SBML Discussion Lists RDF feed

ICSB Tutorial: Modelling and Simulation of Quantitative Biological Models on September 4th, 2013

martin.golebiewski — 2013-04-29T13:18:34-00:00

Dear colleagues, We cordially invite you to this full-day COMBINE (<a href="http://co.mbine.org/" target="_blank">http://co.mbine.org/</a>) tutorial workshop: Modelling and Simulation of Quantitative Biological Models Wednesday, September 4th, 2013 (9:30 - 17:30) Copenhagen (at the Technical University of Denmark) This workshop is a satellite of the 14th International Conference on Systems Biology (ICSB). You can sign in for the tutorial (free of charge) when registering for the conference at <a href="http://www.icsb2013.dk." target="_blank">http://www.icsb2013.dk.</a> Participants will learn setting-up quantitative computer models of biological networks using experimental kinetic data and simulating them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included providing attendees with the necessary skills to enable them to access experimental kinetics data from available resources, assembling computer models with these data and finally simulating the models within different tools. The topics will include: * Using experimental data for setting up quantitative models * Parameter estimation, optimization and model fitting * Simulation, analysis and visualization of biochemical models * Integrated data management and model databases * Community standards and formats for systems biology models Covered tools, platforms, databases and standards: BioModels database: <a href="http://www.ebi.ac.uk/biomodels-main/" target="_blank">http://www.ebi.ac.uk/biomodels-main/</a> CellDesigner: <a href="http://www.celldesigner.org/" target="_blank">http://www.celldesigner.org/</a> COMBINE: <a href="http://co.mbine.org/" target="_blank">http://co.mbine.org/</a> COPASI: <a href="http://www.copasi.org" target="_blank">http://www.copasi.org</a> JWS Online/OneStop: <a href="http://jjj.biochem.sun.ac.za/" target="_blank">http://jjj.biochem.sun.ac.za/</a> SABIO-RK: <a href="http://sabio.h-its.org/" target="_blank">http://sabio.h-its.org/</a> SBML: <a href="http://sbml.org" target="_blank">http://sbml.org</a> SYCAMORE: <a href="http://sycamore.eml.org" target="_blank">http://sycamore.eml.org</a> SysMO-DB: <a href="http://www.sysmo-db.org/" target="_blank">http://www.sysmo-db.org/</a> Virtual Cell (VCell): <a href="http://www.nrcam.uchc.edu/" target="_blank">http://www.nrcam.uchc.edu/</a> Virtual Liver SEEK: <a href="http://seek.virtual-liver.de/" target="_blank">http://seek.virtual-liver.de/</a> Target audience: Modellers and experimentalists with some basic experience in modelling and simulation of biological networks. Tutors: Martin Golebiewski, Frank Bergmann, Akira Funahashi, Noriko Hiroi, Mike Hucka, Nicolas Le Novère, Pedro Mendes, Ion Moraru, Sven Sahle, Jacky Snoep, Dawie van Niekerk, Andreas Weidemann, Katy Wolstencroft Best regards, Martin Golebiewski Phone: +49-6221-533-281 FAX: +49-6221-533-298 Email: <a href="mailto:martin.golebiewski@h-its.org" target="_blank">martin.golebiewski@h-its.org</a> HITS gGmbH Schloss-Wolfsbrunnenweg 35 D-69118 Heidelberg Germany <a href="http://www.h-its.org" target="_blank">http://www.h-its.org</a> _________________________________________________ Amtgericht Mannheim / HRB 337446 Managing Directors: Dr. h.c. Dr.-Ing. E.h. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

HARMONY 2013: May 20-23 in Farmington, CT, USA

Mike Hucka — 2013-02-20T19:26:27-00:00

HARMONY 2013 is kindly being organized by the Virtual Cell group at the University of Connecticut Health Center, USA. It will take place from May 20 to 23. Registration is now open! <a href="http://www.co.mbine.org/events/HARMONY_2013" target="_blank">http://www.co.mbine.org/events/HARMONY_2013</a> ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML Level 3 Hierarchical Model Composition package

Mike Hucka — 2013-02-14T16:52:04-00:00

[This is a belated announcement; this should have been posted on sbml-announce back in November -- MH] The working group for the SBML Level 3 "Hierarchical Model Composition" package is pleased to announce that Version 1 of the specification is now available. You can find a link to the specification, as well as other information, from the 'comp' package status page at <a href="http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Hierarchical_Model_Composition_%28comp%29" target="_blank">http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Hierarchical_Model_Composition_%28comp%29</a> Special thanks to Lucian Smith, Stefan Hoops, Chris Myers, Nicolas Le Novère, Frank Bergmann, Andrew Finney, Martin Ginkel, Jörg Stelling, Ranjit Randhawa, Michael Blinov, Wolfram Liebermeister, and Ion Moraru for their contributions to the development of the 'comp' package over the years, and especially Lucian Smith for pushing the package along through the SBML Development Process and authoring the bulk of the final specification document. Best regards, Mike (on behalf of the 'comp' package working group) ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML Level 3 Flux Balance Constraints package

Mike Hucka — 2013-02-14T16:41:49-00:00

The working group for the SBML Level 3 "Flux Balance Constraints" package is pleased to announce that Version 1 of the specification is now available. You can find a link to the specification, as well as other information, from the 'fbc' package status page at <a href="http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc" target="_blank">http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc</a> Special thanks to Brett Olivier and Frank Bergmann for authoring the specification and pushing the package along through the SBML Development Process. This marks an exciting milestone in the effort to standardize model descriptions and enhance tool interoperability in the constraint-based modeling area. Best regards, Mike (on behalf of Brett and Frank, and the rest of the FBC working group) ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

