2012/10/using-libsbml-from-tomcat.html" target="_blank">http://frank-fbergmann.blogspot.de/2012/10/using-libsbml-from-tomcat.html</a> > > All the best > Frank > >> -----Original Message----- >> From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- >> <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Neil Swainston >> Sent: Sonntag, 21. Oktober 2012 18:47 >> To: <a href="mailto:libsbml-development@caltech.edu" target="_blank">libsbml-development@caltech.edu</a> >> Subject: Re: [libsbml-development] Calling libSBML from a Browser >> >> >> Hi Herbert, >> >> I've used the Java bindings on Tomcat in the past. Can be a bit of a pain, > linking >> to the native libraries but doable. >> >> Depending upon what you're doing, could you use JSBML? Pure Java, so one >> jar in Tomcat and you're done. >> >> Cheers, >> >> Neil. >> ____________________________________________________________ >> To manage your libsbml-development list subscription, visit >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> >> For a web interface to the libsbml-development mailing list, visit >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> >> For questions or feedback about the libsbml-development list, contact > sbml- >> <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Calling libSBML from a Browser

fbergman — 2012-10-22T06:37:39-00:00

I'm sorry that it caused trouble to run libSBML from Tomcat. After hearing this issue some time ago, I spend quite some time investigating the issue. I've put together a brief tutorial that should make it easy for you to get started. <a href="http://frank-fbergmann.blogspot.de/2012/10/using-libsbml-from-tomcat.html" target="_blank">http://frank-fbergmann.blogspot.de/2012/10/using-libsbml-from-tomcat.html</a> All the best Frank > -----Original Message----- > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Neil Swainston > Sent: Sonntag, 21. Oktober 2012 18:47 > To: <a href="mailto:libsbml-development@caltech.edu" target="_blank">libsbml-development@caltech.edu</a> > Subject: Re: [libsbml-development] Calling libSBML from a Browser > > > Hi Herbert, > > I've used the Java bindings on Tomcat in the past. Can be a bit of a pain, linking > to the native libraries but doable. > > Depending upon what you're doing, could you use JSBML? Pure Java, so one > jar in Tomcat and you're done. > > Cheers, > > Neil. > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, contact sbml- > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Need for PHP extension? was [Calling libSBML from a Browser]

b.g.olivier — 2012-10-19T12:39:30-00:00

On 19-10-2012 14:20, Stefan Hoops wrote: > Hello Frank, > > I was more joking than asking for it. But if I would develop a web > application I would choose between the > django (python): <a href="https://www.djangoproject.com/" target="_blank">https://www.djangoproject.com/</a> > or > symfony (php): <a href="http://www.symfony-project.org/" target="_blank">http://www.symfony-project.org/</a> > > frameworks. Thus php bindings would be appreciated. +1 from me, this is potentially very interesting. Brett > Thanks, > Stefan > > > On Fri, 19 Oct 2012 13:49:19 +0200 > "Frank T. Bergmann" <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> wrote: > >>> From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- >>> <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Stefan Hoops >>> [...] The only major web programming language missing would be >>> php :) >>> >> If there is a need it would be possible to also cover PHP. It is just >> that so far the SBML Team has not received requests for a PHP >> extension. Is there such a need? >> >> Thanks >> Frank >> >> ____________________________________________________________ >> To manage your libsbml-development list subscription, visit >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> >> For a web interface to the libsbml-development mailing list, visit >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> >> For questions or feedback about the libsbml-development list, >> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> >> > > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Calling libSBML from a Browser

Neil Swainston — 2012-10-19T12:32:56-00:00

Hi Herbert, I've used the Java bindings on Tomcat in the past. Can be a bit of a pain, linking to the native libraries but doable. Depending upon what you're doing, could you use JSBML? Pure Java, so one jar in Tomcat and you're done. Cheers, Neil.

Re: Need for PHP extension? was [Calling libSBML from a Browser]

Stefan.Hoops — 2012-10-19T12:20:03-00:00

Hello Frank, I was more joking than asking for it. But if I would develop a web application I would choose between the django (python): <a href="https://www.djangoproject.com/" target="_blank">https://www.djangoproject.com/</a> or symfony (php): <a href="http://www.symfony-project.org/" target="_blank">http://www.symfony-project.org/</a> frameworks. Thus php bindings would be appreciated. Thanks, Stefan On Fri, 19 Oct 2012 13:49:19 +0200 "Frank T. Bergmann" <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>> wrote: > > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Stefan Hoops > > [...] The only major web programming language missing would be > > php :) > > > > If there is a need it would be possible to also cover PHP. It is just > that so far the SBML Team has not received requests for a PHP > extension. Is there such a need? > > Thanks > Frank > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > -- Stefan Hoops, Ph.D. Senior Project Associate Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics Facility II Blacksburg, Va 24061, USA Phone: (540) 231-1799 Fax: (540) 231-2606 Email: <a href="mailto:shoops@vbi.vt.edu" target="_blank">shoops@vbi.vt.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Need for PHP extension? was [Calling libSBML from a Browser]

fbergman — 2012-10-19T11:49:19-00:00

> From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Stefan Hoops > [...] The only major web programming language missing would be php :) > If there is a need it would be possible to also cover PHP. It is just that so far the SBML Team has not received requests for a PHP extension. Is there such a need? Thanks Frank ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Calling libSBML from a Browser

hsauro — 2012-10-19T01:25:04-00:00

Thanks for your reply. On the server side I assume you're suggesting setting up libsbml as a web service on a server? What language binds do we have other than Java I guess that could work on the server side? What about on the client side, how might that work? Herbert >From your post it is not immediately clear to me whether you want >to call it on the server side (Webserver) or on the client side >(Browser) since you talk both about browser and ASP. On the server >side you have all the different language bindings available. The >only majorweb programming language missing would be php <img src="images/smiley_icons/icon_smile.gif" border=0 alt="Smile"> >Thanks, >Stefan

Re: Calling libSBML from a Browser

Stefan.Hoops — 2012-10-19T00:50:29-00:00

Hello Herbert, >From your post it is not immediately clear to me whether you want to call it on the server side (Webserver) or on the client side (Browser) since you talk both about browser and ASP. On the server side you have all the different language bindings available. The only major web programming language missing would be php :) Thanks, Stefan On Thu, 18 Oct 2012 17:38:05 -0700 (PDT) hsauro <<a href="mailto:hsauro@kgi.edu" target="_blank">hsauro@kgi.edu</a>> wrote: > > Anyone know what mechanisms exist for calling libSBML from within a > browser? I know Frank Bergmann used a combination of ASP and C# but > is there any other way? eg we were looking at Native Client from > Google but that only runs on Chrome but biggest problem is that the > user has to activate the functionality to make it work. > > Herbert Sauro > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > -- Stefan Hoops, Ph.D. Senior Project Associate Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics Facility II Blacksburg, Va 24061, USA Phone: (540) 231-1799 Fax: (540) 231-2606 Email: <a href="mailto:shoops@vbi.vt.edu" target="_blank">shoops@vbi.vt.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Calling libSBML from a Browser

hsauro — 2012-10-18T18:59:17-00:00

Anyone know what mechanisms exist for calling libSBML from within a browser? I know Frank Bergmann used a combination of ASP and C# but is there any other way? eg we were looking at Native Client from Google but that only runs on Chrome but biggest problem is that the user has to activate the functionality to make it work. Herbert Sauro

Re: Possible bug in SBML_formulaToString

Lucian Smith — 2012-10-08T17:17:27-00:00

* hsauro <<a href="mailto:hsauro@kgi.edu" target="_blank">hsauro@kgi.edu</a>> [2012-10-08 17:30] writes: > > Thanks for the reply. One question, how to I set the L3P_PARSE_LOG_AS_LN option? I looked up the docs but wasn't quite sure what to do? Do I have to recompile libSBML? No, no need to recompile anything; it's just a change in how you call the L3Parser. See: <a href="http://sbml.org/Special/Software/libSBML/docs/cpp-api/_l3_parser_8h.html#a77c72a78afff728a6c569790338f2085" target="_blank">http://sbml.org/Special/Software/libSBML/docs/cpp-api/_l3_parser_8h.html#a77c72a78afff728a6c569790338f2085</a> and <a href="http://sbml.org/Special/Software/libSBML/docs/cpp-api/class_l3_parser_settings.html" target="_blank">http://sbml.org/Special/Software/libSBML/docs/cpp-api/class_l3_parser_settings.html</a> You can change how the string "log(x)" is parsed by providing an 'L3ParserSettings' object. Here's how it would work in C++: string formula = "log(x)"; L3ParserSettings l3ps; l3ps.setParseLog(L3P_PARSE_LOG_AS_LN); ASTNode* rootnode = SBML_parseL3FormulaWithSettings(formula.c_str(), &l3ps); The L3ParserSettings object can also be used to change whether minuses are collapsed ("--x" becomes just "x"); whether units attached to numeric values are parsed; whether 'avogadro' is parsed as a csymbol or not; and to set a Model object the parser will check to see if there are symbols there that should override the default built-in interpretation of any string: if you define your own 'sin' function and your own 'pi' variable, telling the L3ParserSettings object about it will cause "sin(pi)" to be translated as sin </ci> pi </ci> </apply> instead of </apply> -Lucian ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Possible bug in SBML_formulaToString

Sarah Keating — 2012-10-07T12:10:54-00:00

Hi Herbert Just to give you a historical explanation for libSBML's behaviour and a word of warning about using the SBML_formulaToString function. This function was originally written SOLELY to deal with converting files between SBML L2 (with MathML) and SBML L1 (with infix). Its functionality therefore produces infix formula that are compliant with the SBML L1 specification. In L1 log(x) was considered to be the natural log. Thus when the SBML_formulaToString function encounters MathML with ln it "translates" it to the SBML L1 equivalent which is log. You are not the first person to report this as confusing; but whilst libSBML supports l2 to L1 conversion we need this function to work as it does :-) We have recognised that people find this (and its converse SBML_parseFormula) useful functions for situations that are entirely unrelated to SBML L2/L1 issues. Thus we are working on providing this functionality that is not restricted by these issues and that will be customisable to an extent. As Lucian points out to date we have SBML_parseL3Formula which takes infix and returns ASTNodes (the libSBML internal representation of the math). We do not as yet have the math to infix version but are working on this. Sarah ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Possible bug in SBML_formulaToString

hsauro — 2012-10-04T16:07:36-00:00

Thanks for the reply. One question, how to I set the L3P_PARSE_LOG_AS_LN option? I looked up the docs but wasn't quite sure what to do? Do I have to recompile libSBML?

Re: Possible bug in SBML_formulaToString

Lucian Smith — 2012-10-04T04:31:21-00:00

This is an option you can set in the L3 infix-to-MathML parser: whether 'log' turns into 'ln', 'log10', or is an error. However, there is no such option for the mathML-to-infix translator, because a new one has yet to be written. So to keep them compatible, use the 'L3P_PARSE_LOG_AS_LN' option. Then, you'll translate the string "ln(3)" to the MathML ""; The mathML "" will translate to the string "log(3)", but that will in turn translate to "" again, making it round-trip compatible. Once we get the new mathML-to-infix translator released, you'll be able to set 'log' to be whatever you want, and it won't produce the infix 'log(x)' at all: the only written infix will be "ln(x)", "log10(x)", and "log(base, x)" -Lucian * hsauro <<a href="mailto:hsauro@kgi.edu" target="_blank">hsauro@kgi.edu</a>> [2012-10-04 01:38] writes: > > Someone reported to me that when they saved a model using ln() and loaded the model back in, the ln() turned into log(). An example assignment rule where this happens is: > > > > > > > Node1 > </ci> > </apply> > </math> > </assignmentRule> > > I am using libSBML 5.5 calling > > astTree = readMathMLFromString (mathML); > result = SBML_formulaToString (astTree); > > with mathml equal to: > > <?xml version="1.0" encoding="UTF-8"?> > > Node1 </ci> </apply> > </math> > > result equals: 'log(Node1)' instead of 'ln(Node1)' > > Are these the right functions to use, or I am doing something else wrong? > > Current workaround is to use 2.303*log() instead of ln(). > > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Possible bug in SBML_formulaToString

hsauro — 2012-10-03T23:53:48-00:00

Someone reported to me that when they saved a model using ln() and loaded the model back in, the ln() turned into log(). An example assignment rule where this happens is: Node1 </ci> </apply> </math> </assignmentRule> I am using libSBML 5.5 calling astTree = readMathMLFromString (mathML); result = SBML_formulaToString (astTree); with mathml equal to: <?xml version="1.0" encoding="UTF-8"?> Node1 </ci> </apply> </math> result equals: 'log(Node1)' instead of 'ln(Node1)' Are these the right functions to use, or I am doing something else wrong? Current workaround is to use 2.303*log() instead of ln().

Re: Attaching user-data to sbml objects using libsbml

Sarah Keating — 2012-09-24T12:25:34-00:00

Hi Sorry this sat so long without an answer. Actually you have identified a bug (missing function) in the C API. The SBase class does have a userData member but the C API was never extended to allow access to it via C. I have added this to our tracker <a href="https://www.pivotaltracker.com/projects/248655#" target="_blank">https://www.pivotaltracker.com/projects/248655#</a> and so it should be added to the next libsbml release (anticipated the beginning of December.) Thanks for the email. Sarah ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Attaching user-data to sbml objects using libsbml

mihajlv — 2012-09-09T01:07:43-00:00

I was wondering if there is any way that one could attach a user- data to SBML objects. For example on a GObject from glib, there is a void pointer field that you can set to user-data. I am wondering if there is an existing way to do this in libsbml? I am using c.

