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Posts: 2
Registered:
January 2010
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Posts: 967
Registered:
October 2003
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Re: SBML.py cannot be opened?
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28 Jan '10 23:58
 
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Hi there,
I haven't personally installed SynBioSS, so I don't know
what's included in the package, but it's very likely that
you do need to install libSBML separately. Hopefully that
won't be too hard, but before you do, some questions that
will impact the next step are:
1) What platform/operating system are you using?
2) Does SynBioSS say anything about which specific version
of libSBML it is designed for? (It's not necessarily the
case that you can just use the latest version, if the
software hasn't been updated for a while and uses an
older API.)
MH
ajdecker1022> I hope you can bear with me, as I am an
ajdecker1022> absolute beginner with this! So I just
ajdecker1022> tried to install SynBioSS (Synthetic Biology
ajdecker1022> Software Suite) from
ajdecker1022> synbioss.sourceforge.net from the source
ajdecker1022> code. I'm using Ubuntu Linux 9.10 (which I
ajdecker1022> am completely new to as well :-s) However,
ajdecker1022> when attempting to run the synbioss.py
ajdecker1022> script (the main one) I get an error that
ajdecker1022> SBML.py cannot be opened. Then, after I
ajdecker1022> click ok, it complains about a syntax error:
ajdecker1022> The file sbml.py contains the syntax error
ajdecker1022> invalid syntax at line 530, character 45.
ajdecker1022> I'm guessing this is because I did not
ajdecker1022> properly link the SBML software. I know the
ajdecker1022> documentation is online, but I am confused
ajdecker1022> as to how to properly use ldconfig, and I
ajdecker1022> found the manual to be unhelpful.
ajdecker1022>
ajdecker1022> Am I likely correct in thinking that the
ajdecker1022> problem has to do with no proper linking?
ajdecker1022> Can anyone lend a hand?
____________________________________________________________
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For a web interface to the sbml-interoperability mailing list, visit
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For questions or feedback about the sbml-interoperability list,
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Posts: 1
Registered:
January 2010
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Re: SBML.py cannot be opened?
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29 Jan '10 03:57
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I install libsbml-4.0.0, in a Debian squeeze. Try the following:
"ldconfig -v | grep sbml"
And find this line:
"libsbml.so.4 -> libsbml.so.4.0.0"
and if you have it is that you have properly installed the libSBML. Be
carefull with the version, look at this website:
http://synbioss.sourceforge.net/releases/20080910/101-is-up, I with
libSBML 4.0, and the Debian Squezee packages, I worked the last version
of SynbioSS.
Good luck and sorry for me English, Diego.
ajdecker1022 wrote:
> Hello, everyone!
>
> I hope you can bear with me, as I am an absolute beginner with this! So I just tried to install SynBioSS (Synthetic Biology Software Suite) from synbioss.sourceforge.net from the source code. I'm using Ubuntu Linux 9.10 (which I am completely new to as well :-s) However, when attempting to run the synbioss.py script (the main one) I get an error that SBML.py cannot be opened. Then, after I click ok, it complains about a syntax error: The file sbml.py contains the syntax error invalid syntax at line 530, character 45. I'm guessing this is because I did not properly link the SBML software. I know the documentation is online, but I am confused as to how to properly use ldconfig, and I found the manual to be unhelpful.
>
> Am I likely correct in thinking that the problem has to do with no proper linking? Can anyone lend a hand?
>
> Thanks!
>
> Andrew
> ____________________________________________________________
> To manage your sbml-interoperability list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
>
> For a web interface to the sbml-interoperability mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the sbml-interoperability list,
> contact sbml-team@caltech.edu
>
____________________________________________________________
To manage your sbml-interoperability list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
For a web interface to the sbml-interoperability mailing list, visit
http://sbml.org/Forums/
For questions or feedback about the sbml-interoperability list,
contact sbml-team@caltech.edu
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Posts: 2
Registered:
January 2010
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