ICSB/COMBINE Tutorial: Modelling and Simulation of Quantitative Biological Models

martin.golebiewski — 2012-07-31T15:39:47-00:00

A joint tutorial at the International Conference on Systems Biology (ICSB) and the COMBINE 2012 meeting will be of special interest for the SBML community: **** Modelling and Simulation of Quantitative Biological Models: COPASI, CellDesigner, JWS online, SABIO-RK and Virtual Cell **** In this tutorial participants will learn setting-up quantitative computer models of biological networks using experimental kinetic data and simulating them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included providing attendees with the necessary skills to enable them to access experimental kinetics data from available resources, assembling computer models with these data and finally simulating the models within different tools. ** Date and Venue ** Sunday, August 19, 2012, 9:00 am - 2:30 pm Donnelly Centre for Cellular and Biomolecular Research (CCBR) University of Toronto, 160 College Street Toronto M5S 3E1, Canada ** Target audience ** Modellers and experimentalists with some basic experience in modelling and simulation of biological networks The participation is free of charge. Details are in the attached outline. Please register at <a href="https://www.surveymonkey.com/s/icsb2012_workshops" target="_blank">https://www.surveymonkey.com/s/icsb2012_workshops</a> Best regards, Martin Golebiewski (on behalf of the organizers)

Errata for SBML Level 3 Version 1 Core specification

Mike Hucka — 2012-07-04T00:50:40-00:00

The SBML Editors have collected and published a list of officially-recognized issues in the SBML Level 3 Version 1 Core Release 1 specification document. You can view the list by visiting <a href="http://sbml.org/Documents/Specifications#SBML_Level_3" target="_blank">http://sbml.org/Documents/Specifications#SBML_Level_3</a> and clicking on the icon labeled "Errata". As always, we greatly welcome reports of any issues found in the SBML specifications. You can find a link to the issue tracking/reporting system in the same section on the page mentioned above. Thank you. Mike, on behalf of the SBML Editors ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

COMBINE 2012: August 15-19 in Toronto

Mike Hucka — 2012-06-29T18:52:59-00:00

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats, initially in Systems Biology and related fields. The Annual COMBINE forum is a workshop-style event with oral presentations, posters and breakout sessions. The meeting provides an opportunity for those involved in many related standardization and software efforts in systems biology to meet and discuss their efforts, with the aim of working more closely together to ensure smooth interoperability between systems. <a href="http://co.mbine.org/events/COMBINE_2012" target="_blank">http://co.mbine.org/events/COMBINE_2012</a> COMBINE 2012 will take place at The Donnelly Centre building at the University of Toronto from Wednesday August 15 to Sunday Aug. 19, 2012, immediately preceding the 13th International Conference on Systems Biology (<a href="http://icsb2012toronto.com/" target="_blank">http://icsb2012toronto.com/</a>). The COMBINE conference location is a short walk from ICSB events and COMBINE 2012 is an official satellite meeting of ICSB, so you can follow the same travel and accommodation instructions for ICSB and use the same hotel discounts. Registration for COMBINE is $125 (Canadian) to cover costs associated with the meeting, including a workshop dinner and catering. We hope to see you there! ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

HARMONY 2012: May 21-25 in Maastricht

Mike Hucka — 2012-03-08T04:18:41-00:00

*********************************************** Announcing H A R M O N Y 2012 May 21-25, 2012 Maastricht, The Netherlands <a href="http://co.mbine.org/events/HARMONY_2012" target="_blank">http://co.mbine.org/events/HARMONY_2012</a> *********************************************** Dear Colleagues, We are happy to announce that the registration for HARMONY 2012 is open now. HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There is generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. The HARMONY 2012 meeting will be hosted by the Department of Bioinformatics from Maastricht University. The maximum number of participants is 70. Please register using the following form: <a href="http://harmony2012.eventbrite.com" target="_blank">http://harmony2012.eventbrite.com</a> We are trying to get more funding to support the accommodation costs of the participants. We have agreed to special room rates with the Apart Hotel Randwyck and the NH hotel. The participants have to book the hotel rooms themselves. For further information please have a look at <a href="http://www.co.mbine.org/events/HARMONY_2012#Accommodation" target="_blank">http://www.co.mbine.org/events/HARMONY_2012#Accommodation</a> The conference dinner will take place on the evening of Wednesday 23rd May at Ipanema. On the first meeting day (Monday 21st May) there will be an open symposium with tutorials, talks and a reception/poster session in the evening. A full schedule and further information will be provided on the meeting website <a href="http://www.co.mbine.org/events/HARMONY_2012" target="_blank">http://www.co.mbine.org/events/HARMONY_2012</a> We look forward to welcoming you all in Maastricht. For any further questions, please contact us (<a href="mailto:harmony2012@maastrichtuniversity.nl" target="_blank">harmony2012@maastrichtuniversity.nl</a>). Best Regards, Martina, Chris, Gary, Nicolas, Mike ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

COMBINE 2011: September 3-7 in Heidelberg

Mike Hucka — 2011-06-14T22:30:40-00:00

COMBINE 2011, the second international meeting of the COmputational Modeling in BIology NEtwork will take place September 3-7, in Heidelberg, Germany. COMBINE integrates and replaces previous individual meetings of several standardization efforts, including the annual SBML Forum. Registration for COMBINE 2011 is now open. Early bird registration ends July 15, so please register at your earliest convenience. Visit the following web page for the registration link and more information about COMBINE 2011: <a href="http://co.mbine.org/events/COMBINE_2011" target="_blank">http://co.mbine.org/events/COMBINE_2011</a> Attendees are responsible for arranging their own accommodations. We urge you to make your hotel bookings as soon as possible, because Heidelberg in September is a popular tourist destination and hotels fill early. The organizations of COMBINE 2011 are (in alphabetical order): * Gary Bader, University of Toronto, Canadaâ€¨ * Emek Demir, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, USAâ€¨ * Martin Golebiewski, Heidelberg Institute for Theoretical Studies (HITS), Germany â€¨* Michael Hucka, California Institute of Technology (Caltech), USA â€¨* Nicolas Le NovÃ¨re, European Bioinformatics Institute (EMBL-EBI), UKâ€¨ * Sven Sahle, BioQuant at the University of Heidelberg, Germany COMBINE 2011 will be hosted by the Heidelberg Institute for Theoretical Studies (HITS). Thank you, and we hope to see you at COMBINE 2011! ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