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

Karthik Raman — 2012-08-31T03:59:03-00:00

Ah, many thanks for the insights! Best regards, Karthik On Thu, Aug 30, 2012 at 6:30 PM, Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>>wrote: > Good to know it worked out in the end. I believe the issue was that in > your configure line you have a semicolon so instead of: > > > ./configure --with-matlab="/opt/matlab/"; > > > it should have been: > > > ./configure --with-matlab=/opt/matlab > > To explain what happens, is that we then just go to the matlab path/bin, > which in your case would have been > > "/opt/matlab/";/bin > > and of course that would have failed, hence we could not determine the > architecture, as can be seen here > > >>> make -w mexext= TranslateSBML. OutputSBML. > > > The architecture is determined by running matlab one time and querying it > about a number of things. > > Cheers > Frank > > > > On Aug 30, 2012, at 2:31 PM, Karthik Raman wrote: > > > Dear Frank, > > > > Many thanks for your ultra-prompt response; it was quite helpful. > > > > In the end, I did the following: > > > > export CXXFLAGS="/opt/matlab/extern/include/"; > > ./configure --with-matlab="/opt/matlab/"; > > make > > make install > > > > Merely mentioning matlab path did not seem to solve the issue, I think. > > > > Thanks for pointing me in the right direction, > > > > Best, > > Karthik > > > > On Thu, Aug 30, 2012 at 3:21 PM, Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a> > >wrote: > > > >> Hello Karthik, > >> > >> unfortunately the configure script cannot guess where matlab is located. > >> You see this in the output, that it did not locate the mex.h file. > Please > >> re-configure by supplying the matlab root directory to the configure > >> command. It should look something like this: > >> > >> ./configure --with-matlab= > >> > >> for example: > >> > >> ./configure --with-matlab=/opt/R2011b/ > >> > >> Cheers > >> Frank > >> > >> On Aug 30, 2012, at 11:38 AM, Karthik Raman wrote: > >> > >>> Hello, > >>> > >>> I seem to have trouble installing libSBML with matlab bindings on my > >> linux > >>> box running MATLAB R2012a and Ubuntu 12.04 (x64). > >>> > >>> At the end of my ./configure and make, I get the following error: > >>> > >>> ... > >>> make -C matlab -w install > >>> make[3]: Entering directory > >>> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > >>> make -w mexext= TranslateSBML. OutputSBML. > >>> make[4]: Entering directory > >>> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > >>> /home/karthik/libsbml-5.6.0/doltlibtool --mode=compile --tag=CC gcc -I. > >>> -I/home/karthik/libsbml-5.6.0/src -DLINUX -MT TranslateSBML.lo > -MD > >>> -MP -MF ".deps/TranslateSBML.Po" -c -o TranslateSBML.lo TranslateSBML.c > >>> TranslateSBML.c:31:17: fatal error: mex.h: No such file or directory > >>> compilation terminated. > >>> make[4]: *** [TranslateSBML.lo] Error 1 > >>> make[4]: Leaving directory > >> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > >>> make[3]: *** [all] Error 2 > >>> make[3]: Leaving directory > >> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > >>> make[2]: *** [matlab-recurse] Error 2 > >>> make[2]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings' > >>> make[1]: *** [bindings-recurse] Error 2 > >>> make[1]: Leaving directory `/home/karthik/libsbml-5.6.0/src' > >>> make: *** [src-recurse] Error 2 > >>> make: Leaving directory `/home/karthik/libsbml-5.6.0' > >>> > >>> Is there something amiss with my MATLAB install perhaps? I find that > >> there > >>> is a mex.h in /opt/matlab/extern/include/mex.h > >>> > >>> I would appreciate any inputs to help fix this error. > >>> > >>> Sincerely, > >>> Karthik > >>> ____________________________________________________________ > >>> To manage your libsbml-development list subscription, visit > >>> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > >>> > >>> For a web interface to the libsbml-development mailing list, visit > >>> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > >>> > >>> For questions or feedback about the libsbml-development list, > >>> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > >>> > >> > >> ____________________________________________________________ > >> To manage your libsbml-development list subscription, visit > >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > >> > >> For a web interface to the libsbml-development mailing list, visit > >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > >> > >> For questions or feedback about the libsbml-development list, > >> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > >> > >> > > > > > > -- > > --------------------------------------------------------------------- > > Karthik Raman > > Assistant Professor > > BT 104, Department of Biotechnology > > Bhupat and Jyoti Mehta School of Biosciences > > Indian Institute of Technology Madras > > Chennai - 600 036, INDIA > > > > Tel: +91-44-2257-4139 > > Web: <a href="http://www.biotech.iitm.ac.in/Karthik/" target="_blank">http://www.biotech.iitm.ac.in/Karthik/</a> > > --------------------------------------------------------------------- > > ____________________________________________________________ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, > > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > -- --------------------------------------------------------------------- Karthik Raman Assistant Professor BT 104, Department of Biotechnology Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras Chennai - 600 036, INDIA Tel: +91-44-2257-4139 Web: <a href="http://www.biotech.iitm.ac.in/Karthik/" target="_blank">http://www.biotech.iitm.ac.in/Karthik/</a> --------------------------------------------------------------------- ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

fbergman — 2012-08-30T13:00:01-00:00

Good to know it worked out in the end. I believe the issue was that in your configure line you have a semicolon so instead of: > ./configure --with-matlab="/opt/matlab/"; it should have been: > ./configure --with-matlab=/opt/matlab To explain what happens, is that we then just go to the matlab path/bin, which in your case would have been "/opt/matlab/";/bin and of course that would have failed, hence we could not determine the architecture, as can be seen here >>> make -w mexext= TranslateSBML. OutputSBML. The architecture is determined by running matlab one time and querying it about a number of things. Cheers Frank On Aug 30, 2012, at 2:31 PM, Karthik Raman wrote: > Dear Frank, > > Many thanks for your ultra-prompt response; it was quite helpful. > > In the end, I did the following: > > export CXXFLAGS="/opt/matlab/extern/include/"; > ./configure --with-matlab="/opt/matlab/"; > make > make install > > Merely mentioning matlab path did not seem to solve the issue, I think. > > Thanks for pointing me in the right direction, > > Best, > Karthik > > On Thu, Aug 30, 2012 at 3:21 PM, Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>>wrote: > >> Hello Karthik, >> >> unfortunately the configure script cannot guess where matlab is located. >> You see this in the output, that it did not locate the mex.h file. Please >> re-configure by supplying the matlab root directory to the configure >> command. It should look something like this: >> >> ./configure --with-matlab= >> >> for example: >> >> ./configure --with-matlab=/opt/R2011b/ >> >> Cheers >> Frank >> >> On Aug 30, 2012, at 11:38 AM, Karthik Raman wrote: >> >>> Hello, >>> >>> I seem to have trouble installing libSBML with matlab bindings on my >> linux >>> box running MATLAB R2012a and Ubuntu 12.04 (x64). >>> >>> At the end of my ./configure and make, I get the following error: >>> >>> ... >>> make -C matlab -w install >>> make[3]: Entering directory >>> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' >>> make -w mexext= TranslateSBML. OutputSBML. >>> make[4]: Entering directory >>> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' >>> /home/karthik/libsbml-5.6.0/doltlibtool --mode=compile --tag=CC gcc -I. >>> -I/home/karthik/libsbml-5.6.0/src -DLINUX -MT TranslateSBML.lo -MD >>> -MP -MF ".deps/TranslateSBML.Po" -c -o TranslateSBML.lo TranslateSBML.c >>> TranslateSBML.c:31:17: fatal error: mex.h: No such file or directory >>> compilation terminated. >>> make[4]: *** [TranslateSBML.lo] Error 1 >>> make[4]: Leaving directory >> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' >>> make[3]: *** [all] Error 2 >>> make[3]: Leaving directory >> `/home/karthik/libsbml-5.6.0/src/bindings/matlab' >>> make[2]: *** [matlab-recurse] Error 2 >>> make[2]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings' >>> make[1]: *** [bindings-recurse] Error 2 >>> make[1]: Leaving directory `/home/karthik/libsbml-5.6.0/src' >>> make: *** [src-recurse] Error 2 >>> make: Leaving directory `/home/karthik/libsbml-5.6.0' >>> >>> Is there something amiss with my MATLAB install perhaps? I find that >> there >>> is a mex.h in /opt/matlab/extern/include/mex.h >>> >>> I would appreciate any inputs to help fix this error. >>> >>> Sincerely, >>> Karthik >>> ____________________________________________________________ >>> To manage your libsbml-development list subscription, visit >>> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >>> >>> For a web interface to the libsbml-development mailing list, visit >>> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >>> >>> For questions or feedback about the libsbml-development list, >>> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> >>> >> >> ____________________________________________________________ >> To manage your libsbml-development list subscription, visit >> <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> >> >> For a web interface to the libsbml-development mailing list, visit >> <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> >> >> For questions or feedback about the libsbml-development list, >> contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> >> >> > > > -- > --------------------------------------------------------------------- > Karthik Raman > Assistant Professor > BT 104, Department of Biotechnology > Bhupat and Jyoti Mehta School of Biosciences > Indian Institute of Technology Madras > Chennai - 600 036, INDIA > > Tel: +91-44-2257-4139 > Web: <a href="http://www.biotech.iitm.ac.in/Karthik/" target="_blank">http://www.biotech.iitm.ac.in/Karthik/</a> > --------------------------------------------------------------------- > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

Karthik Raman — 2012-08-30T12:31:56-00:00

Dear Frank, Many thanks for your ultra-prompt response; it was quite helpful. In the end, I did the following: export CXXFLAGS="/opt/matlab/extern/include/"; ./configure --with-matlab="/opt/matlab/"; make make install Merely mentioning matlab path did not seem to solve the issue, I think. Thanks for pointing me in the right direction, Best, Karthik On Thu, Aug 30, 2012 at 3:21 PM, Frank T. Bergmann <<a href="mailto:fbergman@caltech.edu" target="_blank">fbergman@caltech.edu</a>>wrote: > Hello Karthik, > > unfortunately the configure script cannot guess where matlab is located. > You see this in the output, that it did not locate the mex.h file. Please > re-configure by supplying the matlab root directory to the configure > command. It should look something like this: > > ./configure --with-matlab= > > for example: > > ./configure --with-matlab=/opt/R2011b/ > > Cheers > Frank > > On Aug 30, 2012, at 11:38 AM, Karthik Raman wrote: > > > Hello, > > > > I seem to have trouble installing libSBML with matlab bindings on my > linux > > box running MATLAB R2012a and Ubuntu 12.04 (x64). > > > > At the end of my ./configure and make, I get the following error: > > > > ... > > make -C matlab -w install > > make[3]: Entering directory > > `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > > make -w mexext= TranslateSBML. OutputSBML. > > make[4]: Entering directory > > `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > > /home/karthik/libsbml-5.6.0/doltlibtool --mode=compile --tag=CC gcc -I. > > -I/home/karthik/libsbml-5.6.0/src -DLINUX -MT TranslateSBML.lo -MD > > -MP -MF ".deps/TranslateSBML.Po" -c -o TranslateSBML.lo TranslateSBML.c > > TranslateSBML.c:31:17: fatal error: mex.h: No such file or directory > > compilation terminated. > > make[4]: *** [TranslateSBML.lo] Error 1 > > make[4]: Leaving directory > `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > > make[3]: *** [all] Error 2 > > make[3]: Leaving directory > `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > > make[2]: *** [matlab-recurse] Error 2 > > make[2]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings' > > make[1]: *** [bindings-recurse] Error 2 > > make[1]: Leaving directory `/home/karthik/libsbml-5.6.0/src' > > make: *** [src-recurse] Error 2 > > make: Leaving directory `/home/karthik/libsbml-5.6.0' > > > > Is there something amiss with my MATLAB install perhaps? I find that > there > > is a mex.h in /opt/matlab/extern/include/mex.h > > > > I would appreciate any inputs to help fix this error. > > > > Sincerely, > > Karthik > > ____________________________________________________________ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, > > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > -- --------------------------------------------------------------------- Karthik Raman Assistant Professor BT 104, Department of Biotechnology Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras Chennai - 600 036, INDIA Tel: +91-44-2257-4139 Web: <a href="http://www.biotech.iitm.ac.in/Karthik/" target="_blank">http://www.biotech.iitm.ac.in/Karthik/</a> --------------------------------------------------------------------- ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

fbergman — 2012-08-30T09:51:28-00:00

Hello Karthik, unfortunately the configure script cannot guess where matlab is located. You see this in the output, that it did not locate the mex.h file. Please re-configure by supplying the matlab root directory to the configure command. It should look something like this: ./configure --with-matlab= for example: ./configure --with-matlab=/opt/R2011b/ Cheers Frank On Aug 30, 2012, at 11:38 AM, Karthik Raman wrote: > Hello, > > I seem to have trouble installing libSBML with matlab bindings on my linux > box running MATLAB R2012a and Ubuntu 12.04 (x64). > > At the end of my ./configure and make, I get the following error: > > ... > make -C matlab -w install > make[3]: Entering directory > `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > make -w mexext= TranslateSBML. OutputSBML. > make[4]: Entering directory > `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > /home/karthik/libsbml-5.6.0/doltlibtool --mode=compile --tag=CC gcc -I. > -I/home/karthik/libsbml-5.6.0/src -DLINUX -MT TranslateSBML.lo -MD > -MP -MF ".deps/TranslateSBML.Po" -c -o TranslateSBML.lo TranslateSBML.c > TranslateSBML.c:31:17: fatal error: mex.h: No such file or directory > compilation terminated. > make[4]: *** [TranslateSBML.lo] Error 1 > make[4]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > make[3]: *** [all] Error 2 > make[3]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings/matlab' > make[2]: *** [matlab-recurse] Error 2 > make[2]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings' > make[1]: *** [bindings-recurse] Error 2 > make[1]: Leaving directory `/home/karthik/libsbml-5.6.0/src' > make: *** [src-recurse] Error 2 > make: Leaving directory `/home/karthik/libsbml-5.6.0' > > Is there something amiss with my MATLAB install perhaps? I find that there > is a mex.h in /opt/matlab/extern/include/mex.h > > I would appreciate any inputs to help fix this error. > > Sincerely, > Karthik > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

