|
| (17 May '13) A new version of the standalone Test Runner for the SBML Test Suite is now available.
|
|
| (17 May '13) An updated set of test cases for the SBML Test Suite is now available.
|
|
| (17 May '13) The specification for Version 1 of the SBML Level 3 Qualitative Models package is available.
|
|
| (1 Mar.'13) Release 2 of the specification for SBML Level 3 Hierarchical Model Composition is now available.
|
|
| (28 Feb.'13) Supports the latest Level 3 fbc specification and includes bug fixes and documentation updates.
|
|
| (18 Feb.'13) Registration is open for the next HARMONY, to be held May 20-23, 2013, in Connecticut, USA.
|
|
| (13 Feb.'13) We have updated the list of publications that are known to support submissions in SBML format.
|
|
| (18 Jan.'13) The 2.3 release adds test cases for the SBML Level 3 packages 'comp' and 'fbc'.
|
|
| (16 Jan.'13) The database of public SBML Test Suite results is now open!
|
|
| (14 Jan.'13) Supports the latest Level 3 comp specification, updates other Level 3 package plug-ins, and fixes bugs.
|
|
| (1 Jan.'13) The 2.2 release brings much-improved plots and a few other changes.
|
|
| (13 Dec.'12) Elections for 2 new SBML Editors for 2013–2015 have begun.
|
|
| (20 Nov.'12) The nomination phase for two new SBML Editors is now open.
|
|
| (17 Nov.'12) The next Hackathon on Resources for Modeling in Biology will be held May 20-23, 2013, in Connecticut, USA.
|
|
| (10 Aug.'12) Changes are limited to fixes to documentation errors.
|
|
| (14 Sep.'12) SBMLeditor, the simple low-level editor for SBML, now supports SBML Level 3 Version 1 Core.
|
|
| (25 Aug.'12) JSBML 0.8, the pure Java SBML API library, provides new features and many bug fixes.
|
|
| (14 Aug.'12) Changes include new test cases, some tag updates and case corrections, and an updated online interface.
|
|
| (3 Aug.'12) libSBML 5.6.0 adds an R interface, improved Python interface, bug fixes, and more.
|
|
| (29 Jun.'12) Registration is now open for COMBINE 2012, being held in Toronto, CA, on Aug. 15–19.
|
|
| (12 May.'12) libSBML 5.5.0 fixes an annotation-handling bug and adds new features, including a new math parser.
|
|
| (11 Apr.'12) The ordering system for the SBML t-shirts is now open, in time for HARMONY 2012!
|
|
| (30 Mar.'12) We need libSBML user's feedback about a new infix formula to MathML parser.
|
|
| (24 Feb.'12) libSBML 5.4.1 fixes a few issues discovered in 5.4.0.
|
|
| (24 Feb.'12) libSBML 5.4.1 fixes a few issues discovered in 5.4.0.
|
|
| (15 Feb.'12) libSBML 5.4 fixes some annotation handling and SBML conversion bugs, and adds APIs and docs.
|
|
| (21 Jan.'12) The latest SBMLToolbox supports the 'fbc' flux balance constraints package for SBML Level 3.
|
|
| (23 Dec.'11) The latest libSBML release adds new features and fixes more bugs.
|
|
| (15 Dec.'11) JSBML is a pure Java library for SBML with an API similar to libSBML's. Release 0.8rc1 is now available.
|
|
| (22 Nov.'11) We are running a survey to set the dates of COMBINE 2012 in Toronto, Canada.
|
|
| (12 Nov.'11) The latest libSBML release adds new features and fixes more bugs.
|
|
| (10 Nov.'11) The nomination phase for one new SBML Editors is now open.
|
|
| (9 Nov.'11) The next Hackathon on Resources for Modeling in Biology will be held May 21-25, 2012, in Maastricht, NL.
|
|
| (25 Aug.'11) The first beta release of libSBML 5.1.0 is now available.
|
|
| (19 Jul.'11) The updated SBMLToolbox 4.0 for MATLAB adds fixes and new features (incl. SBML L3v1 Core support).
|
|
| (14 Jun.'11) Registration is now open for COMBINE 2011, being held in Heidelberg, DE, on Sep. 3–7.