HARMONY 2011: April 18-22 in New York City

Mike Hucka — 2011-01-20T05:00:08-00:00

Announcing H A R M O N Y 2011 Dates: April 18-22, 2011 Place: New York City, USA Website: <a href="http://www.biopax.org/harmony.php" target="_blank">http://www.biopax.org/harmony.php</a> Hosts: CBIO @ Memorial Sloan-Kettering Cancer Center Attendance survey: <a href="http://www.surveymonkey.com/s/V2B7FZN" target="_blank">http://www.surveymonkey.com/s/V2B7FZN</a> As most of you hopefully know, beginning this year, we are moving to making SBML Hackathons be part of a wider-scoped event named HARMONY: the HAckathon on Resources for MOdeliNg in biologY. HARMONY 2011 will take place from April 18-22, at the Memorial Sloan-Kettering Cancer Center, New York City, USA. HARMONY events are joint meetings between the developers of formats and related standards supporting computational modeling in biology, including but not limited to SBML, SBGN, BioPAX, and others. Unlike the annual COMBINE meetings, HARMONY is not a general forum targeting the community of users at large, but rather a technical meeting aimed at bringing together developers of the standards and software implementing them. Please help us make the best possible arrangements for this meeting by registering as soon as you can using the short form at <a href="http://www.surveymonkey.com/s/V2B7FZN" target="_blank">http://www.surveymonkey.com/s/V2B7FZN</a> We hope to see you there! Best regards, Nadia Anwar and Mike Hucka, on behalf of all the organizers

SBML Level 3 Version 1 Core, Release 1 (final)

Mike Hucka — 2010-10-06T05:43:33-00:00

The SBML Editors are pleased to announce the release of the final specification for SBML Level 3 Version 1 Core. It is available now from <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> and the SBML project on SourceForge.net. It will soon be available from Nature Precedings as well. This release of the specification incorporates the results of the community vote held earlier this year regarding changes to the definition of events. That is the most significant change from the candidate release of L3V1 Core. In addition, this release includes are a number of small corrections for errors found in the candidate specification. Note this is not a candidate release: it is a final release. The condition for calling this specification "final" is the availability of at least two software systems that demonstrate (to a reasonable degree) the implementation of the specification. During the development of this specification, two implementations (iBioSim and RoadRunner) tested the new features. In fact, the previous release 1 candidate had at least 3 known implementations (BioUML, iBioSim, RoadRunner). In consideration of all this, the SBML Editors believe it is time to call this release final. We would like to thank all of the many members of the SBML community for their current support and use of SBML. The following people deserve special mention in regards to this specification's release: * Chris Myers for extensive discussions, software implementation and testing of events features and definitions * Sarah Keating for implementing test cases and libSBML support * Allyson Lister, for logging a staggering 40+ bug reports for the previous candidate spec * Nick Juty and Camille Laibe for updates to the SBO annotations sections The SBML Editors ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML 10th Anniversary Symposium

Mike Hucka — 2010-10-04T13:02:47-00:00

------------------------------------------------------ The SBML 10th Anniversary Symposium <a href="http://sbml.org/Events/SBML_10th_Anniversary_Symposium" target="_blank">http://sbml.org/Events/SBML_10th_Anniversary_Symposium</a> ------------------------------------------------------ The first draft definition of the Systems Biology Markup Language (SBML) was produced over the summer 2000. Since that time, it has become a de facto standard in computational systems biology, supported by over 180 software tools, and a catalyst for numerous related standardization efforts. To celebrate ten years of SBML, we are holding a special symposium on the afternoon of October 9th, 2010, in Edinburgh, UK, immediately before ICSB 2010 and after COMBINE 2010. Speakers include: * Hiroaki Kitano * John C. Doyle * Hamid Bolouri * Herbert M. Sauro * Pedro Mendes * Andrew M. Finney * Michael Hucka * Nicolas Le Novère The event will run 13:30 to 18:00, followed by cake and refreshments. The location will be the Informatics Forum: Informatics Forum 10 Crichton Street Edinburgh EH8 9AB The event is open to all. Please join us! Nicolas Le Novère & Mike Hucka ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

REMINDER: Registration to COMBINE2010

Nicolas Le Novere — 2010-08-07T08:53:49-00:00

Announcing the: ############################################### # # # First COMBINE meeting # # # ############################################### Dear Colleague, We are pleased to announce COMBINE 2010, that will take place at the Informatics Forum in Edinburgh, Scotland, on Oct. 6â€“9, 2010. With COMBINE 2010, we are inaugurating a new, broader series of meetings to replace, among other events, the SBML and SBGN Fora or the BioPAX face to face meetings. The new meetings are a recognition of the fact that there are multiple allied standardization efforts that should work together towards smooth interoperability. Moreover, we believe a joined meeting makes good economic sense: compared to multiple separate workshops, they reduce the overall number of meetings, travel, and money spent. To reflect this broad scope, we are calling the new workshop series ''COMBINE'': COMBINE: the COmputational Modeling in BIology NEtwork This first meeting will feature sessions about the following efforts: BioPAX, CellML, SBGN, SBML and SED-ML. In addition, sessions will be dedicated to interconversion (how to generate one format from another) and interoperability (i.e. how to make the formats work together). A more detailed agenda will be announced later. The activities at COMBINE will be similar to typical workshops, with oral and poster presentations, break-out discussions, and more. You can find a webpage describing the meeting at <a href="http://sbml.org/Events/Forums/COMBINE_2010" target="_blank">http://sbml.org/Events/Forums/COMBINE_2010</a> (sbml.org being a temporary location before setting up an independent website for the COMBINE and HARMONY meetings.). In order to be able to tune the agenda of COMBINE and satisfy the largest number of attendees, we need you to register *as soon as possible* at: <a href="http://www.surveymonkey.com/s/9GP9KJ3" target="_blank">http://www.surveymonkey.com/s/9GP9KJ3</a> The organizers: * Nadia Anwar, Sloan Kettering Institute * Emek Demir, Sloan Kettering Institute * Michael Hucka, California Institute of Technology (Caltech) * Camille Laibe, European Bioinformatics Institute (EMBL-EBI) * Nicolas Le NovÃ¨re, European Bioinformatics Institute (EMBL-EBI) * Catherine Lloyd, Auckland Bioengineering Institute * Stuart Moodie, University of Edinburgh * Anatoly Sorokin, University of Edinburgh ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

