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This page is an archive of news announcements made on SBML.org about topics from the SBML-using community. For news specifically about SBML, SBML software, and this site, please see the SBML news page.


SBMLsimulator 1.2.1

(22 Jul.'14) New features and bug fixes in the pure Java simulation library.

libRoadRunner 1.2.3 released

(22 Jul.'14) Updates and bug fixes for this fast SBML simulation library.

CellDesigner 4.4 released

(17 Jul.'14) The new version of the popular modeling environment offers many new features and updates.

SBMLsqueezer 2.0 released

(7 Jul.'14) SBMLqueezer generates rate laws from SBML reactions and other data.

Omix supports SBML

(9 Jun.'14) The new Kinetic Modeling Plug-in for the powerful Omix modeling system supports SBML.

Tellerium 1.1 released

(16 May '14) Tellerium is a new Python environment for systems and synthetic biology modeling and simulation.

libRoadRunner 1.2 released

(13 May '14) Adds prototype Gillespie simulation, plus many bug fixes.

SBMLsimulator 1.2

(30 Apr.'14) This Java-based tool for simulation and parameter estimation has new features and bug fixes.

VCell Short Course

(29 Apr.'14) The 15th Annual Virtual Cell Short Course will be held June 9-11.

New TEDDY release

(27 Apr.'14) An update to the Terminology for the Description of Dynamics is now available.

BioUML 0.9.7

(26 Apr.'14) The new release adds population-based modeling, better handling of huge models, and more.

COPASI 4.12

(18 Apr.'14) The new release adds SED-ML support, new GUI features and new algorithms.

libSEDML 0.3.0

(16 Apr.'14) The new version supports SED-ML Level 1 Version 2, plus bug fixes and new features.

BioModels Database rel. 27

(11 Apr.'14) The latest BioModels Database release has over 500 curated models.

MonaLisa release 3

(20 Mar.'14) This Petri net-based tool for biochemical network analysis has visualization and animation too.

Sim Core Library 1.4

(18 Mar.'14) A new version of the pure-Java Systems Biology Simulation Core Library is available.

MASS Toolbox 1.0.3

(14 Mar.'14) A new Mathematica-based kinetic and constraint-based model building and simulation framework.

ModeRator 2.5.7

(10 Mar.'14) Model Comparator gives insights into the similarity of reconstructions that lack entity identifiers.

SBW 2.10.0 released

(3 Mar.'14) The new version of the Systems Biology Workbench has many new features and updates.

PySB 0.1.11 released

(3 Mar.'14) PySB is a framework for building models of biochemical systems as Python programs.

libRoadRunner 1.0.1 released

(3 Mar.'14) This minor update improves the Windows installer and SBML compatibility.

Antimony 2.5 released

(14 Feb.'14) Antimony offers a human-readable/writeable model definition language with SBML Level 3 'comp' support.

MonaLisa Release 2

(17 Jan.'14) MonaLisa is a Petri net-based tool for visualizing and analyzing biochemical networks.

ModeRator 2.5.5

(6 Jan.'14) The Model Comparator evaluates the similarity of two models in SBML or COBRA formats.

BioUML 0.9.6

(1 Jan.'14) New features in this modeling workbench system include rule-based modeling and Galaxy integration.

libRoadRunner 1.0.0

(20 Dec.'13) A high-performance cross-platform C/C++ library for simulating and analyzing SBML models.

SED-ML L1 V2

(2 Dec.'13) Level 1 Version 2 of the SED-ML specification has been released.

SBW Validator module

(25 Nov.'13) A module to validate SBML files from within SBW has been released by Frank Bergmann.

FluxBalance 1.9

(11 Nov.'13) An updated module for SBW to solve FBC models is now availlable.

BioModels Database rel. 26

(4 Nov.'13) BioModels Database now contains 1085 published models and offers a SPARQL endpoint.

DEDiscover supports SBML

(22 Oct.'13) DEDiscover 2.9 simulates & does parameter estimation on models described by ODEs & delayed differential equations.

SBML2GPML

(12 Sep.'13) This new PathVisio plugin allows SBML models to be imported.

CellNOpt 1.7.7

(12 Aug.'13) This logic-based modeling software system now supports SBML Level 3 Qualitative Models.

iNA 0.4.2 released

(11 Jun.'13) The new release offers a new plot editor and supports multi-core computations on MacOS.

BioUML 0.9.5

(21 Jun.'13) The new release of BioUML passes all tests from the SBML Test Suite 3.0.0.

New PySCeS version

(6 Jun.'13) PySCeS 0.9 offers many new features for simulation, analysis, plotting and file export.

New COPASI version

(22 May '13) COPASI 4.10 build 55 brings a large number of new features in all areas.

pybrn released

(17 May '13) Pybrn is a new Python package for analyzing biochemical reaction networks.

ICSB COMBINE tutorial

(30 Apr.'13) A tutorial on modeling & simulation featuring COMBINE standards will be held at ICSB 2013.

SBMLsimulator 1.1

(27 Apr.'13) A new version of this simulation and parameter optimization software is available.

Simulation Core Library 1.3

(20 Apr.'13) A new release of the Systems Biology Simulation Core Library is now available.

NIGMS front-page feature

(9 Apr.'13) The metabolic network model by Ines et al. has been noted on NIGMS's front page.

BioUML 0.9.4 released

(2 Apr.'13) BioUML is a workbench for modeling in biology; the update adds access to BioStore.

OptFlux 3.0.6

(23 Mar.'13) OptFlux provides numerous tools for in silico metabolic engineering.

RAVEN Toolbox

(22 Mar.'13) The RAVEN Toolbox helps reconstruct metabolic networks using on protein homology.