|
|
| (6 Jun.'11) Changes include addition of SBML L3v1 Core test cases, SED-ML files, and updates to the online interface.
|
|
| (13 Apr.'11) The first full release of the package-aware libSBML 5 series.
|
|
| (29 Mar.'11) A minor update to eradicate a few bugs and compatibility issues.
|
|
| (29 Mar.'11) This year's COMBINE meeting will be held in Heidelberg, Germany, Sep 3–7.
|
|
| (7 Mar.'11) Featuring bug fixes, improvements in behavior, and new standalone Windows binaries for MATLAB and Python.
|
|
| (23 Feb.'11) MathSBML is a Mathematical package for working with SBML. The new version supports Mathematica 8.0.
|
|
| (5 Feb.'11) JSBML is a pure Java library for SBML with an API similar to libSBML's. A beta version is now available.
|
|
| (20 Jan.'11) This year's SBML Hackathon will be held during April 18–22 as part of HARMONY 2011.
|
|
| (4 Jan.'11) The votes are in: Sarah Keating and Chris Myers will be new SBML Editors in 2011!
|
|
| (9 Oct.'10) The count of known SBML-compatible software packages now exceeds 200.
|
|
| (6 Oct.'10) This has additions for the final release of Level 3 Version 1 Core, and bug fixes.
|
|
| (6 Oct.'10) The final SBML Level 3 Version 1 Core specification is now available.
|
|
| (1 Oct.'10) On Oct. 9, there will be a mini-symposium to mark the 10th anniversary of SBML. Join us right before ICSB in Edinburgh!
|
|
| (19 Sep.'10) The list of known issues in the SBML Level 3 Version 1 Core candidate specification has been updated.
|
|
| (25 Aug.'10) This major update to libSBML supports SBML Level 3 Version 1 Core, fixes several bugs, and adds new facilities.
|
|
| (10 Aug.'10) The next SBML Forum Meeting will be integrated into COMBINE 2010, being held in Edinburgh, UK, on Oct. 6–9.
|
|
| (27 Apr.'10) Another minor bug-fix release of our free MATLAB toolbox for SBML is now available.
|
|
| (12 Apr.'10) A minor bug-fix release of our free MATLAB toolbox for SBML is now available.
|
|
| (7 Mar.'10) We have a winner for the SBML L3 Core specification bug-finding contest!
|
|
| (28 Jan.'10) The new SBMLToolbox, a free MATLAB toolbox, adds features, support SBML L2v4 and fixes bugs.
|
|
| (25 Jan.'10) The next Hackathon will be held May 1–4 in Seattle. Please let us know if you're coming.
|
|
| (21 Jan.'10) This release of the libSBML version 4.0.x series fixes many reported small bugs in 4.0.0.
|
|
| (18 Jan.'10) A preview version of libSBML version 5, with a plug-in architecture for Level 3 packages, is now available.
|
|
| (15 Jan.'10) Report bugs in the SBML L3v1C spec. and you may win a $100 gift certificate for Amazon.
|
|
| (12 Jan.'10) We've started a page for longer "elaborations" of some frequently-asked topics.
|
|
| (31 Dec.'09) Release 1 Candidate of the SBML Level 3 Version 1 Core specification is now available.
|
|
| (21 Dec.'09) The votes are in: Jim Schaff and Lucian Smith will be new SBML Editors in 2010!
|
|
| (7 Dec.'09) The results of the survey about the Windows installers for libSBML are in, and we have a contest winner!
|
|
| (25 Nov.'09) We are running a survey to determine what people want in their Windows installers for libSBML.
|
|
| (20 Nov.'09) SBMLeditor is a portable (written in Java), simple, low-level SBML editor. This release supports SBML L2v4 and the latest libSBML.
|
|
| (12 Nov.'09) SourceForge.net has a review system for projects. Please use it to vote & comment on the SBML project!
|
|
| (10 Nov.'09) The nomination phase for two new SBML Editors is now open.
|
|
| (26 Aug.'09) LibSBML is an API library for SBML. This release focuses on reducing opportunities for creating invalid SBML.