3 more errata in SBML Level 2 Version 4

Mike Hucka — 2010-02-10T08:24:22-00:00

I'd to draw people's attention to some recent additions to the official list of errata in the SBML Level 2 Version 4 Release 1 specification. You can find the list at <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> (click on the blue icon next to "Errata" in the Level 2 Version 4 section). At some point in the future, there will be a Release 2 of the specification to fix the errata. As always, we greatly welcome reports of any issues found in the SBML specifications. You can find a link to the issue tracking/reporting system in the same section on the page mentioned above. Thank you. Mike, on behalf of the SBML Editors ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

The 2010 SBML-BioModels.net Hackathon

Mike Hucka — 2010-01-22T23:47:10-00:00

Announcing the ------------------------------------- 2010 SBML & BioModels.net Hackathon ------------------------------------- May 1-4, 2010 University of Washington Seattle, WA, USA Hosted and co-organized by the Sauro Group (<a href="http://sys-bio.org" target="_blank">http://sys-bio.org</a>) *** Planning on attending? PLEASE TELL US using this form: *** <a href="http://tinyurl.com/hackathon2010" target="_blank">http://tinyurl.com/hackathon2010</a> Hackathons are an opportunity to get together with other software developers. This year's event follows last year's approach of combining the traditional SBML Hackathon with the BioModels.net meeting, and this year it will be even more integrated. The "SBML-BioModels.net Hackathon" is an opportunity to gather developers and researchers who use SBML and BioModels.net (BioModels Database, SBO, MIRIAM, SED-ML) resources, to collaborate and exchange ideas and software and thereby accelerate development of both SBML and BioModels.net resources. This year's event is being hosted by the Sauro Group in the University of Washington Department of Bioengineering. A preliminary agenda is now available online at <a href="http://sbml.org/Events/Hackathons/The_2010_SBML-BioModels.net_Hackathon" target="_blank">http://sbml.org/Events/Hackathons/The_2010_SBML-BioModels.net_Hackathon</a> Please tell us if you are planning on attending by filling out the very short attendance survey. This will help us plan an appropriate number of hotel rooms and other things. The survey link is on the event page; here's a shortcut: <a href="http://tinyurl.com/hackathon2010" target="_blank">http://tinyurl.com/hackathon2010</a> We hope to see you all there in 2010! Mike on behalf of the local organizers and the SBML Team ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML Level 3 Version 1 Core, Release 1 Candidate

Mike Hucka — 2010-01-01T04:55:10-00:00

Dear SBML-using community, The SBML Editors are pleased to announce the availability of the Release 1 Candidate specification for SBML Level 3 Version 1 Core. It is now available from <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> and the SBML project on SourceForge.net. It will shortly be available from Nature Precedings as well. This specification is labeled "Release 1 Candidate" until two independent software implementations are reported by the SBML-using community. At that time, if no significant errors are reported, the specification will be considered final. Release 1 of SBML Level 3 Version 1 Core will not be modified further unless errors are found. Please report issues with this specification using the simple, streamlined reporting form indicated on the front page of the specification and on the sbml.org pages. (It's a live link -- just click it to be sent to the web form.) An explanation is warranted regarding one issue: unlike past specification documents, there are no XML Schemas in this one. Our plan is to create and issue the schemas as separate companion documents, and to produce RELAX NG schemas and probably also Schematron schemas, instead of XML Schemas. Thus, there will be forthcoming documents titled "The Systems Biology Markup Language (SBML): RELAX NG Schema for Level 3 Version 1 Core", etc. We would like to thank all of the many members of the SBML community for their current support and use of SBML. (And a special thanks to Nicolas Le Novere for extra feedback this past week.) The 2009 SBML Editors: Mike Hucka Frank Bergmann Sarah M. Keating Stefan Hoops Sven Sahle Darren J. Wilkinson ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

Additional errata for SBML Level 2 Version 4

Mike Hucka — 2009-07-11T16:11:10-00:00

I'd to draw people's attention to some recent additions to the official list of minor errata in the SBML Level 2 Version 4 Release 1 specification. You can find the list at <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> (click on the blue icon next to "Errata" in the Level 2 Version 4 section). At some point in the future, there will be a Release 2 of the specification to fix the errata. As always, we greatly welcome reports of any issues found in the SBML specifications. You can find a link to the issue tracking/reporting system in the same section on the page mentioned above. Thank you. Mike, on behalf of the SBML Editors ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML Forum 2009: September 3-4

