News

Here you will find news about both the SBML project itself (including new developments in SBML and upcoming events such as Forum Meetings), as well as broader news of the SBML-using community.

If you have relevant news you would like to have posted here, please send us email to let us know about it.

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News items are sometimes announced in the sbml-discuss and libsbml-discuss forums but don't get posted here despite our efforts, so you may wish to read the forums too.

If you're looking for more general news relevant to systems biology, including job postings and upcoming conferences, take a look at the sysbio list.

SBML News Community News

2008 SBML Forum Meeting

(27 Jun. '07) The next SBML Forum Meeting will be held in Göteborg, Sweden, August 27–28, as a satellite workshop of ICSB 2008.

Repository converted to SVN

(26 Jun '08) The SBML project source code repository now uses SVN instead of CVS for version control.

SBML.org problems

(29 May '08) A security break-in on the server, followed by a disk failure, caused SBML.org to be off-line for two days while we rebuilt it.

New SBML FAQ

(7 May '08) A greatly revised and rewritten list of FAQs and answers for SBML is now available.

New mailing list introduced

(6 May '08) A new mailing list, libsbml-development, now exists for discussions of libSBML improvement and development.

libsbml-discuss renamed

(6 May '08) The libsbml-discuss mailing list has been renamed to sbml-interoperability.

Old sbml.org failed

(2 Mar.'08) The old sbml.org server failed, so we had to unveil this new site even though some areas are unfinished.

LibSBML 3.1.1 released!

(25 Feb.'26) The latest version of LibSBML, an embeddable, portable API library for working with SBML content, is now available.

SBML Hackathon 2008

(19 Feb.'08) This year's SBML Hackathon will be April (6)–7–8 at Stellenbosh University.

SBMLToolbox 3.0.0 released!

(8 Jan.'26) The latest version of SBMLToolbox, a package for working with SBML models in MATLAB, is now available.

LibSBML 3.1.0 released!

(8 Jan.'26) The latest version of LibSBML, an embeddable, portable API library for working with SBML content, is now available.

New SBML Editors elected

(8 Jan.'08) The results are in, and our two new SBML Editors for 2008-2010 are Sven Sahle and Darren Wilkinson. Three cheers for them!

Dates of next SBML Hackathon

(7 Jan.'08) The results of the recent survey are in, and the dates of the 2008 SBML Hackathon will be April 7–8, with an optional third day on April 6, in Stellenbosh, South Africa.

New website in development

(30 Dec. '07) You're reading this on a completely new site and server for SBML.org. It's still in development but hopefully the site will be ready for public use very soon.

libSBML 3.0.3 released!

(17 Dec. '07) LibSBML 3.0.3 is now available. LibSBML is an embeddable, portable API library for reading, writing and manipulating files and data streams containing SBML content.

MathSBML 2.7.1 released!

(7 Dec. '07) MathSBML 2.7.1 is now available. MathSBML is an open-source package for working with SBML models in Mathematica.

libSBML 3.0.2 released!

(28 Nov. '07) LibSBML 3.0.2 is now available. LibSBML is an embeddable, portable API library for reading, writing and manipulating files and data streams containing SBML content.

libSBML 3.0.1 released!

(19 Oct. '07) LibSBML 3.0.1 is now available. LibSBML is an embeddable, portable API library for reading, writing and manipulating files and data streams containing SBML content.

SBML Level 2 Version 3 Release 2!

(27 Sep. '07) Release 2 of the SBML Level 2 Version 3 specification is now available. It corrects typos and small errors in Release 2.

libSBML 3.0.0 released!

(31 Aug. '07) LibSBML 3.0.0 is now available. LibSBML is an embeddable, portable API library for reading, writing and manipulating files and data streams containing SBML content.

2007 SBML Forum Meeting

(22 Aug. '07) The next SBML Forum Meeting will be held in Long Beach, California, USA, October 5–6, as a satellite workshop of ICSB 2007.

SBML Level 2 Version 3 released!

(16 Jun. '07) Release 1 of the SBML Level 2 Version 3 specification is now available.

2007 SBML Hackathon Coming Soon

(3 Apr. '07) This year's SBML Hackathon will be held at the University of Newcastle, UK. Please join us and don't forget to register ASAP!