Karthik Raman — 2012-08-30T09:38:48-00:00

Hello, I seem to have trouble installing libSBML with matlab bindings on my linux box running MATLAB R2012a and Ubuntu 12.04 (x64). At the end of my ./configure and make, I get the following error: ... make -C matlab -w install make[3]: Entering directory `/home/karthik/libsbml-5.6.0/src/bindings/matlab' make -w mexext= TranslateSBML. OutputSBML. make[4]: Entering directory `/home/karthik/libsbml-5.6.0/src/bindings/matlab' /home/karthik/libsbml-5.6.0/doltlibtool --mode=compile --tag=CC gcc -I. -I/home/karthik/libsbml-5.6.0/src -DLINUX -MT TranslateSBML.lo -MD -MP -MF ".deps/TranslateSBML.Po" -c -o TranslateSBML.lo TranslateSBML.c TranslateSBML.c:31:17: fatal error: mex.h: No such file or directory compilation terminated. make[4]: *** [TranslateSBML.lo] Error 1 make[4]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings/matlab' make[3]: *** [all] Error 2 make[3]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings/matlab' make[2]: *** [matlab-recurse] Error 2 make[2]: Leaving directory `/home/karthik/libsbml-5.6.0/src/bindings' make[1]: *** [bindings-recurse] Error 2 make[1]: Leaving directory `/home/karthik/libsbml-5.6.0/src' make: *** [src-recurse] Error 2 make: Leaving directory `/home/karthik/libsbml-5.6.0' Is there something amiss with my MATLAB install perhaps? I find that there is a mex.h in /opt/matlab/extern/include/mex.h I would appreciate any inputs to help fix this error. Sincerely, Karthik ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Revised experimental files for libSBML-5.6.0

Sarah Keating — 2012-08-09T12:00:23-00:00

-------------------------------------------------------------- Revised experimental files for libSBML-5.6.0 -------------------------------------------------------------- Please note that the libSBML-5.6.0 release has updated the experimental files; both source and binary; that are available with this release. There files are available from <a href="https://sourceforge.net/projects/sbml/files/libsbml/5.6.0/experimental/2012-08-07/" target="_blank">https://sourceforge.net/projects/sbml/files/libsbml/5.6.0/experimental/2012-08-07/</a> ==================================================================== Changes ==================================================================== comp * Bug fixes - The flattening procedure was failing to correctly update references to localParameters within a kineticLaw when the localParameter was either deleted or replaced. This has been fixed. ======================================================= Please report any problems you encounter using libSBML either to the mailing list <a href="mailto:libsbml-team@caltech.edu" target="_blank">libsbml-team@caltech.edu</a> or using the issue tracker for libSBML at <a href="https://sourceforge.net/tracker/?group_id=71971&atid=942737" target="_blank">https://sourceforge.net/tracker/?group_id=71971&atid=942737</a> Thanks LibSBMLTeam ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Release of libSBML-5.6.0

Sarah Keating — 2012-08-03T10:12:46-00:00

--------------------- libSBML-5.6.0 --------------------- We are pleased to announce the release of libSBML-5.6.0 which is available for download from <a href="https://sourceforge.net/projects/sbml/files/libsbml/5.6.0/" target="_blank">https://sourceforge.net/projects/sbml/files/libsbml/5.6.0/</a> ==================================================================== Version 5.6.0 (2012-08-03) ==================================================================== A note on the use of SWIG: All aspects of libSBML-5.6.0 requiring SWIG are known to work with SWIG version 2.0.4. Issues with later versions have been found with respect to some areas of a libSBML build. These will be addressed in future releases but for libSBML-5.6.0 we recommend the use of SWIG 2.0.4. STABLE RELEASE * New features - LibSBML now includes a binding to R (The R Project for Statistical Computing). The binding is generated using SWIG and thus can be built by users. Alternatively, the libSBML-5.6.0 release provides R packages that can be installed directly into R. - During HARMONY 2012, people discussed the issue of providing support for Level 3 Layout in other SBML Level 3 packages. The conclusion was that additional GeneralGlyph elements should be added in order to support references to as-yet unknown types of objects to be defined in Level 3 packages. These additional elements have been included in the libSBML layout code. - Although libSBML GNU makefiles have technically supported Python 3 for some time, there had been no feedback regarding the use of Python 3 until recently. In response to the feedback, we have the updated the build system to facilitate the use of different versions of Python 3. On Windows, the libSBML release also includes prebuilt installers for Python 3.2. - The libSBML 'configure' command now accepts the additional option --with-python-interpreter, which allows you to specify the Python interpreter that should be used. This is useful when a system has multiple versions of Python installed in the same directories, and the version that should be used can be selected by explicitly invoking the desired version. The option takes a full path, as in "--with-python-interpreter=/usr/bin/python2.7". - In order to facilitate the use of identifiers.org URLs, we added an additional function, getSBOTermAsURL, to the SBase class. This function returns a string representation of the SBOTerm in its resolvable identifiers.org URL format; e.g., "<a href="http://identifiers.org/biomodels.sbo/SBO:NNNNNNN" target="_blank">http://identifiers.org/biomodels.sbo/SBO:NNNNNNN</a>" - The use of libSBML get and set functions in Python; a by-product of the use of SWIG; is not particularly intuitive. LibSBML-5.6.0 applies a patch that allows the use of indexing in the python environment i.e. model->getSpecies(0)->getId() can be replaced with model.species[0].id. This patch is limited to Python 2 versions at present. It does not adversely effect existing functions for either Python 2 or Python 3. Many thanks to Gordon Ball (Computational Medicine, Karolinska Institute) for creating and sharing this patch. * Bug fixes - When using a copy of libSBML compiled with Level 3 package support, attributes from the "sbml" namespace were not given a namespace prefix when they should have been. This has been fixed. - The L3Parser had some subtle bugs on some operating systems when dealing with very long numbers or exponentials. These have been tracked down and fixed. - Although libSBML explicitly prevented History or CVTerm objects from being added to the annotation of an object when that object had no metaid attribute value, it was still possible to add History and CVTerm directly to the annotation. This could lead to invalid MIRIAM annotations because they lacked a metaid attribute value. LibSBML now checks that an object to which any MIRIAM compliant annotation is being added has a metaid. - When returning a MIRIAM-compliant annotation, all CVTerms were lost if just one had an invalid qualifier. This has been fixed. - The decompression code uses a macro OF that is not defined for all versions of linux. A definition has been added to avoid problems. Thanks to Kai Wohlfahrt for reporting this. - There was a potential memory leak issue while registering SBMLConverters. Thanks to Akira Funahashi and his team for spotting the problem and supplying a fix. * Configuration/build system changes - As SBML Level 3 packages and their code become available, there is a increasing number of possibilities in the matrix of what a particular instance of libSBML has included. In order to facilitate code that may rely on the presence of one or more packages, the CMake configuration process has been improved to include a set of flags that identify the packages included in a particular build. The file convertLayout.cpp in the examples/c++ directory illustrates the use of these #define's. - The MATLAB bindings failed to build on Mac OS X whenever an Xcode version was used that did not include the Mac OS 10.6 SDK. This has been fixed. - The CMake build system has been made more resilient to finding include files from previous libSBML installations. EXPERIMENTAL RELEASE * New features - The Qualitative Modeling package "qual" is now supported. - The R binding is available for all packages. - 'Groups' package: - At HARMONY it was agreed that the 'group' element needed an additional attribute 'kind'. This has been added. - 'Spatial' package: - There was an issue with the encoding of image data for the spatial package. This has been solved by providing a function that will uncompress the data and return it to the user in a usable form. - 'Comp' package: - Instantiated Model objects in Submodels now are set to have that Submodel as their parent. The SBMLDocument is still set to the document of the original Model, so that its own Submodel references can be properly tracked down. ======================================================= Please report any problems you encounter using libSBML either to the mailing list <a href="mailto:libsbml-team@caltech.edu" target="_blank">libsbml-team@caltech.edu</a> or using the issue tracker for libSBML at <a href="https://sourceforge.net/tracker/?group_id=71971&atid=942737" target="_blank">https://sourceforge.net/tracker/?group_id=71971&atid=942737</a> Thanks LibSBMLTeam ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: gt (x,y) or x > y

fbergman — 2012-07-26T14:58:52-00:00

On Jul 26, 2012, at 4:54 PM, hsauro wrote: > > I am finally implementing an event syntax in the Jarnac scripting language and I was reminded again of a 'something nice to have' in the infix to mathml converter in libSBML which I know we've had to work with in other parts of SBW. At present it is not possible to give the converter something like: > > x > y > > it has to be of the form > > gt (x, y) > > Same goes for logical operators such as and etc. Are there any plans to modify the convertToMathML routine to handle syntax of the former kind? If not are there any suggestions, other than implementing the function syntax, which is not terribly pretty to look at. Hello Herbert, Lucian has implemented an L3 parser that will do what you want. It parses the expressions and returns the syntax trees. However, he did not yet implement the reverse operation. But at least you are half way there! Cheers Frank ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: OF not defined on gentoo linux (zlib + libSBML-5.5.0)

Kai Wohlfahrt — 2012-07-26T10:25:35-00:00

Ebuild and manifest below seem to work (minus python3 support as per my other thread, should be resolved in the next libsbml release). I haven't included doxygen or csharp bindings as I'm not quite clear on how this works. I have not tested any bindings other than python27, but java does compile. I don't have the dependencies to test any others. If there are any problems let me know and I'll try to sort them out. If anybody knows how to generate python3 bindings PLEASE tell me and I will update this to match. Kai Ebuild: # Copyright 1999-2012 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=4 inherit cmake-utils python java-pkg-opt-2 DESCRIPTION="a library for working with SBML-xml files. Contains wrappers for C and C++, as well as SWIG wrappers to C#, Java, MATLAB, Octave, Perl, Python and Ruby." HOMEPAGE="<a href="http://sbml.org/Software/libSBML" target="_blank">http://sbml.org/Software/libSBML</a>" SRC_URI=" <a href="http://downloads.sourceforge.net/project/sbml/${PN}/${PVR}/stable/${PF}-src.tar.gz" target="_blank">http://downloads.sourceforge.net/project/sbml/${PN}/${PVR}/stable/${PF}-src.tar.gz</a> " LICENSE="" SLOT="0" KEYWORDS="~amd64" IUSE="java octave perl python ruby bzip2 zlib" DEPEND="sys-apps/sed dev-lang/swig dev-util/cmake zlib? ( sys-libs/zlib ) perl? ( dev-lang/perl ) ruby? ( dev-lang/ruby ) bzip2? ( app-arch/bzip2 ) octave? ( sci-mathematics/octave )" RDEPEND="${DEPEND} dev-libs/libxml2 java? ( >=virtual/jre-1.6 )" DEPEND="${DEPEND} java? ( >=virtual/jdk-1.6 )" PYTHON_DEPEND="python? 2:2.6" pkg_setup() { if use java; then java-pkg-opt-2_pkg_setup fi if use python; then python_set_active_version 2 fi } src_prepare() { sed -i "1i#ifndef OF\n#define OF(x) x\n#endif" \ src/sbml/compress/ioapi.h || die "sed failed!" } src_configure() { # CMAKE_VERBOSE=OFF local mycmakeargs mycmakeargs+=( $(cmake-utils_use_with java) $(cmake-utils_use_with octave) $(cmake-utils_use_with perl) $(cmake-utils_use_with python) $(cmake-utils_use_with ruby) $(cmake-utils_use_with bzip2) $(cmake-utils_use_with zlib) ) cmake-utils_src_configure } src_install() { cmake-utils_src_install } Manifest: DIST libsbml-5.5.0-src.tar.gz 10036921 RMD160 1f584754c466fa110c9f6f9a5376962d9c7db64b SHA1 c04d16ce36db0a2acf43f99ae5cc4b539973b7c2 SHA256 982fad3a0329e1b3322fcdf6b0783d1e664be2c0301c5322521da42e059a6844 EBUILD libsbml-5.5.0.ebuild 1504 RMD160 e5dc3b0ffb2c56557d62fc1ac28c958ddb322f83 SHA1 886b8ce0a2272c9b12343c7f37398c3e19d7251e SHA256 20cc302560d4d86788b1fd18be51d28c557578725d38067dcd0be195000aab6c ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: OF not defined on gentoo linux (zlib + libSBML-5.5.0)

Johan Hattne — 2012-07-26T04:40:55-00:00

On 25 Jul 2012, at 14:53, Kai Wohlfahrt wrote: > If I understand correctly, the OF macro is a workaround in zlib for very > old (before C-89) compilers (<a href="http://stackoverflow.com/a/7299414/844614" target="_blank">http://stackoverflow.com/a/7299414/844614</a>), > the issue being that this macro is not consistently named accross distros > (_Z_OF for gentoo). Perhaps the macro should be removed if there is not a > compelling reason to keep it? Do your efforts by any chance imply that we could look forward to a Gentoo ebuild for libsbml? // Best wishes; Johan ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

OF not defined on gentoo linux (zlib + libSBML-5.5.0)