|
|
| (22 Aug.'09) A draft specification of SBML Level 3 Core is now available for public review.
|
|
| (30 Jul.'09) LibSBML is an API library for SBML. This release contains several small bug fixes.
|
|
| (11 July '09) A few more issues have been noted recently on the SBML Level 2 Version 4 errata list.
|
|
| (1 Jul. '09) FAQ item #3.6 now features an expanded explanation of SBML Level 2 annotations.
|
|
| (26 Jun. '09) Our Google Analytics tracker reports sbml.org gets nearly 5000 visitors/month, 50% of them new.
|
|
| (25 Jun. '09) There is now a group for SBML on LinkedIn.com, for all you LinkedIn members.
|
|
| (15 Jun.'09) LibSBML is an API library for SBML. The new release features new object constructors.
|
|
| (9 Jun. '09) We've added a new item, #4.20, to the SBML FAQ.
|
|
| (17 May '09) The next SBML Forum Meeting will be held in Stanford, California, USA, Sep. 3–4, as a satellite workshop of ICSB 2009.
|
|
| (16 May '09) We're conducting a survey to assess development goals for libSBML. Please tell us your thoughts!
|
|
| (12 May '09) We're conducting a survey to assess development goals for libSBML. Please tell us your thoughts!
|
|
| (11 May '09) A few issues have been noted recently on the SBML Level 2 Version 4 errata list.
|
|
| (9 May '09) SBML has a news feed on Twitter @sbmlnews.
|
|
| (17 Mar.'09) LibSBML is an API library for SBML. Version 4.0.0's API changes make it harder to create invalid SBML.
|
|
| (3 Mar.'09) LibSBML is an API library for SBML. The new release fixes bugs and a memory leak in 3.3.1.
|
|
| (3 Feb.'09) LibSBML is an API library for SBML. The new release fixes a few bugs in 3.3.0, including a potential crasher.
|
|
| (21 Jan.'09) LibSBML is an API library for working with SBML. New features include support for SBML Level 2 Version 4.
|
|
| (20 Jan. '09) SBML.org now partners with the developers of SBML2LaTeX to provide an online service for generating human-readable reports of SBML files.
|
|
| (22 Dec. '08) Release 1 of the SBML Level 2 Version 4 specification is now available. It corrects a few issues in L2V3 and acts on decisions made by the SBML community.
|
|
| (19 Dec.'08) The votes are in, and Frank Bergmann will be an SBML Editor starting in 2009. Congrats, Frank!
|
|
| (13 Dec.'08) The next SBML Hackathon will be held March 26–28, 2009, at the EBI in Hinxton, UK.
|
|
| (20 Aug.'08) LibSBML is an API library for working with SBML. New features include C# bindings and compressed file support.
|
|
| (28 Jul. '08) KEGG2SBML converts KEGG pathway database files to SBML.
|
|
| (27 Jun. '08) The next SBML Forum Meeting will be held in Gothenburg, Sweden, August 27–28, as a satellite workshop of ICSB 2008.
|
|
| (26 Jun '08) The SBML project source code repository now uses SVN instead of CVS for version control.
|
|
| (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.
|
|
| (7 May '08) A greatly revised and rewritten list of FAQs and answers for SBML is now available.
|
|
| (6 May '08) A new mailing list, libsbml-development, now exists for discussions of libSBML improvement and development.
|
|
| (2 Mar.'08) The old sbml.org server failed, so we had to unveil this new site even though some areas are unfinished.
|
|
| (25 Feb.'26) The latest version of LibSBML, an embeddable, portable API library for working with SBML content, is now available.
|
|
| (8 Jan.'26) The latest version of SBMLToolbox, a package for working with SBML models in MATLAB, is now available.
|
|
| (8 Jan.'26) The latest version of LibSBML, an embeddable, portable API library for working with SBML content, is now available.
|
|
| (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!
|
|
| (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.
|
|
| (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.
|
|
| (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.
|
|
| (7 Dec. '07) MathSBML 2.7.1 is now available. MathSBML is an open-source package for working with SBML models in Mathematica.
|
|
| (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.
|
|
| (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.
|
|
| (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.
|
|
| (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.
|
|
| (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.