SBML Level 2 Version 3 Prerelease

(20 Mar. '07) A public review copy of the SBML Level 2 Version 3 specification is now available. Please send us your comments by Apr. 20.

SBML issue reporting system

(13 Jan. '07) There is now an issue reporting and tracking system available for SBML specifications. Revisions of SBML documents will refer to issues logged in this system.

SBML Level 2 Version 2 Released!

(25 Sep. '06) The final version of the SBML Level 2 Version 2 specification is now available!

SBML Wikipedia entry

(18 Sep. '06) There is now an updated entry for SBML in Wikipedia. Let us know your suggestions for improvements.

SBML Tutorial at ICSB 2006

(8 Sep. '06) Mike Hucka will be leading a tutorial on SBML this year at ICSB 2006 in Japan. The focus will be on the about-to-be-released SBML Level 2 Version 2.

Next 2006 SBML Forum meeting

(30 Jul. '06) The next SBML Forum meeting will be held in Tokyo, Japan, October 12-13, as a satellite workshop of ICSB 2006.

SBML Hackathon 2006

(4 Apr. '06) Visit the SBML Hackathon 2006 page for more info about the event happening this week in Nové Hrady, Czech Republic.

New SBML Online Validator!

(6 Mar. '06) SBML.org has a slick new online SBML validator, complete with remote API. Check it out!

MathSBML Vers. 2.5.7 Released!

(4 Feb. '06) The SBML Team released version 2.5.7 of MathSBML, a full-featured package for working with SBML in the Mathematica environment. The new version fixes a small bug in stoichiometry matrix calculations.

SBToolbox2 version 2.0

(6 Jun.'08) The latest version of SBToolbox adds GUIs, new optimization methods, and new sensitivity analysis methods.

Cell Illustrator 4.0

(14 May.'08) BioBase has released version 4.0 of Cell Illustrator. It supports importing SBML.

COPASI user workshop

(23 Apr.'08) The COPASI team will hold a 3-day workshop July 22–24, 2008, at the VBI in Virginia.

Computational Cell Biology course

(22 Apr.'08) The application deadline for the 3-week intensive computational cell biology course at CSHL is April 30.

SBW 2.7.7 released

(2 Apr.'08) A new release of SBW (version 2.7.7) is available and offers many new features and improvements.

COPASI 4.3 released

(25 Mar.'08) A new stable release of COPASI (version 4.3) is available and offers many new features and improvements.

SBToolbox2 version 1.1

(21 Mar.'08) The latest version of SBToolbox adds support for several SBML constructs such as delays and "fast" reactions.

Cell Cycle supports SBML

(12 Feb.'08) The Cell Cycle Database collects genes, proteins and models of the cell cycle and provides a user-friendly web interface. It supports SBML.

PottersWheel 1.5 released

(27 Jan.'08) PottersWheel is a multi-experiment fitting toolbox that supports SBML. The new version includes identifiability analysis.

SBToolbox2 released

(18 Jan.'08) The rewritten SBToolbox and companion add-on package (SBPD) offer powerful features for biological modeling in MATLAB.

PhysioLab Modeler supports SBML

(10 Jan.'08) Entelos's PhysioLab Modeler, a powerful whole-organism simulation and analysis system, now imports and exports SBML.

SIGNALIGN supports SBML

(9 Jan.'08) SIGNALIGN is a new tool for alignment and prediction of biochemical pathways. It supports input in SBML format.

BiologicalNetworks supports SBML

(27 Nov. '07) BiologicalNetworks provides visualization and analysis services and an information management framework for PathSys, an integrated data resource.

Medicel supports SBML

(19 Nov. '07) Medicel is a software suite providing an integrated data model and data + method + application integration for biological research. Medicel Integrator and Medicel Pathway now support SBML.

NEMO compiler supports SBML

(31 Oct. '07) RANGE is generator of random transcription networks and NEMO is a network motif language. The NEMO compiler can now emit SBML.

New version of SBW

(25 Oct. '07) The SBW Development Team has released SBW version 2.7.6. SBW is a software communications framework allowing different tools to be networked.

New version of VCell

(5 Oct. '07) The VCell project has released both a stable and a new beta release of VCell. Among the new features are improved SBML compatibility.