Kai Wohlfahrt — 2012-07-25T21:53:48-00:00

Hi all, I had some errors with compiling libSBML with zlib support, but was able to fix it by inserting the following lines into the top of ioapi.h: #ifndef OF #define OF(x) x #endif If I understand correctly, the OF macro is a workaround in zlib for very old (before C-89) compilers (<a href="http://stackoverflow.com/a/7299414/844614" target="_blank">http://stackoverflow.com/a/7299414/844614</a>), the issue being that this macro is not consistently named accross distros (_Z_OF for gentoo). Perhaps the macro should be removed if there is not a compelling reason to keep it? Kai Errors for reference are: In file included from /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/zip.h:58:0, from /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/zipfstream.h:64, from /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/InputDecompressor.cpp:44: /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:38:44: error: expected initializer before ‘OF’ /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:39:44: error: expected initializer before ‘OF’ /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:40:45: error: expected initializer before ‘OF’ /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:41:44: error: expected initializer before ‘OF’ /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:42:44: error: expected initializer before ‘OF’ /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:43:45: error: expected initializer before ‘OF’ /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:44:49: error: expected initializer before ‘OF’ /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:48:5: error: ‘open_file_func’ does not name a type /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:49:5: error: ‘read_file_func’ does not name a type /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:50:5: error: ‘write_file_func’ does not name a type /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:51:5: error: ‘tell_file_func’ does not name a type /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:52:5: error: ‘seek_file_func’ does not name a type /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:53:5: error: ‘close_file_func’ does not name a type /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:54:5: error: ‘testerror_file_func’ does not name a type /home/kai/libsbml/libsbml-5.5.0/src/sbml/compress/ioapi.h:60:26: error: expected initializer before ‘OF’ [loads more of "error: expected initializer before ‘OF’ " ] make[2]: *** [src/CMakeFiles/sbml.dir/sbml/compress/InputDecompressor.cpp.o] Error 1 make[1]: *** [src/CMakeFiles/sbml.dir/all] Error 2 make: *** [all] Error 2 ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

gt (x,y) or x > y

hsauro — 2012-07-25T21:26:26-00:00

I am finally implementing an event syntax in the Jarnac scripting language and I was reminded again of a 'something nice to have' in the infix to mathml converter in libSBML which I know we've had to work with in other parts of SBW. At present it is not possible to give the converter something like: x > y it has to be of the form gt (x, y) Same goes for logical operators such as and etc. Are there any plans to modify the convertToMathML routine to handle syntax of the former kind? If not are there any suggestions, other than implementing the function syntax, which is not terribly pretty to look at. Herbert Sauro

Re: New reply to Re: Installing libsbml5.5 for Python by fbergman

Neil Swainston — 2012-07-23T09:01:08-00:00

Hi Frank, Thanks for the heads-up. In the meantime, I cracked it. I was actually installing it for a colleague who had an old version kicking around the dusty corridors of her installation. It's all sorted now. Thanks for your help. Neil. Neil Swainston, PhD Research Fellow Manchester Institute of Biotechnology University of Manchester Manchester M1 7DN United Kingdom On 21 Jul 2012, at 08:59, <a href="mailto:sbml-forum-admins@caltech.edu" target="_blank">sbml-forum-admins@caltech.edu</a> wrote: > > Subject: Re: Installing libsbml5.5 for Python Author: fbergman Date: Sat, 21 July 2012 00:59 > Hello Neil, > > Unfortunately your previous mail does not contain enough information to > troubleshoot what was going on. As first guess, it would seem that you are > running this on OSX Lion (10.7). So if you like you could use the pre-built > python bindings for that OS that we distribute with the DMG, simply run the > installer and then set the PYTHONPATH to the > /usr/local/lib/python2.7/site-packages/libsbml directory prior to running > python ... then you get: > > $ PYTHONPATH=/usr/local/lib/python2.7/site-packages/libsbml > /usr/bin/python2.7 > Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) > [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on > darwin > Type "help", "copyright", "credits" or "license" for more information. > >>> from libsbml import * > >>> print getLibSBMLDottedVersion() > 5.5.0 > >>> > > If that is not the case, please let us know precisely which python version > you are running, and how you compiled the python bindings. > > Cheers > Frank > > > -----Original Message----- > > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Neil Swainston > > Sent: Saturday, July 21, 2012 3:49 AM > > To: <a href="mailto:libsbml-development@caltech.edu" target="_blank">libsbml-development@caltech.edu</a> > > Subject: [libsbml-development] Installing libsbml5.5 for Python > > > > > > Hi all, > > > > Cutting my teeth on Python and am currently experiencing the proverbial > "dead > > parrot". > > > > All seems to build fine, but when attempting to 'import libsbml' at the > python > > prompt, I'm getting the following error: > > > > vpn155:libsbml-5.5.0 nataliestanford$ python Python 2.7.3 > > (v2.7.3:70274d53c1dd, Apr 9 2012, 20:52:43) [GCC 4.2.1 (Apple Inc. build > > 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" > for > > more information. > > import libsbml > > Fatal Python error: PyThreadState_Get: no current thread Abort trap > > > > I'm guessing that this is some horrible incompatibility between the Python > > bindings and the library file, but not knowing my way around Python, I'm > taking > > the easy way out and asking you guys. > > > > Thanks as always for any help. > > > > Neil. > > ____________________________________________________________ > > To manage your libsbml-development list subscription, visit > > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > > > For a web interface to the libsbml-development mailing list, visit > > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > > > For questions or feedback about the libsbml-development list, contact > sbml- > > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > > [ Reply ][ Quote ][ View Topic/Message ][ Unsubscribe from this thread ] ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Installing libsbml5.5 for Python

fbergman — 2012-07-21T07:59:43-00:00

Hello Neil, Unfortunately your previous mail does not contain enough information to troubleshoot what was going on. As first guess, it would seem that you are running this on OSX Lion (10.7). So if you like you could use the pre-built python bindings for that OS that we distribute with the DMG, simply run the installer and then set the PYTHONPATH to the /usr/local/lib/python2.7/site-packages/libsbml directory prior to running python ... then you get: $ PYTHONPATH=/usr/local/lib/python2.7/site-packages/libsbml /usr/bin/python2.7 Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from libsbml import * >>> print getLibSBMLDottedVersion() 5.5.0 >>> If that is not the case, please let us know precisely which python version you are running, and how you compiled the python bindings. Cheers Frank > -----Original Message----- > From: <a href="mailto:libsbml-development-bounces@caltech.edu" target="_blank">libsbml-development-bounces@caltech.edu</a> [mailto:libsbml- > <a href="mailto:development-bounces@caltech.edu]" target="_blank">development-bounces@caltech.edu]</a> On Behalf Of Neil Swainston > Sent: Saturday, July 21, 2012 3:49 AM > To: <a href="mailto:libsbml-development@caltech.edu" target="_blank">libsbml-development@caltech.edu</a> > Subject: [libsbml-development] Installing libsbml5.5 for Python > > > Hi all, > > Cutting my teeth on Python and am currently experiencing the proverbial "dead > parrot". > > All seems to build fine, but when attempting to 'import libsbml' at the python > prompt, I'm getting the following error: > > vpn155:libsbml-5.5.0 nataliestanford$ python Python 2.7.3 > (v2.7.3:70274d53c1dd, Apr 9 2012, 20:52:43) [GCC 4.2.1 (Apple Inc. build > 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for > more information. > import libsbml > Fatal Python error: PyThreadState_Get: no current thread Abort trap > > I'm guessing that this is some horrible incompatibility between the Python > bindings and the library file, but not knowing my way around Python, I'm taking > the easy way out and asking you guys. > > Thanks as always for any help. > > Neil. > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, contact sbml- > <a href="mailto:team@caltech.edu" target="_blank">team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Installing libsbml5.5 for Python

Neil Swainston — 2012-07-19T16:42:09-00:00

Hi all, Cutting my teeth on Python and am currently experiencing the proverbial "dead parrot". All seems to build fine, but when attempting to 'import libsbml' at the python prompt, I'm getting the following error: vpn155:libsbml-5.5.0 nataliestanford$ python Python 2.7.3 (v2.7.3:70274d53c1dd, Apr 9 2012, 20:52:43) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information. import libsbml Fatal Python error: PyThreadState_Get: no current thread Abort trap I'm guessing that this is some horrible incompatibility between the Python bindings and the library file, but not knowing my way around Python, I'm taking the easy way out and asking you guys. Thanks as always for any help. Neil.

SBML to dot conversion

am2ta — 2012-06-13T17:59:29-00:00

Hey SBML team I recently downloaded PYGL metabolic pathway in SBML format from reactome database. I wanted to incorporate the pathway into my existing model, which is written in the DOT language. DOT language is provided by GraphViz which makes network reconstruction much simpler. Therefore, to incorporate the SBML pathway in DOT language, I had to convert the SBML format to DOT format. I have been unsuccessful in converting it by using XSLTPROC command in Linux. Does anyone have any ideas of how to effect this conversion? I tried converting the SBML file using some of the style sheets from SBML.org, viz. sbml_dot.xsl through the command XSLTPROC. It is not working. Could you tell me the best way to do it? Or which is the best stylesheet to use. I attach my xml file to this forum so that you guys can try the conversion yourself and tell me if you are successful. Any help in this regard is appreciated. Annamalai

Re: Matlab binding in Ubuntu

fbergman — 2012-06-05T06:38:59-00:00

Hello Javier, thank you so much for letting us know. This issue is fixed in SVN. Can you please delete the line 29 in > /home/tamames/soft/libsbml-5.5.0/src/sbml/annotation/RDFAnnotation.h (the comment that starts with // ) That will sort the issue for now â€¦ please let us know if you face further problems Thanks Frank On Jun 5, 2012, at 3:50 AM, Javier wrote: > > Hello friends > > I am trying to install libsbml with Matlab bindings in my Ubuntu 64 machine. After configure --with-matlab, which runs fine, make fails with the following error message. Could you please provide any hint on how to fix this? > > Thank you very much in advance! > > Best, > > Javier > > * Creating mex files in /home/tamames/soft/libsbml-5.5.0/src/bindings/matlab > - Building TranslateSBML ... > In file included from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBase.h:131, > from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBMLDocument.h:259, > from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBMLTypes.h:34, > from TranslateSBML.c:38: > /home/tamames/soft/libsbml-5.5.0/src/sbml/annotation/RDFAnnotation.h:29: error: expected identifier or Ã¢Â€Â˜(Ã¢Â€Â™ before Ã¢Â€Â˜/Ã¢Â€Â™ token > In file included from /home/tamames/soft/libsbml-5.5.0/src/sbml/Compartment.h:318, > from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBMLTypes.h:51, > from TranslateSBML.c:38: > /home/tamames/soft/libsbml-5.5.0/src/sbml/annotation/RDFAnnotation.h:29: error: expected identifier or Ã¢Â€Â˜(Ã¢Â€Â™ before Ã¢Â€Â˜/Ã¢Â€Â™ token > > mex: compile of ' "TranslateSBML.c"' failed. > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Matlab binding in Ubuntu

Javier — 2012-06-04T12:58:19-00:00

Hello friends I am trying to install libsbml with Matlab bindings in my Ubuntu 64 machine. After configure --with-matlab, which runs fine, make fails with the following error message. Could you please provide any hint on how to fix this? Thank you very much in advance! Best, Javier * Creating mex files in /home/tamames/soft/libsbml-5.5.0/src/bindings/matlab - Building TranslateSBML ... In file included from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBase.h:131, from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBMLDocument.h:259, from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBMLTypes.h:34, from TranslateSBML.c:38: /home/tamames/soft/libsbml-5.5.0/src/sbml/annotation/RDFAnnotation.h:29: error: expected identifier or â€˜(â€™ before â€˜/â€™ token In file included from /home/tamames/soft/libsbml-5.5.0/src/sbml/Compartment.h:318, from /home/tamames/soft/libsbml-5.5.0/src/sbml/SBMLTypes.h:51, from TranslateSBML.c:38: /home/tamames/soft/libsbml-5.5.0/src/sbml/annotation/RDFAnnotation.h:29: error: expected identifier or â€˜(â€™ before â€˜/â€™ token mex: compile of ' "TranslateSBML.c"' failed.

Re: Issues installing libsbml java binding

fbergman — 2012-06-04T12:00:44-00:00

Hello Arnaud, Sorry for the confusion. I believe the issues are the following: On Windows: please put the SBML_DIR\bindings\java directory into your PATH (as that is where the sbml.dll is located that is necessary to run) On Ubuntu please ensure that the actual Jar file is located in the CLASSPATH (from the deb file it will be in /usr/share/java/libsbmlj.jar) In general the following batch file allows you to ascertain that the libsbml java distribution is working. It will simply compile a distributed example and run it afterwards. If you want to change the JVM / libSBML version simply alter the first two definitions: ------------------- snip @echo off REM REM ONLY CHANGE THE NEXT TWO LINES TO YOUR SYSTEM REM (be sure to match 64bit JVMs with 64bit SBML) SET JDK_HOME=C:\Program Files (x86)\Java\jdk1.7.0_04 SET SBML_HOME=C:\Program Files (x86)\SBML\libSBML-5.5.0-libxml2-x86 REM SET UP ADDITIONAL FILES SET JAVAC=%JDK_HOME%\bin\javac SET JAVA=%JDK_HOME%\bin\java SET SBML_CP=%SBML_HOME%\bindings\java\libsbmlj.jar SET EXAMPLE=printSBML SET EXAMPLE_SOURCE=%SBML_HOME%\examples\java\%EXAMPLE%.java SET EXAMPLE_FILE=%SBML_HOME%\examples\sample-models\from-spec-level2\events.xml REM COMPILE cd %TEMP% copy /y "%EXAMPLE_SOURCE%" %EXAMPLE%.java "%JAVAC%" -classpath "%SBML_CP%" %EXAMPLE%.java REM RUN SET PATH=%SBML_HOME%\bindings\java;%PATH% "%JAVA%" -classpath "%SBML_CP%";. %EXAMPLE% "%EXAMPLE_FILE%" pause ------------------- snap Cheers Frank On Jun 1, 2012, at 6:32 PM, Arnaud LEGENDRE wrote: > Hello, > > i am not sure to post in the right list, but feel free to redirect me... > > I have issues making the binding of libsbml with Java work, both under > windows7 64 and ubuntu12.04 64 > >> On windows, i have installed from the regular installer, checking the > option for the java binding. The libraries are hence stored in > C:\Program Files\SBML\libSBML-5.5.0-libxml2-x64 > > I have Java runtime v1.7.0_003, and javac 1.7.0_03 > > i configured my environment variables (system ones) with : > > Path = ;C:\Program Files\SBML\libSBML-5.5.0-libxml2-x64\lib > CLASSPATH = ;C:\Program > Files\SBML\libSBML-5.5.0-libxml2-x64\bindings\java\libsbmlj.jar > > my program, that properly worked on former machines keeps returning: > > import org.sbml.libsbml.*; > > Error: could not link with the libSBML library. It is likely > your LD_LIBRARY_PATH environment variable does not include > the directory containing the libsbml library file. > Java Result: 1 > >> On ubuntu, i tried to install both from the .deb package and > re-compilation of sources (with-xerces and with-java): > > java version "1.6.0_24" > OpenJDK Runtime Environment (IcedTea6 1.11.1) (6b24-1.11.1-4ubuntu3) > OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode) > > in my .bashrc file > > #PATH FOR LIBSBML > export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib:/usr/lib32:/usr/lib64:/usr/local/lib:/usr/share/java:/usr/share:/usr/share/java/:/usr/local/share/java > export > CLASSPATH=$CLASSPATH:/usr/share/java/:/usr/lib:/usr/lib32:/usr/lib64:/usr/local/lib:/usr/share/java:/usr/share:/usr/share/java/:/usr/local/share/java > > i tried with versions 86 and 64 of libsbml, and restarted a couple of > times, but with no success ... > > I'd be greatfull if you gave me some ideas ! > regards, > Arnaud > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Issues installing libsbml java binding