|
|
| (16 Jun. '07) Release 1 of the SBML Level 2 Version 3 specification is now available.
|
|
| (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!
|
|
| (25 Sep. '06) The final version of the SBML Level 2 Version 2 specification is now available!
|
|
| (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.
|
|
| (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.
|
|
|
| (17 May '13) Pybrn is a new Python package for analyzing biochemical reaction networks.
|
|
| (30 Apr.'13) A tutorial on modeling & simulation featuring COMBINE standards will be held at ICSB 2013.
|
|
| (27 Apr.'13) A new version of this simulation and parameter optimization software is available.
|
|
| (9 Apr.'13) The metabolic network model by Ines et al. has been noted on NIGMS's front page.
|
|
| (2 Apr.'13) BioUML is a workbench for modeling in biology; the update adds access to BioStore.
|
|
| (23 Mar.'13) OptFlux provides numerous tools for in silico metabolic engineering.
|
|
| (22 Mar.'13) The RAVEN Toolbox helps reconstruct metabolic networks using on protein homology.
|
|
| (20 Mar.'13) BudHat is a web interface for visualizing differences between models.
|
|
| (18 Mar.'13) iNA enables parameter scans for noise estimation in biochemical networks.
|
|
| (14 Mar.'13) The Systems Biology Ontology web services and online browser have been updated.
|
|
| (13 Mar.'13) BiNoM is a Cytoscape plug-in that features SBML support and many capabilities.
|
|
| (6 Mar.'13) The MIRIAM Registry, a set of online services for the generation of persistent identifiers, has had a site redesign.
|
|
| (4 Mar.'13) Antimony offers a human-readable/writeable model definition language with SBML Level 3 'comp' support.
|
|
| (3 Mar.'13) The Recon 2 consensus reconstruction of the human metabolic network has been published.
|
|
| (5 Feb.'13) The MATLAB Glycosylation Network Analysis Toolbox (GNAT) helps create, visualize and simulate glycosylation reaction networks.
|
|
| (1 Feb.'13) This release adds SED-ML export and updates several other components.
|
|
| (27 Jan.'13) This update to the portable, full-featured SBML ODE simulator adds C# bindings and new integrators.
|
|
| (14 Dec.'12) This Java-based library provides exhaustive simulation support for SBML and includes SED-ML support .
|
|
| (12 Dec.'12) The latest release adds new models and the availability of models in RDF/XML format.
|
|
| (6 Dec.'12) A new version of the consensus yeast metabolic network reconstruction has been released.
|
|
| (13 Nov.'12) This release adds parameter scans, editing for stochastic modelling, & support for SBML shorthand.
|
|
| (13 Aug.'12) Supports units, submodels, and the current SBML 'comp' draft specification.
|
|
| (11 Aug.'12) The latest release adds new models and new services, esp. for the Path2Models project.
|
|
| (31 Jul. '12) BioPAX2SBML translates BioPAX into SBML Level 3 with the provisional 'qual' package.
|
|
| (3 Jul. '12) iNA performs efficient analysis of intrinsic noise in biochemical networks using the System Size Expansion.
|
|
| (18 Jun. '12) CySBML is a Cytoscape plugin for importing and displaying SBML files. This is a bug-fix release.
|
|
| (9 Jun. '12) Newly-released KEGGTranslator 2.0 supports SBML Level 3 and BioPAX, and features many enhancements.
|
|
| (8 Jun. '12) PyDSTool is a Python-based dynamical systems tool with many features. It supports SBML.
|
|
| (20 May '12) The latest release adds over 142,000 models
from Path2Models, and the use of the CC0 license.
|
|
| (27 Mar.'12) MesoRD is a stochastic simulator for reactions and diffusion.
|
|
| (2 Mar.'12) The new all-Java SBMLsimulator implements full SBML support and passes the entire SBML Test Suite.
|
|
| (12 Feb.'12) The latest SBW features an updated JDesigner, improved SBML support in RoadRunner, and more!
|
|
| (8 Feb.'12) The latest release adds 68 models, more annotations, and the use of identifiers.org.
|
|
| (3 Feb.'12) JSim version 2.06 includes fixes to its interpretation of SBML.