New version of COPASI

(5 Oct. '07) The COPASI project has released development version Build 23, featuring several new capabilities and improvements to SBML compatibility.

acslXtreme supports SBML

(30 Aug. '07) acslXtreme is a modeling, execution and analysis environment for continuous dynamic systems and processes. It now supports importing SBML models.

Genetdes supports SBML

(5 Jul. '07) The new software package Genetdes automatically designs transcriptional networks with desired behaviors. It reads and writes SBML.

RMBNToolbox

(25 Jun. '07) A new MATLAB-based toolbox for generating random models for biochemical networks, the RMBNToolbox, is now available. It supports SBML.

SBW 2.7.1 released

(1 Jun. '07) The SBW Team have released version 2.7.1 of the Systems Biology Workbench (SBW), a software framework for heterogeneous application interoperability.

COPASI 4.1 Build 21 Released

(21 May '07) COPASI version 4.1 (build 21) has been released. COPASI is a free, general simulator for systems biology with a large number of features.

VANTED supports SBML

(3 Apr. '07) VANTED is a network editing and visualization system with features for network-integrated visualization of data from experiments and simulations.

RSBML, a package for R

(29 Mar. '07) RSBML is a package that allows SBML to be imported into R either as an S4 object or a Bioconductor graph object.

Xholon supports SBML

(27 Mar. '07) Xholon is an open-source, general-purpose modeling and simulation tool. It can read models created using UML, among other things.

MIRIAM web services

(15 Jan. '07) The MIRIAM project (Minimal Information Requested in the Annotation of Models) now has web services and other resources online.

SBO online services

(15 Jan. '07) The Systems Biology Ontology (SBO) has an updated browser and now provides web services, OWL export and more.

BioModels Database 7th Release

(5 Jan. '07) BioModels Database is a free, public data resource containing published mathematical models of biological interest. The 7th release is now available.

BioNetGen@VCell Release

(6 Oct. '06) BioNetGen@VCell is a new release of BioNetGen, a tool for automatically generating a reaction network from user-specified rules for biomolecular interactions on the level of protein domains.

PottersWheel supports SBML

(4 Oct. '06) PottersWheel 1.2 beta, a MATLAB systems biology toolbox, supports model creation, fitting data, and designing new experiments.

Cyto-Sim Announced

(21 Jul. '06) Cyto-Sim is a simulator for compartmental models containing membranes with peripheral and integral proteins.

SBML-PET Announced

(8 May '06) SBML-PET is a parameter estimation tool that uses SBML and can work with a variety of types of models.

JSim supports SBML

(8 May '06) JSim is a Java-based simulation system for building and analyzing quantitative models.

SBW 2.5.5 Released

(19 Apr. '06) A new release of SBW (the Systems Biology Workbench) is now available. It features significant new capabilities and new modules.

WebCell Supports SBML

(19 Apr. '06) WebCell is a web-based simulation environment for biochemical networks. It supports exploration and analysis of steady-state and dynamic behaviors.

Introducing CLEML

(21 Mar. '06) The Carbon Labeling Experiment Markup Language (CLEML) annotates SBML with formal descriptions of structure and states of systems in carbon labeling experiments. A software library, libCLEML, is available.

COPASI RC1

(21 Feb. '06) COPASI is a biochemical modeling software package and successor to the popular Gepasi. It supports SBML.

SBMLMerge Test Release

(16 Feb. '06) SBMLmerge is a tool for assisting users in merging SBML files. It is now available for testing from the Max Planck Institute for Molecular Genetics.

SABIO-RK Supports SBML

(15 Feb. '06) The SABIO-Reaction Kinetics database from EML is a web-based system containing data about biochemical reactions. A beta test is under way now.

BioModels Database 4th Release

(31 Jan. '06) BioModels Database is a free, public data resource containing published mathematical models of biological interest. The 4th release is now available.

SBliD announced

(20 Jan. '06) SBliD ("SBML-like Database" framework) is a generic web-based database framework whose specifications are close to SBML. It was developed by a team at CNRS and Joseph Fourier University (France).

BioModels Database paper published!

(9 Jan. '06) The first paper about BioModels Database has been published in Nucleic Acids Research v. 34, D689-D691.

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This page was last modified 05:48, 10 March 2008.


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