Arnaud LEGENDRE — 2012-06-01T16:32:48-00:00

Hello, i am not sure to post in the right list, but feel free to redirect me... I have issues making the binding of libsbml with Java work, both under windows7 64 and ubuntu12.04 64 > On windows, i have installed from the regular installer, checking the option for the java binding. The libraries are hence stored in C:\Program Files\SBML\libSBML-5.5.0-libxml2-x64 I have Java runtime v1.7.0_003, and javac 1.7.0_03 i configured my environment variables (system ones) with : Path = ;C:\Program Files\SBML\libSBML-5.5.0-libxml2-x64\lib CLASSPATH = ;C:\Program Files\SBML\libSBML-5.5.0-libxml2-x64\bindings\java\libsbmlj.jar my program, that properly worked on former machines keeps returning: import org.sbml.libsbml.*; Error: could not link with the libSBML library. It is likely your LD_LIBRARY_PATH environment variable does not include the directory containing the libsbml library file. Java Result: 1 > On ubuntu, i tried to install both from the .deb package and re-compilation of sources (with-xerces and with-java): java version "1.6.0_24" OpenJDK Runtime Environment (IcedTea6 1.11.1) (6b24-1.11.1-4ubuntu3) OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode) in my .bashrc file #PATH FOR LIBSBML export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib:/usr/lib32:/usr/lib64:/usr/local/lib:/usr/share/java:/usr/share:/usr/share/java/:/usr/local/share/java export CLASSPATH=$CLASSPATH:/usr/share/java/:/usr/lib:/usr/lib32:/usr/lib64:/usr/local/lib:/usr/share/java:/usr/share:/usr/share/java/:/usr/local/share/java i tried with versions 86 and 64 of libsbml, and restarted a couple of times, but with no success ... I'd be greatfull if you gave me some ideas ! regards, Arnaud ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Memory leak on libsbml-5.5.0

Mike Hucka — 2012-05-30T22:34:59-00:00

Thanks for spotting this providing a patch! MH On Wed, 30 May 2012 23:58:22 +0900, Akira Funahashi wrote: > Hi, > > I'm writing this email on behalf of Akito Tabira <<a href="mailto:mythosil2008@gmail.com" target="_blank">mythosil2008@gmail.com</a>>, > who found and wrote a patch for memory leak of current libsbml. > (He was a graduate student in our lab until this March) > Akito found that there is a small memory leak on libsbml-5.4.1, and there > still exists on current libsbml-5.5.0. > > Here I attach a patch for libsbml-5.5.0, which will correctly free the > allocated memory. > He confirmed that the leak will be eliminated with this patch through > valgrind. > This patch might also work on libsbml-5.4.1 and further. > > Best, > -- > Akira > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Memory leak on libsbml-5.5.0

Akira Funahashi — 2012-05-30T14:58:22-00:00

Hi, I'm writing this email on behalf of Akito Tabira <<a href="mailto:mythosil2008@gmail.com" target="_blank">mythosil2008@gmail.com</a>>, who found and wrote a patch for memory leak of current libsbml. (He was a graduate student in our lab until this March) Akito found that there is a small memory leak on libsbml-5.4.1, and there still exists on current libsbml-5.5.0. Here I attach a patch for libsbml-5.5.0, which will correctly free the allocated memory. He confirmed that the leak will be eliminated with this patch through valgrind. This patch might also work on libsbml-5.4.1 and further. Best, -- Akira

Re: Survey for L3 Parser

myers — 2012-05-14T16:22:23-00:00

I imagine the tricky bit is you don't know which form the user used to enter it, so you have to pick one form to present back. I would prefer the infix though as the present back as it is the more natural. Right now, it presents back the old form, so I look forward to the reverse translation. Chris On May 14, 2012, at 8:33 AM, Lucian Smith wrote: > * Chris J. Myers <<a href="mailto:myers@ece.utah.edu" target="_blank">myers@ece.utah.edu</a>> [2012-05-14 07:04] writes: >> I tried it out. What are all the symbols supported? > > All the listed symbols are at: > > <a href="http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html#a58e584e7c21801b34d79fed7a7c05ac8" target="_blank">http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html#a58e584e7c21801b34d79fed7a7c05ac8</a> > > and include all the MathML symbols plus the various SBML csymbols. > Booleans and inequalities are &&, ||, !, ==, !=, <, > , <=, and >=. > >> What is the technical challenge to the reverse translation? > > Technically, the problem is 'not enough hours in the day'. > > -Lucian > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Survey for L3 Parser

Lucian Smith — 2012-05-14T14:33:56-00:00

* Chris J. Myers <<a href="mailto:myers@ece.utah.edu" target="_blank">myers@ece.utah.edu</a>> [2012-05-14 07:04] writes: > I tried it out. What are all the symbols supported? All the listed symbols are at: <a href="http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html#a58e584e7c21801b34d79fed7a7c05ac8" target="_blank">http://sbml.org/Software/libSBML/docs/cpp-api/_l3_parser_8h.html#a58e584e7c21801b34d79fed7a7c05ac8</a> and include all the MathML symbols plus the various SBML csymbols. Booleans and inequalities are &&, ||, !, ==, !=, <, > , <=, and >=. > What is the technical challenge to the reverse translation? Technically, the problem is 'not enough hours in the day'. -Lucian ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Survey for L3 Parser

myers — 2012-05-14T06:01:01-00:00

I tried it out. What are all the symbols supported? What is the technical challenge to the reverse translation? Chris Sent from my iPhone On May 12, 2012, at 2:07 AM, Lucian Smith <<a href="mailto:lpsmith@spod-central.org" target="_blank">lpsmith@spod-central.org</a>> wrote: > Just as a followup to this: the new L3 Parser is now released as part of > libsbml 5.5! The survey was good, because it showed a pretty deep level > of mixed feelings about how things should work, and in the end, we put the > decisions back in your hands: "log(x)" translates to the base-10 log by > default, but can be set to translate to the natural log or as an error if > you want, and minuses are left expanded by default, but can be collapsed > with a different setting if needed. > > It was also good to know that the mathml-to-infix translator was not > critical for most of you, and you would be happy with just the > infix-to-mathml parser for now. So that's what we gave you! > > Thanks for your responses! > > -Lucian > > > * Lucian Smith <<a href="mailto:lpsmith@spod-central.org" target="_blank">lpsmith@spod-central.org</a>> [2012-03-29 17:24] writes: >> After years of threatening to do so, I finally wrote the basics of an L3 >> infix-to-mathml parser. Thanks to all of you who wrote in with >> suggestions the last time I mentioned this; your suggestions have been >> incorporated into the current development version. >> >> Now we have a few more questions we want your input on, and have created a >> short 3-question survey for it: >> >> <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> >> >> More detail is at the survey itself, but basically, the questions are: >> >> 1) Should "log(x)" translate to natural log, base-10 log, or be illegal? >> 2) How critical is a mathml-to-infix L3 translator to the usefulness of >> the infix-to-mathml L3 translator? >> 3) Does it matter to you if "-4" is translated as 'minus(4)' (in the >> mathml)? >> >> Thank you! If you have any additional questions, feel free to ask here. >> >> -Lucian > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Survey for L3 Parser

Lucian Smith — 2012-05-12T00:07:34-00:00

Just as a followup to this: the new L3 Parser is now released as part of libsbml 5.5! The survey was good, because it showed a pretty deep level of mixed feelings about how things should work, and in the end, we put the decisions back in your hands: "log(x)" translates to the base-10 log by default, but can be set to translate to the natural log or as an error if you want, and minuses are left expanded by default, but can be collapsed with a different setting if needed. It was also good to know that the mathml-to-infix translator was not critical for most of you, and you would be happy with just the infix-to-mathml parser for now. So that's what we gave you! Thanks for your responses! -Lucian * Lucian Smith <<a href="mailto:lpsmith@spod-central.org" target="_blank">lpsmith@spod-central.org</a>> [2012-03-29 17:24] writes: > After years of threatening to do so, I finally wrote the basics of an L3 > infix-to-mathml parser. Thanks to all of you who wrote in with > suggestions the last time I mentioned this; your suggestions have been > incorporated into the current development version. > > Now we have a few more questions we want your input on, and have created a > short 3-question survey for it: > > <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> > > More detail is at the survey itself, but basically, the questions are: > > 1) Should "log(x)" translate to natural log, base-10 log, or be illegal? > 2) How critical is a mathml-to-infix L3 translator to the usefulness of > the infix-to-mathml L3 translator? > 3) Does it matter to you if "-4" is translated as 'minus(4)' (in the > mathml)? > > Thank you! If you have any additional questions, feel free to ask here. > > -Lucian ____________________________________________________________ To manage your sbml-interoperability list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability</a> For a web interface to the sbml-interoperability mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-interoperability list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Survey for L3 Parser

Lucian Smith — 2012-05-12T00:07:34-00:00

Just as a followup to this: the new L3 Parser is now released as part of libsbml 5.5! The survey was good, because it showed a pretty deep level of mixed feelings about how things should work, and in the end, we put the decisions back in your hands: "log(x)" translates to the base-10 log by default, but can be set to translate to the natural log or as an error if you want, and minuses are left expanded by default, but can be collapsed with a different setting if needed. It was also good to know that the mathml-to-infix translator was not critical for most of you, and you would be happy with just the infix-to-mathml parser for now. So that's what we gave you! Thanks for your responses! -Lucian * Lucian Smith <<a href="mailto:lpsmith@spod-central.org" target="_blank">lpsmith@spod-central.org</a>> [2012-03-29 17:24] writes: > After years of threatening to do so, I finally wrote the basics of an L3 > infix-to-mathml parser. Thanks to all of you who wrote in with > suggestions the last time I mentioned this; your suggestions have been > incorporated into the current development version. > > Now we have a few more questions we want your input on, and have created a > short 3-question survey for it: > > <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> > > More detail is at the survey itself, but basically, the questions are: > > 1) Should "log(x)" translate to natural log, base-10 log, or be illegal? > 2) How critical is a mathml-to-infix L3 translator to the usefulness of > the infix-to-mathml L3 translator? > 3) Does it matter to you if "-4" is translated as 'minus(4)' (in the > mathml)? > > Thank you! If you have any additional questions, feel free to ask here. > > -Lucian ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Release of libSBML-5.5.0