|
|
| (2 Feb.'12) The Flux Analysis & Modeling Environment is a web-based system for working with stoichiometric models.
|
|
| (22 Jan.'12) Python-based StochPy provides many stochastic simulation algorithms + unique analysis tools.
|
|
| (24 Dec.'11) The latest release of COPASI features updates to the GUI and simulation engine.
|
|
| (16 Dec.'11) SBML2LaTeX translates SBML files to LaTeX reports. This version uses JSBML and adds more features.
|
|
| (18 Nov.'11) SurreyFBA performs constraint-based simulations and network map visualization, and can import SBML.
|
|
| (31 Oct.'11) The new release adds preliminary support for SED-ML and other improvements all around.
|
|
| (26 Oct.'11) The Advanced Model Identification using Global Optimization toolbox for MATLAB supports SBML.
|
|
| (6 Oct.'11) The latest update to the popular GUI-based modeling system adds database connections, SBGN improvements and SED-ML support.
|
|
| (23 Sep.'11) Antimony, the human-readable model definition language system, now implements a draft of SBML composition.
|
|
| (15 Sep.'11) modelMaGe can automatically generate reduced SBML models based on a given master model.
|
|
| (3 Sep.'11) BioModels Database, release 20, features 65 new models and performance improvements!
|
|
| (1 Sep. '11) identifiers.org is a dereferenceable version of MIRIAM URIs, suitable for SBML models and more.
|
|
| (30 Aug. '11) The update to the iPathways iPhone/iPad app adds more pathways & new interface features.
|
|
| (24 Aug.'11) SBW has an updated JDesigner and Jarnac, and improved support for SBGN-ML, SED-ML and SBRML.
|
|
| (1 Aug. '11) The latest COPASI release has tons of features and updates including SBML L3 support.
|
|
| (29 Jul. '11) MEMOSys is a platform for genome-scale metabolic models.
|
|
| (19 Jul. '11) Facile is a command line tool that generates networks in SBML, XPP, MATLAB and other formats.
|
|
| (3 Jul. '11) PRISM 4.0 is a probabilistic model checker that supports SBML input.
|
|
| (29 Jun. '11) MatCont is a MATLAB package for studying parameterized continuous and discrete dynamical systems.
|
|
| (15 Jun. '11) iPathways is an iPhone/iPad app for browsing map diagrams created in CellDesigner.
|
|
| (13 Jun. '11) STEPS can do stochastic simulation of reaction-diffusion systems in arbitrary 3D geometries.
|
|
| (1 Jun. '11) Systrip is a new, open-source, visual environment for analyzing time-series data from biological networks.
|
|
| (13 May '11) BioUML workbench 0.9.2 will support reading CellDesigner diagrams and displaying them in SBGN format.
|
|
| (29 Mar.'11) SBML-PET-API is a parallel parameter estimation tool for SBML models.
|
|
| (21 Mar.'11) Creates an ontology-based representation of SBML models, for verification and querying.
|
|
| (29 Mar.'11) The version 1.1 specification for SED-ML is now available!
|
|
| (21 Mar.'11) ONDEX is a data integration platform enabling diverse data sets to be linked and visualized.
|
|
| (18 Mar.'11) SBW has an updated JDesigner, improved SBML event handling, and SBGN-ML and SED-ML 1.1 support.
|
|
| (8 Mar.'11) SBML2LaTeX is now a pure Java program. Version 0.9.8 offers new features + SBML Level 3 support.
|
|
| (8 Mar.'11) Metannogen assists you or a team in manually annotating SBML files.
|
|
| (6 Feb.'11) The LibSBGN project has released a specification for SBGN-ML as well as LibSBGN Java and LibSBGN C++.
|
|
| (26 Jan.'11) BRENDA is a well-known comprehensive enzyme information system. It now supports output in SBML.
|
|
| (20 Jan.'11) BioSyS performs distributed simulations using grid computing systems and offers many analysis features.
|
|
| (19 Jan.'11) ProMoT lets you model and simulate complex biological systems. The new version has improved SBML support.
|
|
| (11 Jan.'11) SurreyFBA performs constraint-based simulations and network map visualization, and can import SBML.