Mike Hucka — 2009-05-17T22:44:52-00:00

-------------------------------------------------------- 14th Workshop on Software Platforms for Systems Biology: The SBML Forum Meeting -------------------------------------------------------- September 3 & 4, 2009 (as a workshop at ICSB 2009, <a href="http://icsb-2009.org" target="_blank">http://icsb-2009.org</a>) Location: Stanford University California, USA General information page: <a href="http://sbml.org/Events/Workshops/The_14th_SBML_Forum_Meeting" target="_blank">http://sbml.org/Events/Workshops/The_14th_SBML_Forum_Meeting</a> The next annual SBML Forum Meeting will be held in California, USA, as a satellite workshop of ICSB 2009. The exact agenda has not yet been set and depends in part on the wishes of the attendees; a more detailed agenda for the meeting is forthcoming. If you are planning on attending, please fill out the survey form at the URL given above as soon as possible. As in past SBML Forum meetings, there will be a block of time available during the meeting for people to give short presentations (5-10 minutes) to the audience on the following topics: SBML-enabled applications, the use of SBML to integrate different applications, proposals for SBML extensions, proposals for standards that compliment SBML, announcements of software or standards or events of interest to SBML users, and general experiences of using SBML "in the field". The survey page provides the opportunity for you to indicate if you would like to make a presentation. We regret that we have no travel support available for this meeting, and hope that potential attendees can extend their ICSB 2009 stay (for those who are going to ICSB) in order to attend. You are not required to attend ICSB 2009 in order to attend the SBML Forum. However, ICSB 2009 requires that all workshop attendees register and pay a small fee (US $45) to defray costs of facilities and other expenses. To do that, please visit <a href="http://icsb-2009.org" target="_blank">http://icsb-2009.org</a> and follow the registration link. We hope to hear from you soon. The SBML Team ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

New errata for SBML Level 2 Version 4

Mike Hucka — 2009-05-12T04:45:59-00:00

I'd to draw people's attention to the recent official issuance of some minor errata statements for the SBML Level 2 Version 4 Release 1 specification. You can find the list at <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> (click on the blue icon next to "Errata" in the Level 2 Version 4 section). At some point in the future, there will be a Release 2 of the specification to fix the errata. As always, we greatly welcome reports of any issues found in the SBML specifications. You can find a link to the issue tracking/reporting system in the same section on the page mentioned above. Thank you. Mike, on behalf of the SBML Editors ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML Level 2 Version 4 specification released

Mike Hucka — 2008-12-23T05:59:33-00:00

Dear SBML-using community, The SBML Editors are pleased to announce the release of the SBML Level 2 Version 4 specification, now available from <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> as well as the SBML project on SourceForge.net. This new version incorporates changes requested by the SBML community via past votes and SBML Forum meetings, as well as numerous smaller corrections for inconsistencies. The following is a short summary of the major changes; more explanations of the changes are provided in Appendix G of the document, and the textual changes (relative to L2 V3 Release 2) are marked in red throughout the document. The details of all major issues are also logged as tracker items in the SBML issue tracker (<a href="http://sbml.org/issue-tracker" target="_blank">http://sbml.org/issue-tracker</a>) under the category "Level 2 Version 3". - Unit consistency is not *required* for a valid SBML model, following the decision made via a vote taken in late 2007. - Removal of prohibition on forward references in user-defined function definitions. - Removal of prohibition on forward references in the Compartment 'outside' attribute. - Corrections to small syntax error in the RDF defined for annotations. - New flag "useValuesFromTriggerTime" on Event allows a model to indicate when EventAssignment formulas are meant to be evaluated. - Clarification about the relationship of compartment sizes when one compartment is outside of another. - Addition of new MIRIAM qualifiers. - Updates for SBO and values allowed for sboTerm. - Removal of irrelevant or no longer applicable validation rules, and addition of new rules for the changes above. - "Built-in SBML units" are now called "predefined SBML units", to be (hopefully) more clear. - Other minor corrections and edits. Please report issues with the SBML Level 2 Version 4 specification using the issue-tracker. We would like to thank all of the many members of the SBML community for their current support and use of SBML. Mike Hucka Nicolas Le Novere Sarah Keating Stefan Hoops Sven Sahle Darren Wilkinson ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML Hackathon 2009: March 26-28

Mike Hucka — 2008-12-10T22:20:07-00:00

Announcing the ------------------- SBML Hackathon 2009 ------------------- <a href="http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon" target="_blank">http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon</a> March 26-28 European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Hosted and co-organized by the Le Novere group (<a href="http://ebi.ac.uk/compneur" target="_blank">http://ebi.ac.uk/compneur</a>) SBML Hackathons are an opportunity to get together with other software developers who use SBML as their model exchange format. The objective of the meeting is to collaborate and exchange ideas and software to accelerate development of SBML-enabled software. The 2009 SBML Hackathon will be held at the familiar EBI in Hinxton, UK, which was also the site of the 2004 SBML Hackathon. The EBI is the home of many SBML-related efforts and resources, including the BioModels Database, the Systems Biology Ontology, MIRIAM Resources, and more. This year's event will be immediately followed by the BioModels Annual Meeting, held March 28-30. Interested persons may register for one or both events using the registration page at <a href="http://moourl.com/sb2009" target="_blank">http://moourl.com/sb2009</a> This year's Hackathon is also preceded by BioSysBio on March 23-25 in Cambridge (<a href="http://conferences.theiet.org/biosysbio/" target="_blank">http://conferences.theiet.org/biosysbio/</a>) and will be followed shortly thereafter by the combined CellML-SBGN-SBO-MIRIAM-BioPAX super-workshop in Auckland, New Zealand, April 5 (<a href="http://www.cellml.org/workshop/workshop2009/" target="_blank">http://www.cellml.org/workshop/workshop2009/</a>) Please visit the SBML Hackathon 2009 information page for more information, and please make sure to fill out the registration form as soon as you can: <a href="http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon" target="_blank">http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon</a> We will have a limited amount of travel support funding available for the SBML/BioModels events. We emphasize *limited amount*. If you truly need it, please get in touch with us as soon as possible and we will try to work something out. We hope to see you all there in 2009! Mike, the Le Novere group, and the SBML Team ____________________________________________________________ To manage your sbml-announce list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sbml-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sbml-announce</a> For a web interface to the sbml-announce mailing list, visit <a href="http://sbml.org/Forums/" target="_blank">http://sbml.org/Forums/</a> For questions or feedback about the sbml-announce list, contact <a href="mailto:sbml-team@caltech.edu" target="_blank">sbml-team@caltech.edu</a>