Sarah Keating — 2012-05-11T12:06:32-00:00

--------------------- libSBML-5.5.0 --------------------- We are pleased to announce the release of libSBML-5.5.0 which is available for download from <a href="https://sourceforge.net/projects/sbml/files/libsbml/5.5.0/" target="_blank">https://sourceforge.net/projects/sbml/files/libsbml/5.5.0/</a> ========================================== Version 5.5.0 (2012-05-11) ========================================== STABLE RELEASE * Revision of annotation and SBML MIRIAM RDF Following discussions on the libsbml-development mailing list we have adjusted the way functions affecting annotations interact with the SBML MIRIAM RDF classes for History and CVTerms. - Previously any annotation was assessed and if it contained MIRIAM RDF the corresponding classes were created and the original annotation XMLNodes relating to these objects was removed from the annotation. When the annotation was retrieved the xml was reconstructed from the History and CVTerm classes. This is no longer the case. In 5.5 we have changed the code so that the MIRIAM objects are created BUT the original annotation remains intact. It is only reconstructed if the code has directly altered the History or CVTerm classes via the class API, otherwise the original annotation is returned. - We reassessed the use of the appendAnnotation function. Previously any annotation was appended regardless of whether the existing annotation already contained a top level element with the same namespace. We considered this to be a bug, since it would result in invalid SBML. Thus, the appendAnnotation function now checks whether there is an existing top-level element with the same namespace of any it is to append and does not append if it encounters a duplicate. It returns an OperationReturnValue of LIBSBML_DUPLICATE_ANNOTATION_NS to indicate this to the user. - In our reassessment of appendAnnotation we came to the conclusion that it was virtually impossible to correctly determine the intent of the user in cases where both the existing and appending annotation contained RDF that complied with the SBML MIRIAM RDF History or CVTerms. Thus the appendAnnotation function no longer treats RDF as a "special" case. If there is existing RDF, no further RDF will be appended. Users wishing to alter existing History or CVTerms should use the API provided or construct their own annotation and use the setAnnotation function. - New functions removeTopLevelAnnotationElement(std::string name) and replaceTopLevelAnnotationElement(XMLNode* annotation) have been introduced to allow users to remove or replace a single top level annotation element whilst conserving any other annotation that may be present. * New features - There is now a version of the infix to MathML parser that is independent of L1 constructs. This parser is available as three functions: SBML_parseL3Formula(""), SBML_parseL3FormulaWithModel("", Model*) and SBML_parseL3FormulaWithSettings("", L3ParserSettings *). There is a new object L3ParserSettings that allows the user to tailor the results of the function, for example to parse "log" as natural log or log base 10; to allow users to enter units on numbers as "10m" or to disable this feature along with some other options. - The getLine() and getColumn() functions did on some occasions return a maximum int value when the correct lines and columns could not be determined. This produced inconsistent behaviour as some XML parsers return '0' as if they cannot determine location. This has been unified and libSBML's getLine()/getColumn() will now return '0' if the location is unknown. - There is a new class SBMLDocumentPluginNotRequired which allows a package code to derive from an object where the required attribute is considered 'false' until it has been set. Note this is not a "default" value it is just the value with which the boolean attribute is initialised. The existing SBMLDocumentPlugin class assumes a value of 'true'. This is in fact a change in behaviour but since users should set this value it should not cause a problem. * Bug fixes - Tracker issue#3509843 The annotation element in SBML should contain only elements. Schema validation reports this but libSBML was not. This has been corrected. Thanks to Camille Laibe for still running schema validation and reporting the issue. - There was a subtle bug involving accessing a NULL ModelHistory object. This has been fixed. - Area units were not being properly converted between SBML Levels. They are now. - An AST plus or times node that was created with more than two children was written out as only having two children; thus losing information. This behaviour has been corrected. - Functions used to add objects to other objects in libSBML check that the SBML Level/Version/Namespaces of the objects correspond. However these checks were imposing the condition that the number of namespaces on both objects be the same. This is not a necessary condition and the code has been relaxed. Thanks to Chris Myers for pointing it out. - In XML if the sbml element is not prefixed but the only declaration of the sbml namespace is, then technically the sbml element has not been placed into the sbml namespace. LibSBML was failing to report this. This has now been fixed. - There was a curious indentation issue that arose if notes used text as child elements of an element that also had another non-text child element. This could proliferate and cause models where the indentation ran into the thousands of spaces. This has been sorted out and no longer happens. * Miscellaneous - The uninstallation instructions were out of date. This is now updated, for example to mention that the Mac OS X installer does in fact provide an uninstall script. * Configuration/build system changes - Doxygen versions 1.7 and 1.8 are now supported, but due to differences in the new version, older versions of Doxygen are no longer supported. The 'configure' script will now only accept version 1.7 at minimum. - Some changes have been made to facilitate building libSBML with the Borland compiler. This included standardising the use of #ifdefined rather than using #if. Thanks to Totte Karlsson for the effort of getting this to work. - The CMake build has been updated to facilitate the use of the Intel compiler. EXPERIMENTAL RELEASE * New features - New macros provided so that SBMLNamespaces objects may easily be created to allow package elements to be extended by other packages (for example: a comp:modelDefinition to have a layout:listOfLayouts). These macros now used throughout package system when creating new package elements. - In 'comp': - ExternalModelDefinitions have a new function, 'getReferencedModel' that tries to find the referenced document and model, if the reference URI is a 'file' type. If the SBMLDocument has its fileURI set, this will use that to search for relative filenames. - With the above in place, automated flattening now works with ExternalModelDefinitions that point to local files. - May now use ModelDefinitions to create the main Model of an SBMLDocument. ======================================================= Please report any problems you encounter using libSBML either to the mailing list <a href="mailto:libsbml-team@caltech.edu" target="_blank">libsbml-team@caltech.edu</a> or using the issue tracker for libSBML at <a href="https://sourceforge.net/tracker/?group_id=71971&atid=942737" target="_blank">https://sourceforge.net/tracker/?group_id=71971&atid=942737</a> Thanks LibSBMLTeam ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Standardising #if and #if defined

Sarah Keating — 2012-04-17T11:04:15-00:00

It has been on our radar for a while and was recently pointed out by Totte as a problem for the Borland compiler that libSBML is not consistent in the use of #if (WIN32) or #if defined (WIN32). We propose to standardise on #if defined (WIN32) but wanted to check whether people were in the habit of using #define WIN32 0 which of course means that the change in libSBML could potentially change functionality for people. We will at the same time standardise any use of #if and defines (__cplusplus is also used inconsistently). Let us know if you have any objections to this change. Thanks The LibSBML Team ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: [python-libsbml]how to get reactant/product from a reaction?

Sarah Keating — 2012-04-16T09:55:03-00:00

Hi Thanks for your interest and taking the time to pose the question. The SpeciesReference objects that are in the listOfProducts/Reactants are not required to have an id. They use the species attribute to refer to the id of the species in the listOfSpecies that they represent. Using product.getSpecies() in your code should work. Hope this helps. Sarah On 16/04/2012 10:03, ç”°é²äº¦ wrote: > > I have a human SBML files(Recon 1) from BiGG database, and I want to extract reactant and product id in reactions.I tried the following code, but it didn't work:----- reader = SBMLReader() doc = reader.readSBML([filename]) model = doc.getModel() Reactions = model.getListOfReactions() for reaction in Reactions: products=reaction.getListOfProducts() for product in products: print product.getId()----There is no result for all reactions. When I tried 'reaction.getId()', I could get the id of a reaction, but it doesnot work in species. I think get product and reactant from a reaction mast be a simple task in libSBML. Anyone knows how to do this in python-libsbml? Thank you for your help. > > > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

[python-libsbml]how to get reactant/product from a reaction?

tlytiger — 2012-04-16T09:03:59-00:00

I have a human SBML files(Recon 1) from BiGG database, and I want to extract reactant and product id in reactions.I tried the following code, but it didn't work:----- reader = SBMLReader() doc = reader.readSBML([filename]) model = doc.getModel() Reactions = model.getListOfReactions() for reaction in Reactions: products=reaction.getListOfProducts() for product in products: print product.getId()----There is no result for all reactions. When I tried 'reaction.getId()', I could get the id of a reaction, but it doesnot work in species. I think get product and reactant from a reaction mast be a simple task in libSBML. Anyone knows how to do this in python-libsbml? Thank you for your help.

Re: [sbml-interoperability] Survey for L3 Parser

Mike Hucka — 2012-04-09T03:10:56-00:00

On Sun, 8 Apr 2012 18:02:21 -0700 (PDT), pax wrote: > At least 10 people! We care about libSBML. However, we are currently > doing our own infix to mathML conversions. I can fill out the survey > (and will) but we don't use these particular functions. Hi Pax! OK, fair enough :-). Thanks for filling out the survey! MH ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: [libsbml-development] Survey for L3 Parser

Mike Hucka — 2012-04-09T03:10:56-00:00

On Sun, 8 Apr 2012 18:02:21 -0700 (PDT), pax wrote: > At least 10 people! We care about libSBML. However, we are currently > doing our own infix to mathML conversions. I can fill out the survey > (and will) but we don't use these particular functions. Hi Pax! OK, fair enough :-). Thanks for filling out the survey! MH ____________________________________________________________ To manage your sbml-interoperability list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability</a> For a web interface to the sbml-interoperability mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-interoperability list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: [sbml-interoperability] Survey for L3 Parser

pax — 2012-04-06T15:37:33-00:00

At least 10 people! We care about libSBML. However, we are currently doing our own infix to mathML conversions. I can fill out the survey (and will) but we don't use these particular functions. pax

Re: [libsbml-development] Survey for L3 Parser

Mike Hucka — 2012-04-05T17:16:25-00:00

So, what this basically means is, only 9 people in the world care about libSBML. Seriously, people? 9? There are more of you, aren't there? I hope? MH > So, we have some preliminary results from this (thanks to the nine of you > who filled it out), ____________________________________________________________ To manage your sbml-interoperability list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability</a> For a web interface to the sbml-interoperability mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-interoperability list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: [sbml-interoperability] Survey for L3 Parser

Mike Hucka — 2012-04-05T17:16:25-00:00

So, what this basically means is, only 9 people in the world care about libSBML. Seriously, people? 9? There are more of you, aren't there? I hope? MH > So, we have some preliminary results from this (thanks to the nine of you > who filled it out), ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: [sbml-interoperability] Survey for L3 Parser

Lucian Smith — 2012-04-04T20:39:13-00:00

So, we have some preliminary results from this (thanks to the nine of you who filled it out), and responses are somewhat mixed, but revealing. If you haven't responded yet and have an opinion, now is the time to voice it, either by replying here or on the survey itself (or both!) The survey URL is <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> Here's the current rough consensus on the questions: 1) "How should we interpret 'log(x)'?" There is at least one 'Unacceptable' response for each of the three options, so it seems it will be impossible to please everyone. However, a begrudging consensus is forming around "log(x) should be log10(x)" with 6/9 responders saying this was preferred or acceptable. One argument brought up was that the MathML standard for the '' function with no defined base defaults to base 10, so since SBML hitched its wagon to MathML a long time ago, this seems like a reasonable externally-defined standard. 2) "Is the infix-to-mathML parser useful without the corresponding mathML-to-infix translator?" Overwhelmingly, the answer here is 'yes' or 'it doesn't matter'--this is good to know, and we'll be releasing the L3 parser without waiting to simultaneously release the to-infix translator. 3) "Should "-4' be translated as such inside a element, or should it use ?" Most people don't care, and other opinion is evenly split. Thanks for your responses! -Lucian * Lucian Smith <<a href="mailto:lpsmith@spod-central.org" target="_blank">lpsmith@spod-central.org</a>> [2012-03-29 17:24] writes: > After years of threatening to do so, I finally wrote the basics of an L3 > infix-to-mathml parser. Thanks to all of you who wrote in with > suggestions the last time I mentioned this; your suggestions have been > incorporated into the current development version. > > Now we have a few more questions we want your input on, and have created a > short 3-question survey for it: > > <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> > > More detail is at the survey itself, but basically, the questions are: > > 1) Should "log(x)" translate to natural log, base-10 log, or be illegal? > 2) How critical is a mathml-to-infix L3 translator to the usefulness of > the infix-to-mathml L3 translator? > 3) Does it matter to you if "-4" is translated as 'minus(4)' (in the > mathml)? > > Thank you! If you have any additional questions, feel free to ask here. > > -Lucian > ____________________________________________________________ > To manage your sbml-interoperability list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability</a> > > For a web interface to the sbml-interoperability mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the sbml-interoperability list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Survey for L3 Parser

Lucian Smith — 2012-04-04T20:39:13-00:00

So, we have some preliminary results from this (thanks to the nine of you who filled it out), and responses are somewhat mixed, but revealing. If you haven't responded yet and have an opinion, now is the time to voice it, either by replying here or on the survey itself (or both!) The survey URL is <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> Here's the current rough consensus on the questions: 1) "How should we interpret 'log(x)'?" There is at least one 'Unacceptable' response for each of the three options, so it seems it will be impossible to please everyone. However, a begrudging consensus is forming around "log(x) should be log10(x)" with 6/9 responders saying this was preferred or acceptable. One argument brought up was that the MathML standard for the '' function with no defined base defaults to base 10, so since SBML hitched its wagon to MathML a long time ago, this seems like a reasonable externally-defined standard. 2) "Is the infix-to-mathML parser useful without the corresponding mathML-to-infix translator?" Overwhelmingly, the answer here is 'yes' or 'it doesn't matter'--this is good to know, and we'll be releasing the L3 parser without waiting to simultaneously release the to-infix translator. 3) "Should "-4' be translated as such inside a element, or should it use ?" Most people don't care, and other opinion is evenly split. Thanks for your responses! -Lucian * Lucian Smith <<a href="mailto:lpsmith@spod-central.org" target="_blank">lpsmith@spod-central.org</a>> [2012-03-29 17:24] writes: > After years of threatening to do so, I finally wrote the basics of an L3 > infix-to-mathml parser. Thanks to all of you who wrote in with > suggestions the last time I mentioned this; your suggestions have been > incorporated into the current development version. > > Now we have a few more questions we want your input on, and have created a > short 3-question survey for it: > > <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> > > More detail is at the survey itself, but basically, the questions are: > > 1) Should "log(x)" translate to natural log, base-10 log, or be illegal? > 2) How critical is a mathml-to-infix L3 translator to the usefulness of > the infix-to-mathml L3 translator? > 3) Does it matter to you if "-4" is translated as 'minus(4)' (in the > mathml)? > > Thank you! If you have any additional questions, feel free to ask here. > > -Lucian > ____________________________________________________________ > To manage your sbml-interoperability list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability</a> > > For a web interface to the sbml-interoperability mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the sbml-interoperability list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> ____________________________________________________________ To manage your sbml-interoperability list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability</a> For a web interface to the sbml-interoperability mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-interoperability list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Survey for L3 Parser

Lucian Smith — 2012-03-29T16:24:17-00:00

After years of threatening to do so, I finally wrote the basics of an L3 infix-to-mathml parser. Thanks to all of you who wrote in with suggestions the last time I mentioned this; your suggestions have been incorporated into the current development version. Now we have a few more questions we want your input on, and have created a short 3-question survey for it: <a href="http://www.surveymonkey.com/s/YG76BDG" target="_blank">http://www.surveymonkey.com/s/YG76BDG</a> More detail is at the survey itself, but basically, the questions are: 1) Should "log(x)" translate to natural log, base-10 log, or be illegal? 2) How critical is a mathml-to-infix L3 translator to the usefulness of the infix-to-mathml L3 translator? 3) Does it matter to you if "-4" is translated as 'minus(4)' (in the mathml)? Thank you! If you have any additional questions, feel free to ask here. -Lucian ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

PyDev: Unresolved import: libsbml

ls233 — 2012-03-26T03:58:33-00:00

I use PyDev for Eclipse as my main Python IDE (Windows). I have libsbml 5.4.1 installed and working properly with the IDLE (Python 2.7). PyDev for Eclipse however complains - Unresolved import: libsbml. Anybody uses PyDev with libsbml? thanks German