|
|
| (25 Dec.'10) Cain is an application for stochastic simulations. This new version adds improved support for SBML.
|
|
| (20 Dec.'10) PINT can integrate SBML files from different sources and explore phenotypic outcomes implied by particular conditions.
|
|
| (16 Nov.'10) Omix is an editor for metabolic network diagrams and a customizable, scriptable visualization framework.
|
|
| (16 Nov.'10) Snoopy is a graphical tool for working with biomolecular networks as Petri nets.
|
|
| (3 Nov.'10) The new version of the Reactome open-source, manually curated pathway database features many updates.
|
|
| (26 Oct.'10) FASIMU is a free simulation and analysis framework for FBA offering a range of new computational methods.
|
|
| (9 Oct.'10) The latest release of
iBioSim supports SBML Level 3 Version 1 and includes many enhancements.
|
|
| (7 Oct.'10) This development release of COPASI supports SBML Level 3 Version 1 and includes many enhancements.
|
|
| (1 Oct.'10) The latest release of BioModels Database adds 157 new models, new conversions for Octave and BioPAX, and more.
|
|
| (26 Sep.'10) Cain is an application for stochastic simulations. This new version adds support for events.
|
|
| (24 Sep.'10) The newest release of BioUML adds tons of new features and updates.
|
|
| (13 Sep.'10) JigCell is a Java-based model development tool and ODE-based simulator. Among other things, it supports SBML Events.
|
|
| (10 Aug.'10) PRISM is a probabilistic model checker. The new release supports SBML.
|
|
| (9 Aug.'10) MetNetMaker creates metabolic networks from KEGG LIGAND for FBA in the COBRA toolbox.
|
|
| (3 Aug.'10) CRdata.org is a free, open-source, cloud-based simulation, analysis and sharing system for R, Bioconductor and SBML users.
|
|
| (31 Jul.'10) SBW now supports SBML Level 3 Core (Final Candidate 1), and has an improved Simulation Tool and other updates.
|
|
| (22 Jul.'10) The new stable release of COPASI adds support for events, new stochastic algorithms, and SBML L2v4.
|
|
| (30 Jun.'10) CellDesigner is a full-featured modeling environment with a GUI. This release adds SBML L2v4, SABIO-RK, MIRIAM, PANTHER, SBGN and other support.
|
|
| (31 May.'10) Cain is a stochastic simulator with highly efficient implementations of many methods.
|
|
| (10 May.'10) SBW is a component-based application framework. The update improves support for simulation of SBML models and Windows 7 support.
|
|
| (2 May.'10) There will be a Cell Behavior Ontology (CBO) and Standards for Multicellular Model Specification workshop @ ICSB 2010.
|
|
| (2 May.'10) Workshop on "Developing multi-scale, multi-cell developmental and biomedical simulations with CompuCell3D and SBW" in August.
|
|
| (27 Apr.'10) The latest release of BioModels Database adds 20 new models and many software improvements.
|
|
| (23 Apr.'10) sbmltidy is a simple script to run tidy to reformat an SBML file.
|
|
| (3 Apr.'10) SBMLsqueezer generates rate laws from SBML reactions based on SBO annotations.
|
|
| (10 Feb.'10) The MIASE effort has a new website, connected to BioModels.net.
|
|
| (1 Jan.'10) Cain is a stochastic simulator with highly efficient implementations of many methods.
|
|
| (30 Nov.'09) BioUML, the Java-based modeling platform, now has a web edition.
|
|
| (29 Oct.'09) BioMet Toolbox is a web-based toolbox for analyzing genome-scale models.
|
|
| (27 Oct.'09) modelMaGe can generate models and fit models to data.
|
|
| (27 Oct.'09) CycSim is a pathway genome simulator supporting constraint-based models of metabolism.
|
|
| (19 Oct.'09) TEDDY is an ontology for describing behaviors & other aspects of dynamical systems.
|
|
| (18 Oct.'09) Antimony is a human-readable model definition language and accompanying editor.
|
|
| (17 Sep.'09) BridgeDB is a library for finding and manipulating identifiers. It supports MIRIAM URIs.
