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The Systems Biology Markup Language
The Systems Biology Markup Language

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Release 2 of the SBML Level 3 Version 1 specification has been issued.

Release 2 contains many clarifications to the text of L3V1R1. In addition, a few restrictions (concerning units and annotations) have been relaxed but there are no SBML feature changes. Any existing valid SBML L3V1 document continues to be valid and any existing implementation supporting L3V1 continues to do so.

The SBML Editors would like to thank all the people who have offered feedback during the process and are looking forward to any reports of implementations supporting the Release Candidate L3V2 specification.

Here is a direct link to the specification document:

http://sbml.org/specifications/sbml-level-3/version-1/core/release-2/sbml-level-3-version-1-core-release-2.pdf

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Online SBML Validator updated
Thanks to the hard work of Frank Bergmann and Sarah Keating, the Online SBML Validator at http://sbml.org/Facilities/Validator/ has been updated in several respects:

1) For models that use not-yet-officially-finalized SBML Level 3 packages, the validator now performs validation against the draft specifications by using RELAX NG schemas. (This behavior can be turned off using a checkbox on the front page.)

2) For models that use version 2 of the FBC package for SBML Level 3, the validator additionally offers to send the model to the BiGG validator maintained by the Palsson group at UCSD.

3) It now runs on much faster hardware.

Please let us know if you encounter any issues with the new system or have any questions or suggestions.

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This year's Google Summer of Code students have started coding! Here's a list of who they are, their mentors, and their blog pages.

* Hovakim Grabski (Frank Bergmann)
"Java support for Deviser, a code generation system for SBML libraries"
http://hgrabski.blogspot.de

* Kaito Ii (Akira Funahashi)
"Interconvertible Layout software for CellDesigner"
http://kaitoii.blogspot.jp/

* Devesh Khandelwal (Zachary King)
"Visual Biology with Escher"
https://github.com/devkhan/EscherConverter/wiki

* Tramy Nguyen (Michael Hucka)
"Interconversion between the systems biology modeling formats SBML and BioPAX"
http://www.async.ece.utah.edu/~tramyn/gsoc

* Roman Schulte (Andreas Dräger)
"Offline SBML validation in the Java-based JSBML library"
http://romanschulte.blogspot.de

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BioModels Database 30th release
The BioModels Team has made release #30 of the database: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20160510

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LibSBML 5.13.0 released
Adds support for SBML Level 3 Groups, fixes bugs, and more.

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SBML Level 3 Groups package released
The SBML Editors and the working group for the SBML Level 3 "Groups" package are pleased to announce that Version 1 of the specification is now available.  You can find the document at its resolvable URI

  http://identifiers.org/combine.specifications/sbml.level-3.version-1.groups.version-1.release-1

You can also find a link to the specification, as well as other information, from the 'groups' package status page at 
  http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/groups

The package authors would like to thank Andreas Dräger, Ben Heavner, Brett Olivier, Kieran Smallbone, and Anna Zhukova for their work in implementing 'Groups' support in their own software tools.

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The 2016 summer school on whole-cell modeling is taking place next month in Barcelona:

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Conference on computational modeling with COPASI, May 12-13, in Manchester: http://buff.ly/1RRkKWI
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FAIRDOM launched a webinar series about life science data and model management. Steven Wiley speaks on Monday 25th – http://buff.ly/1T6yZXW

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BioSharing is conducting a survey about a registry of standards. If you use any standard in life sciences at all, you really should fill out the survey: https://www.surveymonkey.co.uk/r/BioSharingStandardsRegistry
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