Re: libSBML using Borland, Codegear compiler

Mike Hucka — 2012-03-13T00:12:54-00:00

Hi Totte, Thank you very much for this information and for working on the compatibility with the Borland compiler! We'll aim to incorporate these changes in a future libSBML release. Best regards, MH -- Mike Hucka, Ph.D. <a href="mailto:mhucka@caltech.edu" target="_blank">mhucka@caltech.edu</a> Member of the Professional Staff, Engineering and Applied Science The California Institute of Technology On Sat, 10 Mar 2012 11:41:15 -0800, Totte Karlsson wrote: > Hi, > I recently needed to compile libSBML using the Borland Compiler. As > different > compilers, catches different problems I expected that some fixes would be > necessary. Surprisingly, consider the number of lines of code in > libSBML, they > where not that many or hard to fix. > > The problems where in these areas: > 1) #defines Visual Studio and other compilers(?) accept the (non-standard) > #if WIN32 > > while CG don't. All such constructs needed to be changed to > #ifdef WIN 32 > or #if defined(WIN32) > > 2) returns from ?: statements. The two operands need to be of the same type. > 3) isnan is not defined for borland > 4) tolower/toupper type cast > 5) Some other peculiar errors > > For the curious, I compiled the "fixes", and not so pretty > "quick-fixes" on this > page: > <a href="http://www.monkisoft.com/wp/archive/compile-libsbml-with-codegear-xe-compiler/" target="_blank">http://www.monkisoft.com/wp/archive/compile-libsbml-with-codegear-xe-compiler/</a> > > Hopefully, later on, this page will be obsolete.. > > Cheers, > Totte > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

libSBML using Borland, Codegear compiler

totte_karlsson — 2012-03-10T19:41:15-00:00

Hi, I recently needed to compile libSBML using the Borland Compiler (CodeGear, CG). As different compilers, catches different problems I expected that some fixes would be necessary. Surprisingly, consider the number of lines of code in libSBML, they where not that many or hard to fix. The problems where in these areas: 1) #defines Visual Studio and other compilers(?) accept the (non-standard) #if WIN32 while CG don't. All such constructs needed to be changed to #ifdef WIN 32 or #if defined(WIN32) 2) returns from ?: statements. The two operands need to be of the same type. 3) isnan is not defined for borland 4) tolower/toupper type cast 5) Some other peculiar errors For the curious, I compiled the "fixes", and not so pretty "quick-fixes" on this page: <a href="http://www.monkisoft.com/wp/archive/compile-libsbml-with-codegear-xe-compiler/" target="_blank">http://www.monkisoft.com/wp/archive/compile-libsbml-with-codegear-xe-compiler/</a> Hopefully, later on, this page will be obsolete.. Cheers, Totte ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

Sarah Keating — 2012-03-08T08:48:15-00:00

Dear "people who use libSBML to interact with annotations" Thank you very much for the feedback . After carefully considering everything that has been suggested so far, we have identified the following development goals for libSBML. Already done: ------------------- LibSBML-5.4.0 reduced the rigidity with which the RDF parser looked for a MIRIAM compliant annotation and added a number of warnings that will be logged when a document is read in to tell the user that the objects created are not fully valid. Short term (libSBML-5.5) : ----------------------------------- Change the existing behaviour so that we do not remove and reconstruct RDF UNLESS a user has specifically interacted with the annotation or the MIRIAM_RDF objects ModelHistory and CVTerm. This means the XMLNode originally read in is only ever altered by the user, which currently is not the case. This will address the issues about losing information in the majority of cases. Longer term (libSBML-6) : ------------------------------------ 1) Explore further the concept of including a full RDF parser or at least facilitating access to a full RDF parser from within libsbml to allow users to interact with RDF annotations directly as RDF. 2) Within the "Running states" concept <a href="http://sbml.org/SBML_Projects/libSBML/Development/Running_states" target="_blank">http://sbml.org/SBML_Projects/libSBML/Development/Running_states</a> provide options for users to apply a state relating to how they wish to interact with annotations. This would allow users to specify whether libsbml never attempt to parser the RDF; only parse the RDF is a fully MIRIAM compliant Description element is found; parse any RDF that might be a MIRIAN RDF element regardless of validity etc. ----------------------------------------- We hope these measures will ultimately address the needs/desires of all users. Thanks libSBML Team ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

Sarah Keating — 2012-02-29T09:15:42-00:00

Hi Nico >> Only when libSBML writes out a model does it reconstruct the RDF from >> the ModelHistory/CVTerm elements. >> > > I though that they were methods to get the whole annotation as XML. > > SBase.getAnnotation() or SBase.getAnnotationString() return only the non > RDF part of the annotation ? > If there is a way to get the full annotation, then people can do > whatever they want with it afterwards. > There are indeed methods that get the whole annotation. The getAnnotation methods will reconstruct the RDF so the returned XMLNode/string is the whole annotation. > And do the SBase. setAnnotation methods parse the RDF part if there is > some RDF ? Similarly if you use setAnnotation this method will parse any RDF MIRIAM information it finds in the argument. Sorry if I was not clear :-( Sarah ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

rodrigue — 2012-02-27T10:33:33-00:00

On 25/02/12 10:13, Sarah Keating wrote: > Hi > > Thanks for the feedback so far ... now I have another couple of questions > > As Stefan knows IMHO libSBML has no intention of becoming an RDF parser > or indeed incorporating a full rdf parsing library into the libsbml > distribution. :-) I feel this is over and above the need for libSBML to > support the SBML specification. > > Maybe other people have thoughts on that ?? > > Just to reiterate what libSBML does when it encounters an RDF block. > > It parses the block, > if it decides there is a MIRIAM compliant annotation > it creates a ModelHistory/List of CVTerms > and REMOVES the relevant RDF from the annotation block. > > The user is left with the ModelHistory/List of CVTerms objects and an > XMLNode that represents the remaining annotation including a RDF block > with any of the RDF that was not MIRIAM compliant. If the only > annotation was the MIRIAM annotation, then you get the objects and no > XMLNode at all. > > Only when libSBML writes out a model does it reconstruct the RDF from > the ModelHistory/CVTerm elements. > > Originally my post was trying to ascertain where people felt libSBML > should draw the line between parsing or not parsing an RDF annotation > i.e. how strict should the decision making process used by libsbml to > decide it has a MIRIAM compliant annotation actually be. > > However I'm getting the impression that the overall approach might be > counter productive to people who wish to use do more than this with RDF > annotations. > > Does it cause issues for people that libsbml removes the XML > representation of the MIRIAM annotations ? And if so, how major an issue > is this ? I though that they were methods to get the whole annotation as XML. SBase.getAnnotation() or SBase.getAnnotationString() return only the non RDF part of the annotation ? If there is a way to get the full annotation, then people can do whatever they want with it afterwards. And do the SBase. setAnnotation methods parse the RDF part if there is some RDF ? Nico ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

curoli — 2012-02-25T12:14:40-00:00

Hello Sarah, All, If you already have an XML tree in memory, as libSBML does, turning the RDF/XML portion into an RDF graph in memory is not a big deal. An experienced programmer could read the RDF/XML specs [1] in the morning and write the parser in the afternoon. I'd feel strongly tempted to do just that, except that I haven't touched C++ in years and become rusty. RDF libraries tend to be large due to all the things you can do with RDF (reasoning, SPARQL, database, ontology building, and support for half a dozen or more serialization formats). There may be an RDF library in C++ that allows you to isolate the RDF/XML parser and use only that (in Java, that would be Sesame). RDF would not be an SBML/libSBML issue if you would provide a complete RDF document (not just a fragment) and made no mention of what you expect in the RDF. But you don't and you do, so it is your responsibility. Take care Oliver [1] <a href="http://www.w3.org/TR/rdf-syntax-grammar/" target="_blank">http://www.w3.org/TR/rdf-syntax-grammar/</a> On Sat, Feb 25, 2012 at 5:13 AM, Sarah Keating <<a href="mailto:skeating@caltech.edu" target="_blank">skeating@caltech.edu</a>> wrote: > Hi > > Thanks for the feedback so far ... now I have another couple of questions > > As Stefan knows IMHO libSBML has no intention of becoming an RDF parser > or indeed incorporating a full rdf parsing library into the libsbml > distribution. :-) I feel this is over and above the need for libSBML to > support the SBML specification. > > Maybe other people have thoughts on that ?? > > Just to reiterate what libSBML does when it encounters an RDF block. > > It parses the block, > if it decides there is a MIRIAM compliant annotation > it creates a ModelHistory/List of CVTerms > and REMOVES the relevant RDF from the annotation block. > > The user is left with the ModelHistory/List of CVTerms objects and an > XMLNode that represents the remaining annotation including a RDF block > with any of the RDF that was not MIRIAM compliant. If the only > annotation was the MIRIAM annotation, then you get the objects and no > XMLNode at all. > > Only when libSBML writes out a model does it reconstruct the RDF from > the ModelHistory/CVTerm elements. > > Originally my post was trying to ascertain where people felt libSBML > should draw the line between parsing or not parsing an RDF annotation > i.e. how strict should the decision making process used by libsbml to > decide it has a MIRIAM compliant annotation actually be. > > However I'm getting the impression that the overall approach might be > counter productive to people who wish to use do more than this with RDF > annotations. > > Does it cause issues for people that libsbml removes the XML > representation of the MIRIAM annotations ? And if so, how major an issue > is this ? > > > Thanks > > Sarah > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > -- Oliver Ruebenacker, Computational Cell Biologist Virtual Cell (<a href="http://vcell.org" target="_blank">http://vcell.org</a>) SBPAX: Turning Bio Knowledge into Math Models (<a href="http://www.sbpax.org" target="_blank">http://www.sbpax.org</a>) <a href="http://www.oliver.curiousworld.org" target="_blank">http://www.oliver.curiousworld.org</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

Sarah Keating — 2012-02-25T10:13:35-00:00

Hi Thanks for the feedback so far ... now I have another couple of questions As Stefan knows IMHO libSBML has no intention of becoming an RDF parser or indeed incorporating a full rdf parsing library into the libsbml distribution. :-) I feel this is over and above the need for libSBML to support the SBML specification. Maybe other people have thoughts on that ?? Just to reiterate what libSBML does when it encounters an RDF block. It parses the block, if it decides there is a MIRIAM compliant annotation it creates a ModelHistory/List of CVTerms and REMOVES the relevant RDF from the annotation block. The user is left with the ModelHistory/List of CVTerms objects and an XMLNode that represents the remaining annotation including a RDF block with any of the RDF that was not MIRIAM compliant. If the only annotation was the MIRIAM annotation, then you get the objects and no XMLNode at all. Only when libSBML writes out a model does it reconstruct the RDF from the ModelHistory/CVTerm elements. Originally my post was trying to ascertain where people felt libSBML should draw the line between parsing or not parsing an RDF annotation i.e. how strict should the decision making process used by libsbml to decide it has a MIRIAM compliant annotation actually be. However I'm getting the impression that the overall approach might be counter productive to people who wish to use do more than this with RDF annotations. Does it cause issues for people that libsbml removes the XML representation of the MIRIAM annotations ? And if so, how major an issue is this ? Thanks Sarah ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

Stefan.Hoops — 2012-02-24T21:49:23-00:00

Hello All, On Fri, 24 Feb 2012 10:58:52 -0500 Oliver Ruebenacker <<a href="mailto:curoli@gmail.com" target="_blank">curoli@gmail.com</a>> wrote: > Hello, > > I would suggest to have the following functionalities coexisting so > that they can be used separately from each other: > > (1) methods to access the complete RDF data as a graph of RDF nodes, > and to find statements containing given nodes, classes, properties or > data types. libsbml must not do that. There exist libraries (e.g. Redland <a href="http://librdf.org/" target="_blank">http://librdf.org/</a>) for this. As long as libsbml keeps providing the full rdf you simply feed it to your preferred rdf support library. > (2) methods that return classes, properties and data types that are > used to represent ModelHistory or CVTerm objects or other objects of > interest. yes > (3) methods to read, write, modify, yes for the ModelHistory or CVTerm objects > validate maybe > attempt to repair definitely no automatic repair. > ModelHistory or CVTerm objects or other objects objects of interest in > the RDF data. Thanks, Stefan -- Stefan Hoops, Ph.D. Senior Project Associate Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics Facility II Blacksburg, Va 24061, USA Phone: (540) 231-1799 Fax: (540) 231-2606 Email: <a href="mailto:shoops@vbi.vt.edu" target="_blank">shoops@vbi.vt.edu</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