|
|
| (12 Sep.'09) DOTcvpSB is a MATLAB-based dynamic optimization tool for models.
|
|
| (8 Sep.'09) MetExplore is a web system to help map metabolomics experiments onto metabolic networks.
|
|
| (2 Sep.'09) BioModels Database, a free database of published models, now contains 231 curated and 198 uncurated models.
|
|
| (28 Aug.'09) CellDesigner is a modeling tool with a GUI. This release adds SBML L2v4, SABIO-RK, SBGN and other support.
|
|
| (28 Aug.'09) BioUML is a Java-based integrated workbench for systems biology. This release adds many powerful new features.
|
|
| (19 Aug.'09) Model Format OWL (MFO) is an expression of SBML in OWL. It now supports all constructs in SBML.
|
|
| (19 Aug.'09) SBW is a component-based application framework. The update improves support for SBML "events" & the proposed layout/render extension.
|
|
| (7 Aug.'09) SBGN (The Systems Biology Graphical Notation) is a visual notation for diagrams in systems biology.
|
|
| (29 Jul.'09) Cain is a stochastic simulator with highly efficient implementations of many methods.
|
|
| (16 Jun.'09) BioModels Database, a free database of published models, now contains 216 curated and 196 uncurated models.
|
|
| (25 Apr.'09) GNU MCSim lets you design statistical or simulation models & perform Bayesian inference.
|
|
| (24 Apr.'09) Tutorial & workshop on SRI's Pathway Tools and BioCyc database in August '09.
|
|
| (23 Apr.'09) Cain is a stochastic simulator with highly efficient implementations of many methods.
|
|
| (26 Mar.'09) A new version of DSMTS (a discrete stochastic test suite) is available for Level 2 Version 4. Plus: an updated SBML shorthand.
|
|
| (25 Mar.'09) BioModels Database, a free database of published models, now contains 211 curated and 124 uncurated models.
|
|
| (16 Mar.'09) Cain is a stochastic simulator implementing many methods, including tau-leaping.
|
|
| (9 Mar.'09) An open-source package for both deterministic and stochastic modeling, ByoDyn features a GUI, facilities for designing experiments, a web service, and more.
|
|
| (3 Mar.'09) The Systems Biology Workbench is a component-based application framework. New features include improved simulator and auto-layout performance.
|
|
| (26 Feb.'09) BioModels Database, a free, public resource, now has a mirror site at Caltech for better load balancing.
|
|
| (13 Feb.'09) The new release of SABIO-RK, a database of biochemical reactions and kinetics, features improved performance, plus updates to the web services & SBML output facilities.
|
|
| (13 Dec.'08) The latest update of the Systems Biology Ontology sports an updated interfaces and new vocabulary branches.
|
|
| (13 Dec.'08) The latest BioUML has architectural improvements, parameter fitting, and new database interfaces.
|
|
| (3 Dec.'08) BioModels Database, a free, public resource, now contains 208 curated and 85 uncurated models, totalling over 34 000 reactions.
|
|
| (20 Nov.'08) Cain is an optimized stochastic simulator implementing many methods, including tau-leaping.
|
|
| (3 Nov.'08) SynBioSS is a suite for generating and simulating synthetic biological networks.
|
|
| (1 Nov.'08) GNA models and simulates qualitative genetic regulatory networks. It supports SBML.
|
|
| (27 Oct.'08) ConsensusPathDB contains human pathways of metabolisms, signal transduction and gene regulation.
|
|
| (18 Sep.'08) The latest stable (4.5) and beta (4.6) versions of the Virtual Cell are now available.
|
|
| (9 Sep.'08) The new release of SBMLeditor, an XML editor for SBML files, fixes bugs and uses libSBML 3.0.2.
|
|
| (21 Aug. '08) BioModels Database is a public resource containing published mathematical models of biological interest.
|
|
| (20 Aug.'08) The latest COPASI adds MIRIAM support and bug fixes.
|
|
| (19 Aug.'08) iBioSim is a tool for analyzing and designing genetic circuit models. It features virtually complete support for all of SBML L2v3.
|
|
| (18 Aug.'08) The Systems Biology Workbench is a component-based application framework. The new release adds many exciting across-the-board feature enhancements.