SBML Forum 2008: Aug. 27-28

Mike Hucka — 2008-05-02T19:07:59-00:00

-------------------------------------------------------- 13th Workshop on Software Platforms for Systems Biology: The SBML Forum Meeting -------------------------------------------------------- August 27 & 28, 2008 (as a workshop at ICSB 2008, http://icsb-2008.org) Location: Gothenburg Convention Centre Gothenburg, Sweden Workshop registration page: http://sbml.org/Events/Workshops/The_13th_SBML_Forum_Meeting/Survey General information page: http://sbml.org/Events/Workshops/The_13th_SBML_Forum_Meeting The next annual SBML Forum Meeting will be held in Gothenburg, Sweden, as a satellite workshop of ICSB 2008. The exact agenda has not been set and depends in part on the wishes of the attendees; a more detailed agenda for the meeting is forthcoming. If you are planning on attending, please fill out the form at the URL given above as soon as possible. We regret that we have no travel support available for this meeting, and hope that potential attendees can extend their ICSB 2008 stay in order to attend. We will, however, arrange for coffee breaks and (hopefully) some meals. As in past SBML Forum meetings, there will be a block of time available during the meeting for people to give short presentations (5-10 minutes) to the audience on the following topics: SBML-enabled applications, the use of SBML to integrate different applications, proposals for SBML extensions, proposals for standards that compliment SBML, announcements of software or standards or events of interest to SBML users, and general experiences of using SBML "in the field". The registration page provides the opportunity for you to indicate if you would like to make a presentation. We hope to hear from you soon. The SBML Team ____________________________________________________________ To manage your sbml-announce list subscription, visit https://utils.its.caltech.edu/mailman/listinfo/sbml-announce For a web interface to the sbml-announce mailing list, visit http://sbml.org/Forums/ For questions or feedback about the sbml-announce list, contact sbml-team@caltech.edu

SBML Hackathon 2008: April (6)-7-8

Mike Hucka — 2008-02-19T18:38:58-00:00

Announcing the ------------------- SBML Hackathon 2008 ------------------- April (6)-7-8 Stellenbosch University Stellenbosch, South Africa http://www.jjj.sun.ac.za/hackathon/ Hosted by the JJJ Group, Stellenbosch University SBML Hackathons are an opportunity to get together with other software developers who use SBML as their model exchange format. The objective of the meeting is to collaborate and exchange ideas and software to accelerate development of SBML-enabled software. This year's Hackathon will also include discussions of the upcoming SBML Test Suite and plans for modularizing libSBML to support SBML Level 3. The SBML Hackathon will be at Stellenbosch University. The local organizers this year are Jannie Hofmeyr, Johann Rohwer and Brett Olivier. The city of Stellenbosch is located approximately 30 kilometers from Cape Town, South Africa. A few pictures and some brief information can be found here: http://www.stellenboschwriters.com/stboschm.html SBML Hackathons have traditionally been two-day events, but with the growth of the global SBML effort, the growing size of the SBML community, and the distances some people have to travel to reach the event, we are experimenting this year with 2.5 days by adding an optional half day beginning on the afternoon of April 6. (Having the extra day in front also accounts for the fact that many flights to South Africa are overnight flights arriving in the morning on April 6.) We anticipate being able to cover the cost of local accommodations, local ground transportation at Stellenbosch, and some meals, for academic attendees. Transportation to/from Stellenbosch and other remaining costs will be partly the responsibility of attendees, although the Caltech group anticipates being able to provide a portion of the funding for those who cannot attend otherwise. If you will be attending the Hackathon, please fill out the following 2 short surveys: About your attendance: http://tinyurl.com/yrtcoe About your flight schedule: http://tinyurl.com/294nnu Best regards, Mike (on behalf of everyone) ____________________________________________________________ To manage your sbml-announce list subscription, visit https://utils.its.caltech.edu/mailman/listinfo/sbml-announce For a web interface to the sbml-announce mailing list, visit http://sbml.org/forums/ For questions or feedback about the sbml-announce list, contact sbml-team@caltech.edu.

Release 2 of SBML Level 2 Version 3 is now available

Mike Hucka — 2007-09-28T16:51:22-00:00

Dear SBML community, The SBML Editors are pleased to release a minor update to the SBML Level 2 Version 3 specification, in the form of Release 2. This release makes no SBML language changes that were not intended to be in Release 1; rather, it makes corrections for issues and errors that have come to light since the announcement of Release 1. These issues are documented in detail in the new Appendix H of the document and can also be found online at the following URL: http://sbml.org/specifications/sbml-level-2/version-3/errata/ There are some particularly unfortunate typographical errors in the examples and explanations of SBML reactions in the first release of Level 2 Version 3, so if you have been scratching your head over some of the equations in Release 1, the Release 2 update may resolve the questions for you. A PDF version of the SBML Level 2 Version 3 specification is available for immediate download from SourceForge at http://sourceforge.net/project/showfiles.php?group_id=71971 The file is called "sbml-level-2-version-3-rel-2.pdf". You can also find a direct link at http://sbml.org/specifications/sbml-level-2/version-3 Please report any issues you find in the new release using the online tracker at http://sbml.org/issue-tracker The SBML Editors. ____________________________________________________________ To manage your sbml-announce list subscription, visit https://utils.its.caltech.edu/mailman/listinfo/sbml-announce For a web interface to the sbml-announce mailing list, visit http://sbml.org/forums/ For questions or feedback about the sbml-announce list, contact sbml-team@caltech.edu.