curoli — 2012-02-24T15:58:52-00:00

Hello, I would suggest to have the following functionalities coexisting so that they can be used separately from each other: (1) methods to access the complete RDF data as a graph of RDF nodes, and to find statements containing given nodes, classes, properties or data types. (2) methods that return classes, properties and data types that are used to represent ModelHistory or CVTerm objects or other objects of interest. (3) methods to read, write, modify, validate or attempt to repair ModelHistory or CVTerm objects or other objects objects of interest in the RDF data. Take care Oliver On Fri, Feb 24, 2012 at 10:30 AM, Nicolas Rodriguez <<a href="mailto:rodrigue@ebi.ac.uk" target="_blank">rodrigue@ebi.ac.uk</a>> wrote: > On 22/02/12 14:08, Stefan Hoops wrote: >> On 2/22/12 4:26 AM, Sarah Keating wrote: >>> Dear "people who use libSBML to interact with annotations" >>> >>> There were recently a couple of issues logged on the sourceforge tracker >>> reporting situations in which libSBML completely lost annotations :-( >>> >>> <a href="http://sourceforge.net/tracker/?func=detail&aid=3482279&group_id=71971&atid=942737" target="_blank">http://sourceforge.net/tracker/?func=detail&aid=3482279&group_id=71971&atid=942737</a> >>> >>> <a href="http://sourceforge.net/tracker/?func=detail&aid=3482668&group_id=71971&atid=942737" target="_blank">http://sourceforge.net/tracker/?func=detail&aid=3482668&group_id=71971&atid=942737</a> >>> >>> We have addressed these issues in libSBML-5.4.0 but they raise a wider >>> issue that we would like your input on. >>> >>> When libSBML reads annotations it makes a decision on whether an rdf >>> element is intended to be a 'ModelHistory' element or a 'CVTerm' element >>> or whether it is some other rdf that should be stored but generally ignored. >>> >>> One of the issues raised was that when the annotation did not represent >>> a completely valid ModelHistory it got lost, as libSBML initially >>> decided it was a ModelHistory, parsed it as such and then rejected the >>> ModelHistory element. We addressed this by allowing a ModelHistory >>> element that is technically invalid to be stored and giving the user a >>> warning that this had been done. >>> >>> However, this actually requires 'intelligence' on the part of libSBML. >>> We would like people's thoughts on this? >>> >>> As background note that in the SBML specification Section 6 on >>> annotations, the syntax for the RDF Annotation elements are shown; with >>> the symbol +++ used to indicate where it is valid to have other elements. >>> >>> The question is : >>> >>> When libSBML encounters an RDF annotation that 'might' represent a >>> ModelHistory but is not complete OR has extra information where it is >>> not considered valid - what should we do ? >>> >>> OPTION 1: If the RDF has some of the elements of a Model History we >>> parse it into the ModelHistory object; even if that object is not valid. >>> >>> Advantages: The user then has access to the API to interact with the >>> Model History object (and hopefully fix it !) >>> >>> Disadvantages: Potentially roundtrip invalid Model History objects and >>> if there was additional information where it is not valid to have >>> additional information this information still gets lost. > > I would be for option 1, but without the disavantages !! If they are > missing bits > libSBML shoud read the remaining information but if they are additional > information, then > it should be read as XMLNode only (a validation warning would be nice in > this case) > > And I think the SBML specs should change as well to make it clear that > the main elements in the History are > optional (creator, created and modified date). > As History can be made on any elements (would be nice to deprecate > ModelHistory in libSBML and replace it by History by the way) > may be some software/tool would want to store only the modified dates, > some only the people that have done modifications and some will handle both. > > >>> OPTION 2: If the RDF does not constitute a complete valid ModelHistory >>> element then it gets treated as another RDF annotation (i.e. stored as >>> XMLNodes). >>> >>> Advantages: Any additional information to a Model History is preserved. >>> >>> Disadvantages: It is much harder to edit the annotation when stored as >>> XML and if you did then use the API to create a new Model History this >>> would take precedence >>> >>> >>> In an ideal world libSBML would allow you to specify which type of >>> behaviour you would prefer. >>> >>> But for the moment, we would like comments on the two options above. >>> >> I actually think that there is a 3rd option. >> a) do not parse the ...</rdf:RDF> element >> b) allow the user to query, set and enumerate the graph created from the >> element for SBML MIRIAM compliant information. > > Having this functionality would probably be nice for some users but it > should not replace > the creation of objects that are more easy to manipulate, in my opinion. > >> The benefits of this approach are >> 1) round tripping is assured since nothing happens to the >> element if the user does not modify it. >> 2) Since the graph is agnostic to what constitutes SBML MIRIAM >> information non-compliant information is preserved even if you modify >> the graph by adding, changing or removing MIRIAM compliant information. >> >> This is what we implemented in COPASI. It requires that you create a >> graph on demand but that is straight forward please have a look at the >> COPASI code in the MIRIAM subfolder. Since COPASI is released under the >> Artistic License 2.0 you are even free to use it :) >> >>> Also, in relation to Option 1, we would like comment on how close to a >>> ModelHistory object does an annotation have to be for libSBML to assume >>> that this is what it is intended to be. For example, is this a >>> ModelHistory annotation or an alternative RDF annotation ? >>> >>> >>> >>> 2010-07-23T17:43:40Z</dcterms:W3CDTF> >>> </dcterms:modified> >>> </rdf:Description> >>> > > This is a valid element History for me (and it should be valid as well > in the future SBML specs) > > Thanks, > Nico > > ____________________________________________________________ > To manage your libsbml-development list subscription, visit > <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> > > For a web interface to the libsbml-development mailing list, visit > <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> > > For questions or feedback about the libsbml-development list, > contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a> > -- Oliver Ruebenacker, Computational Cell Biologist Virtual Cell (<a href="http://vcell.org" target="_blank">http://vcell.org</a>) SBPAX: Turning Bio Knowledge into Math Models (<a href="http://www.sbpax.org" target="_blank">http://www.sbpax.org</a>) <a href="http://www.oliver.curiousworld.org" target="_blank">http://www.oliver.curiousworld.org</a> ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

rodrigue — 2012-02-24T15:30:49-00:00

On 22/02/12 14:08, Stefan Hoops wrote: > On 2/22/12 4:26 AM, Sarah Keating wrote: >> Dear "people who use libSBML to interact with annotations" >> >> There were recently a couple of issues logged on the sourceforge tracker >> reporting situations in which libSBML completely lost annotations :-( >> >> <a href="http://sourceforge.net/tracker/?func=detail&aid=3482279&group_id=71971&atid=942737" target="_blank">http://sourceforge.net/tracker/?func=detail&aid=3482279&group_id=71971&atid=942737</a> >> >> <a href="http://sourceforge.net/tracker/?func=detail&aid=3482668&group_id=71971&atid=942737" target="_blank">http://sourceforge.net/tracker/?func=detail&aid=3482668&group_id=71971&atid=942737</a> >> >> We have addressed these issues in libSBML-5.4.0 but they raise a wider >> issue that we would like your input on. >> >> When libSBML reads annotations it makes a decision on whether an rdf >> element is intended to be a 'ModelHistory' element or a 'CVTerm' element >> or whether it is some other rdf that should be stored but generally ignored. >> >> One of the issues raised was that when the annotation did not represent >> a completely valid ModelHistory it got lost, as libSBML initially >> decided it was a ModelHistory, parsed it as such and then rejected the >> ModelHistory element. We addressed this by allowing a ModelHistory >> element that is technically invalid to be stored and giving the user a >> warning that this had been done. >> >> However, this actually requires 'intelligence' on the part of libSBML. >> We would like people's thoughts on this? >> >> As background note that in the SBML specification Section 6 on >> annotations, the syntax for the RDF Annotation elements are shown; with >> the symbol +++ used to indicate where it is valid to have other elements. >> >> The question is : >> >> When libSBML encounters an RDF annotation that 'might' represent a >> ModelHistory but is not complete OR has extra information where it is >> not considered valid - what should we do ? >> >> OPTION 1: If the RDF has some of the elements of a Model History we >> parse it into the ModelHistory object; even if that object is not valid. >> >> Advantages: The user then has access to the API to interact with the >> Model History object (and hopefully fix it !) >> >> Disadvantages: Potentially roundtrip invalid Model History objects and >> if there was additional information where it is not valid to have >> additional information this information still gets lost. I would be for option 1, but without the disavantages !! If they are missing bits libSBML shoud read the remaining information but if they are additional information, then it should be read as XMLNode only (a validation warning would be nice in this case) And I think the SBML specs should change as well to make it clear that the main elements in the History are optional (creator, created and modified date). As History can be made on any elements (would be nice to deprecate ModelHistory in libSBML and replace it by History by the way) may be some software/tool would want to store only the modified dates, some only the people that have done modifications and some will handle both. >> OPTION 2: If the RDF does not constitute a complete valid ModelHistory >> element then it gets treated as another RDF annotation (i.e. stored as >> XMLNodes). >> >> Advantages: Any additional information to a Model History is preserved. >> >> Disadvantages: It is much harder to edit the annotation when stored as >> XML and if you did then use the API to create a new Model History this >> would take precedence >> >> >> In an ideal world libSBML would allow you to specify which type of >> behaviour you would prefer. >> >> But for the moment, we would like comments on the two options above. >> > I actually think that there is a 3rd option. > a) do not parse the ...</rdf:RDF> element > b) allow the user to query, set and enumerate the graph created from the > element for SBML MIRIAM compliant information. Having this functionality would probably be nice for some users but it should not replace the creation of objects that are more easy to manipulate, in my opinion. > The benefits of this approach are > 1) round tripping is assured since nothing happens to the > element if the user does not modify it. > 2) Since the graph is agnostic to what constitutes SBML MIRIAM > information non-compliant information is preserved even if you modify > the graph by adding, changing or removing MIRIAM compliant information. > > This is what we implemented in COPASI. It requires that you create a > graph on demand but that is straight forward please have a look at the > COPASI code in the MIRIAM subfolder. Since COPASI is released under the > Artistic License 2.0 you are even free to use it :) > >> Also, in relation to Option 1, we would like comment on how close to a >> ModelHistory object does an annotation have to be for libSBML to assume >> that this is what it is intended to be. For example, is this a >> ModelHistory annotation or an alternative RDF annotation ? >> >> >> >> 2010-07-23T17:43:40Z</dcterms:W3CDTF> >> </dcterms:modified> >> </rdf:Description> >> This is a valid element History for me (and it should be valid as well in the future SBML specs) Thanks, Nico ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Release of libSBML-5.4.1

Sarah Keating — 2012-02-24T09:07:39-00:00

--------------------- libSBML-5.4.1 --------------------- We are pleased to announce the release of libSBML-5.4.1 which is available for download from <a href="https://sourceforge.net/projects/sbml/files/libsbml/5.4.1/" target="_blank">https://sourceforge.net/projects/sbml/files/libsbml/5.4.1/</a> NOTE: This is a bug fix only release. Due to technical reasons we are unable at this moment in time to produce installers for Linux. We apologise to those users who find these useful. Please be assured that we will continue to provide these as soon as our technical difficulties have been resolved. ======================================================= Version 5.4.1 (2012-02-24) ======================================================= STABLE RELEASE * Bug fixes - The MATLAB binding function isSBML_Model had a subtle bug that meant it could crash in certain circumstances. This has been addressed. Thanks to Ying Zhang for the report. - When determining units from rate rules unit checking failed to catch the case where time had been redefined as dimensionless. This is now fixed. Thanks to Kieran Smallbone for reporting it. - Documentation files for MATLAB were missing from the dmg installers for MacOS. This has been fixed. - 'getElementBySId' could potentially return initial assignments, event assignments, assignment rules, and rate rules that assigned *to* the SId in question, instead of returning the actual element with the SId. This has been fixed. EXPERIMENTAL RELEASE * Bug fixes - LibSBML will now automatically register any packages that are enabled in code. Previously libSBML could be built including package code but users needed to perform an additional step to actually use it. This was causing some confusion. - In the Hierarchical Model Composition package (comp), flattening routines have been made more robust, and now should handle arbitrarily-deep nested models, both for simple aggregation, and for replacements of arbitrarily-deep elements. ======================================================= Please report any problems you encounter using libSBML either to the mailing list <a href="mailto:libsbml-team@caltech.edu" target="_blank">libsbml-team@caltech.edu</a> or using the issue tracker for libSBML at <a href="https://sourceforge.net/tracker/?group_id=71971&atid=942737" target="_blank">https://sourceforge.net/tracker/?group_id=71971&atid=942737</a> Thanks Frank, Sarah & Mike ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Re: Handling of annotations

Camille Laibe — 2012-02-23T17:26:38-00:00

Hi Sarah, I think the best solution is the one suggested by Stefan. If that cannot be implemented in libSBML (for whatever reason), I would prefer the option 2, mainly because there is no potential loss of information (however, the case when one creates a new Model history would need to be smartly implemented in order to not mess up the previous records). Maybe the main question is: how strict do you want libSBML to be? Some reports (at least the one I submitted), were clearly about something that is not SBML compliant according to the specs (but was perfectly valid RDF). It was about annotation (so something that does not interfere with the model per se) and somebody did consider this additional information useful enough to make the effort to add it, so I think it would be nice if we could not lose it. To summarise: considering valid RDF annotations, it would be fine if libSBML did not provide easy access to elements that are not described in the specs, but all should be kept. Cheers. -- Camille Laibe BioModels.net Coordinator European Bioinformatics Institute, Cambridge (UK) ____________________________________________________________ To manage your libsbml-development list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/libsbml-development" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/libsbml-development</a> For a web interface to the libsbml-development mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the libsbml-development list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

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Re: Possible bug in SBML_formulaToString

Re: Possible bug in SBML_formulaToString

Possible bug in SBML_formulaToString

Re: Attaching user-data to sbml objects using libsbml

Attaching user-data to sbml objects using libsbml

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

Re: libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

libSBML MATLAB bindings in x64 Ubuntu 12.04/Matlab R2012a

Revised experimental files for libSBML-5.6.0

Release of libSBML-5.6.0

Re: gt (x,y) or x &gt; y

Re: OF not defined on gentoo linux (zlib + libSBML-5.5.0)

Re: OF not defined on gentoo linux (zlib + libSBML-5.5.0)

OF not defined on gentoo linux (zlib + libSBML-5.5.0)

gt (x,y) or x > y

Re: New reply to Re: Installing libsbml5.5 for Python by fbergman

Re: Installing libsbml5.5 for Python

Installing libsbml5.5 for Python

SBML to dot conversion

Re: Matlab binding in Ubuntu

Matlab binding in Ubuntu

Re: Issues installing libsbml java binding

Issues installing libsbml java binding

Re: Memory leak on libsbml-5.5.0

Memory leak on libsbml-5.5.0

Re: Survey for L3 Parser

Re: Survey for L3 Parser

Re: Survey for L3 Parser

Re: Survey for L3 Parser

Re: Survey for L3 Parser

Release of libSBML-5.5.0

Standardising #if and #if defined

Re: [python-libsbml]how to get reactant/product from a reaction?

[python-libsbml]how to get reactant/product from a reaction?

Re: gt (x,y) or x > y