|
|
| (5 Jul.'08) SBMLeditor is an XML editor for SBML files. The new release fixes some bugs and adds updates for MIRIAM.
|
|
| (4 Aug.'08) CellDesigner is a popular biochemical network modeling tool with a powerful graphical interface.
|
|
| (11 Jul.'08) SYCAMORE is a web-based system providing access to software for modeling, viewing and simulating biochemical systems.
|
|
| (6 Jun.'08) The latest version of SBToolbox adds GUIs, new optimization methods, and new sensitivity analysis methods.
|
|
| (23 Apr.'08) The COPASI team will hold a 3-day workshop July 22–24, 2008, at the VBI in Virginia.
|
|
| (22 Apr.'08) The application deadline for the 3-week intensive computational cell biology course at CSHL is April 30.
|
|
| (2 Apr.'08) A new release of SBW (version 2.7.7) is available and offers many new features and improvements.
|
|
| (25 Mar.'08) A new stable release of COPASI (version 4.3) is available and offers many new features and improvements.
|
|
| (21 Mar.'08) The latest version of SBToolbox adds support for several SBML constructs such as delays and "fast" reactions.
|
|
| (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.
|
|
| (27 Jan.'08) PottersWheel is a multi-experiment fitting toolbox that supports SBML. The new version includes identifiability analysis.
|
|
| (18 Jan.'08) The rewritten SBToolbox and companion add-on package (SBPD) offer powerful features for biological modeling in MATLAB.
|
|
| (9 Jan.'08) SIGNALIGN is a new tool for alignment and prediction of biochemical pathways. It supports input in SBML format.
|
|
| (27 Nov. '07) BiologicalNetworks provides visualization and analysis services and an information management framework for PathSys, an integrated data resource.
|
|
| (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.
|
|
| (31 Oct. '07) RANGE is generator of random transcription networks and NEMO is a network motif language. The NEMO compiler can now emit SBML.
|
|
| (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.
|
|
| (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.
|
|
| (5 Oct. '07) The COPASI project has released development version Build 23, featuring several new capabilities and improvements to SBML compatibility.
|
|
| (30 Aug. '07) acslXtreme is a modeling, execution and analysis environment for continuous dynamic systems and processes. It now supports importing SBML models.
|
|
| (5 Jul. '07) The new software package Genetdes automatically designs transcriptional networks with desired behaviors. It reads and writes SBML.
|
|
| (25 Jun. '07) A new MATLAB-based toolbox for generating random models for biochemical networks, the RMBNToolbox, is now available. It supports SBML.
|
|
| (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.
|
|
| (3 Apr. '07) VANTED is a network editing and visualization system with features for network-integrated visualization of data from experiments and simulations.
|
|
| (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.
|
|
| (27 Mar. '07) Xholon is an open-source, general-purpose modeling and simulation tool. It can read models created using UML, among other things.
|
|
| (15 Jan. '07) The MIRIAM project (Minimal Information Requested in the Annotation of Models) now has web services and other resources online.
|
|
| (5 Jan. '07) BioModels Database is a free, public data resource containing published mathematical models of biological interest. The 7th release is now available.
|
|
| (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.
|
|
| (4 Oct. '06) PottersWheel 1.2 beta, a MATLAB systems biology toolbox, supports model creation, fitting data, and designing new experiments.
|
|
| (21 Jul. '06) Cyto-Sim is a simulator for compartmental models containing membranes with peripheral and integral proteins.
|
|
| (8 May '06) SBML-PET is a parameter estimation tool that uses SBML and can work with a variety of types of models.
|
|
| (8 May '06) JSim is a Java-based simulation system for building and analyzing quantitative models.
|
|
| (19 Apr. '06) WebCell is a web-based simulation environment for biochemical networks. It supports exploration and analysis of steady-state and dynamic behaviors.
|
|
| (21 Feb. '06) COPASI is a biochemical modeling software package and successor to the popular Gepasi. It supports SBML.
|
|
| (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.
|
|
| (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.
|
|
| (31 Jan. '06) BioModels Database is a free, public data resource containing published mathematical models of biological interest. The 4th release is now available.
|
|
| (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).
|
|