SBML Forum 2007: Oct. 5-6

Mike Hucka — 2007-08-23T06:01:26-00:00

-------------------------------------------------------- 12th Workshop on Software Platforms for Systems Biology: The SBML Forum Meeting -------------------------------------------------------- October 5 & 6, 2007 (immediately following ICSB 2007, http://icsb-2007.org) Location: Long Beach Convention Center Long Beach, California Workshop registration page: http://surveymonkey.com/s.aspx?sm=XEp1nZuPNCdEPpPfJpMqDQ_3d_3d General information page: http://www.sbml.org/workshops/twelfth/ The next annual SBML Forum Meeting will be held in Long Beach, California, USA, as a satellite workshop of ICSB 2007. Although the exact agenda has not been set and depends in part on the wishes of the attendees, this next Forum meeting will likely focus on moving forward with SBML Level 3 development. A more detailed agenda for the meeting will be forthcoming. If you are planning on attending, please fill out the form at the URL given above as soon as possible. We regret that we have no travel support available for this meeting, and hope that potential attendees can extend their ICSB 2007 stay in order to attend. As in past SBML Forum meetings, there will be a block of time available during the meeting for people to give short presentations (5-10 minutes) to the audience on the following topics: SBML-enabled applications, the use of SBML to integrate different applications, proposals for SBML extensions, proposals for standards that compliment SBML, announcements of software or standards or events of interest to SBML users, and general experiences of using SBML "in the field". The registration page provides the opportunity for you to indicate if you would like to make a presentation. We hope to hear from you soon. The SBML Team ____________________________________________________________ To manage your sbml-announce list subscription, visit https://utils.its.caltech.edu/mailman/listinfo/sbml-announce For a web interface to the sbml-announce mailing list, visit http://sbml.org/forums/ For questions or feedback about the sbml-announce list, contact sbml-team@caltech.edu.

SBML Level 2 Version 3 specification released

Mike Hucka — 2007-06-16T23:16:25-00:00

Dear SBML-using community, The SBML Editors are pleased to announce the release of the SBML Level 2 Version 3 specification, now available from http://sbml.org/documents/ as well as the SBML project on SourceForge.net. This new version of the SBML Level 2 specification incorporates many corrections and clarifications. The following is a short summary of some of the major changes; a more detailed list is provided in Appendix G of the document. - Placement of the 'sboTerm' attribute on SBase instead of only some individual object classes, and expansion of the SBO hierarchy and the mapping of SBML objects to SBO - Removal of 'timeUnits' from Event - Removal of 'spatialSizeUnits' from Species - Explanations of some differences in data type definitions between XML Schema and MathML - Explanation of the units assumed for literal numbers appearing in mathematical expressions, along with corrections to validation rules. - Explanations of the units required by various MathML operators and other constructs - Corrections to the definitions of some primitive data types - Addition of more guidelines about the content of elements. - Addition of more validation rules - Complete redrawing of all class definition diagrams to use more proper UML Please report issues with the SBML L2v3 specification using the reporting facilities at http://sbml.org/issue-tracker We would like to thank all of the many members of the SBML community for their current support and use of SBML. Mike Hucka Nicolas Le Novere Sarah Keating Stefan Hoops Andrew Finney ____________________________________________________________ To manage your sbml-announce list subscription, visit https://utils.its.caltech.edu/mailman/listinfo/sbml-announce For a web interface to the sbml-announce mailing list, visit http://sbml.org/forums/ For questions or feedback about the sbml-announce list, contact sbml-team@caltech.edu. [Note added by moderator 2007-Jun-25: the original message had an incorrect subject line. This archived message has been edited to make the correction, thereby hopefully reducing confusion and making search easier for users of this web forum. The original message is still untouched in the sbml-announce@caltech.edu mailing list archive. -- Mike Hucka]

SBML Hackathon 2007: June 7-8

Mike Hucka — 2007-04-13T22:34:04-00:00

[I neglected to post this here last month; my apologies. --MH] Announcing the ------------------- SBML Hackathon 2007 ------------------- June 7-8, 2007 Newcastle University, UK http://www.mas.ncl.ac.uk/~ncsg3/hackathon07/ Hosted by the University of Newcastle upon Tyne, UK We are pleased to announce that a site and dates have been selected for the 2007 SBML Hackathon. The local organizers this year are Colin Gillespie and Darren Wilkinson of the School of Mathematics & Statistics at Newcastle University. SBML Hackathons are an opportunity to get together with other software developers who use SBML as their model exchange format. The objective of the meeting is to collaborate and exchange ideas and software to accelerate development of SBML-enabled software. This year's Hackathon main them will be the new SBML Level 2 Version 3 and working with the (soon-to-be-released) final libSBML 3.0. IMPORTANT: if you will be attending, please help us plan local accommodations by filling out a very brief survey: http://www.surveymonkey.com/s.asp?u=188773526823 We anticipate being able to cover the cost of local accommodations, local ground transportation at Newcastle, and some meals, for academic attendees. Transportation to/from Newcastle and other remaining costs will be the responsibility of attendees. Newcastle, UK, is located in the northeastern region of England, and has excellent links with the rest of the UK and Europe by air, road, sea and rail. Please see the Hackathon web page for more information about the location: http://www.mas.ncl.ac.uk/~ncsg3/hackathon07/ You are encouraged to make flight reservations as soon as possible because prices will likely increase in the coming weeks. Join us at the 2007 SBML Hackathon! -- Mike Hucka and Colin Gillespie ____________________________________________________________ To manage your sbml-announce list subscription, visit https://utils.its.caltech.edu/mailman/listinfo/sbml-announce For a web interface to the sbml-announce mailing list, visit http://sbml.org/forums/ For questions or feedback about the sbml-announce list, contact sbml-team@caltech.edu.

Survey: SBML L2V2R2 versus L2V3 (deadline Feb.8)

Mike Hucka — 2007-02-05T07:34:26-00:00

[This should have been posted to sbml-announce sooner. Very sorry. It went to sbml-discuss but announcements of votes are also supposed to go to sbml-announce. -- MH] Dear SBML Community, The discussion topic that produced the most significant debate at the SBML Forum last October concerned the inadequacy of the current L2V2 spec's use of the sboTerm attribute. Specifically, the realization was that it needs to be placed on several SBML elements where it is not currently available. This can be done in one of two ways: either the definitions of the individual objects where sboTerm is missing can be redefined on a case-by-case basis, or sboTerm can be moved to the SBase abstract class as an optional attribute. In either case, the changes are backward compatible in the sense that XML files containing sboTerm attributes as currently defined in L2V2 would still be exactly valid under either version of the fix. However, and more seriously, either approach undeniably changes the SBML object model. This has put the SBML Editors in a bit of a quandary. The guidelines under which we have been *trying* to work is that changes to the syntax of SBML would only occur between Versions within Levels (or else changing whole Levels). The changes that are needed now come at the request of SBML users, and are necessary to actually use SBO properly. Further, some groups have begun using SBO, which is making a fix an urgent matter. The changes *could* be done by making them in a revision of L2V2 (i.e., in Level 2 Version 2 Revision 2), but that would violate (so soon!) the guidelines we were trying to establish for good SBML development. Under those guidelines, these kinds of syntax changes *should* be done as a new Version (so, Level 2 Version 3). But if we create a Level 2 Version 3 so soon after Level 2 Version 2 was released, will that leave a bad impression and result in people losing confidence? In defense of producing Level 2 Version 3, we note that (1) it appears few people have worked on L2V2 support anyway, apparently because most developers are waiting for a final libSBML release with L2V2 support; (2) the SBML issue tracker on http://sbml.org/issue-tracker now has numerous small (albeit simple) changes on the table, including a significant number of additional validation rules, which suggests that producing a Level 2 Version 3 wouldn't be a bad idea; (3) a Level 2 Version 3 specification could be produced very quickly given the relatively simple changes on the table; and (4) if it were done immediately, the difference between L2V2 and a new L2V3 would be small enough that even if someone was in the middle of implementing L2V2 support, they would probably not feel it is a difficult set of changes to make to move to L2V3. Either way, we believe we can produce a new document in February, because of point #3 above. So, here is our question for you. Assuming that either alternative results in a release of an SBML specification quickly, which of the following would you prefer is done? 1) Bend the guidelines and issue the changes as Revision 2 of Level 2 Version 2, or 2) Issue the changes as SBML Level 2 Version 3. Please cast your votes by Feb. 8 using the following page: http://www.surveymonkey.com/s.asp?u=872673185384 The SBML Level 2 Version 2 specification is at: http://prdownloads.sourceforge.net/sbml/sbml-level-2-version-2-rev1.pdf?download Thank you, The SBML Editors (Mike Hucka, Nicolas Le Novere, Sarah Keating, Stefan Hoops, Andrew Finney)

SBML Forum 2006: Oct. 12-13

Mike Hucka — 2006-10-01T19:47:24-00:00

-------------------------------------------------------- 11th Workshop on Software Platforms for Systems Biology: The SBML Forum Meeting -------------------------------------------------------- October 12 & 13, 2006 (immediately following ICSB 2006) Location: National Museum of Emerging Science & Innovation ("MeSci") Tokyo, Japan General information, agenda and registration page: http://www.sbml.org/workshops/eleventh/ The next annual SBML Forum Meeting will be held in Tokyo, Japan, as a satellite workshop of ICSB 2006. The venue will be "MeSci"/Miraikan (http://www.miraikan.jst.go.jp), a favorite location of past events in Japan. Please note that, like some other ICSB workshops, the venue is actually in Tokyo and not Yokohama (where ICSB itself will be held), which means that you will probably want to change hotels. A preliminary agenda is available on the meeting info page, http://www.sbml.org/workshops/eleventh/. The first day will be largely devoted to software talks from delegates, talks about SBML experiences, a review of the final SBML Level 2 Version 2 specification, and related topics. The second day will be largely devoted to SBML Level 3. Prior to coming to the meeting, we strongly advise attendees to print the detailed directions to the venue that we have provided at http://www.sbml.org/workshops/eleventh/. (See the section titled "Location" on that page.) If you are planning on attending, please fill out the form at http://www.surveymonkey.com/s.asp?u=694632374913 if you have not already done so. We regret that we have no travel support available for this meeting, and hope that attendees can extend their ICSB 2006 stay in order to attend. See you at the meeting! The SBML Team

Introducing the 'sbml-announce' mailing list

Mike Hucka — 2006-09-27T06:43:07-00:00

In our continuing efforts to improve communications with the SBML user community and revise the development process to make it more transparent, accountable, timely and relevant, we have introduced a new mailing list: sbml-announce@caltech.edu This is a broadcast-only mailing list for important announcements concerning the Systems Biology Markup Language (SBML). The release of new documents as well as errata and revisions to old documents will be announced here. We request that everyone who uses SBML in their software or their work please sign up for the sbml-announce mailing list, so that we may keep you informed about important developments. This is not a discussion list. It is strictly moderated by humans to filter out any off-topic postings. Only the SBML editors may post to the list. Only announcements of the highest importance to SBML will be posted, including: * Releases of specifications for new SBML Levels & Versions * Disclosure of errata and subsequent issue of SBML revisions * Requests for proposals for SBML technical development * Voting topics and deadlines for SBML development issues * Upcoming SBML community events (Forums and Hackathons) The list membership will be kept confidential and will not be intentionally disclosed beyond the SBML editors and their immediate assistants. The list will not be used for advertising. In keeping with our normal policy, the list is opt-in only; no one has been subscribed. You must subscribe yourself using the following registration page: https://utils.its.caltech.edu/mailman/listinfo/sbml-announce The goal is to move announcement-only type postings to sbml-announce and *not* cross-post them to sbml-discuss. (Example: announcements of meetings and new SBML specification documents do not need to be cross-posted.) A very few types of postings may end up being cross-posted if it makes sense to do so. (Example: requests for proposals of technical development may lead to discussions, so it makes sense to have them show up on sbml-discuss.) In summary, the goal is to keep cross-posting to a minimum. Consequently, everyone should subscribe to sbml-announce regardless of whether they are on sbml-discuss or libsbml-discuss. Thank you, Mike -- Mike Hucka, Ph.D. <mhucka@caltech.edu> tel +1.626.395.8128 Senior Research Fellow, Control and Dynamical Systems Co-director, Biological Network Modeling Center The Beckman Institute @ The California Institute of Technology