New version of BudHat

(20 Mar.'13) BudHat is a web interface for visualizing differences between models.

iNA 0.4.1 released

(18 Mar.'13) iNA enables parameter scans for noise estimation in biochemical networks.

SBO updated

(14 Mar.'13) The Systems Biology Ontology web services and online browser have been updated.

BiNoM 2.0 released

(13 Mar.'13) BiNoM is a Cytoscape plug-in that features SBML support and many capabilities.

MIRIAM Registry updated

(6 Mar.'13) The MIRIAM Registry, a set of online services for the generation of persistent identifiers, has had a site redesign.

Antimony 2.4 released

(4 Mar.'13) Antimony offers a human-readable/writeable model definition language with SBML Level 3 'comp' support.

Human metabolic network

(3 Mar.'13) The Recon 2 consensus reconstruction of the human metabolic network has been published.

GNAT released

(5 Feb.'13) The MATLAB Glycosylation Network Analysis Toolbox (GNAT) helps create, visualize and simulate glycosylation reaction networks.

CellDesigner 4.3 released

(1 Feb.'13) This release adds SED-ML export and updates several other components.

LibSBMLSim 1.1.0 released

(27 Jan.'13) This update to the portable, full-featured SBML ODE simulator adds C# bindings and new integrators.

Systems Biology Simulation Core Library v.1.2

(14 Dec.'12) This Java-based library provides exhaustive simulation support for SBML and includes SED-ML support .

BioModels Database rel. 24

(12 Dec.'12) The latest release adds new models and the availability of models in RDF/XML format.

Yeast metabolic model updated

(6 Dec.'12) A new version of the consensus yeast metabolic network reconstruction has been released.

iNA 0.4 released

(13 Nov.'12) This release adds parameter scans, editing for stochastic modelling, & support for SBML shorthand.

Antimony 2.3 beta

(13 Aug.'12) Supports units, submodels, and the current SBML 'comp' draft specification.

BioModels Database rel. 23

(11 Aug.'12) The latest release adds new models and new services, esp. for the Path2Models project.

BioPAX2SBML 1.0 released

(31 Jul. '12) BioPAX2SBML translates BioPAX into SBML Level 3 with the provisional 'qual' package.

iNA supports SBML

(3 Jul. '12) iNA performs efficient analysis of intrinsic noise in biochemical networks using the System Size Expansion.

CySBML 1.2 released

(18 Jun. '12) CySBML is a Cytoscape plugin for importing and displaying SBML files. This is a bug-fix release.

KEGGtranslator 2.0

(9 Jun. '12) Newly-released KEGGTranslator 2.0 supports SBML Level 3 and BioPAX, and features many enhancements.

PyDSTool supports SBML

(8 Jun. '12) PyDSTool is a Python-based dynamical systems tool with many features. It supports SBML.

Wolfram SystemModeler

(30 May '12) Wolfram's new SystemModeler supports SBML!

BioModels Database rel. 22

(20 May '12) The latest release adds over 142,000 models

from Path2Models, and the use of the CC0 license.

MesoRD 1.0 released

(27 Mar.'12) MesoRD is a stochastic simulator for reactions and diffusion.

SBMLsimulator released!

(2 Mar.'12) The new all-Java SBMLsimulator implements full SBML support and passes the entire SBML Test Suite.

SBW 2.9.0 released!

(12 Feb.'12) The latest SBW features an updated JDesigner, improved SBML support in RoadRunner, and more!

BioModels Database rel. 21

(8 Feb.'12) The latest release adds 68 models, more annotations, and the use of identifiers.org.

JSim 2.06 released

(3 Feb.'12) JSim version 2.06 includes fixes to its interpretation of SBML.

FAME released

(2 Feb.'12) The Flux Analysis & Modeling Environment is a web-based system for working with stoichiometric models.

StochPy 1.0.4 released

(22 Jan.'12) Python-based StochPy provides many stochastic simulation algorithms + unique analysis tools.

COPASI 4.8 (Build 35)

(24 Dec.'11) The latest release of COPASI features updates to the GUI and simulation engine.

SBML2LaTeX 0.9.9 released

(16 Dec.'11) SBML2LaTeX translates SBML files to LaTeX reports. This version uses JSBML and adds more features.

SurreyFBA 1.32 released

(18 Nov.'11) SurreyFBA performs constraint-based simulations and network map visualization, and can import SBML.

BioUML 0.9.3b released

(31 Oct.'11) The new release adds preliminary support for SED-ML and other improvements all around.

AMIGO released!

(26 Oct.'11) The Advanced Model Identification using Global Optimization toolbox for MATLAB supports SBML.

CellDesigner 4.2 released!

(6 Oct.'11) The latest update to the popular GUI-based modeling system adds database connections, SBGN improvements and SED-ML support.

Antimony 2.0 & 2.1 beta

(23 Sep.'11) Antimony, the human-readable model definition language system, now implements a draft of SBML composition.

modelMaGe 1.0

(15 Sep.'11) modelMaGe can automatically generate reduced SBML models based on a given master model.

BioModels Database rel. 20

(3 Sep.'11) BioModels Database, release 20, features 65 new models and performance improvements!

identifiers.org in beta

(1 Sep. '11) identifiers.org is a dereferenceable version of MIRIAM URIs, suitable for SBML models and more.

iPathways 1.2 released

(30 Aug. '11) The update to the iPathways iPhone/iPad app adds more pathways & new interface features.

SBW 2.8.3 Released

(24 Aug.'11) SBW has an updated JDesigner and Jarnac, and improved support for SBGN-ML, SED-ML and SBRML.

COPASI 4.7 (34) released!

(1 Aug. '11) The latest COPASI release has tons of features and updates including SBML L3 support.

MEMOSys supports SBML

(29 Jul. '11) MEMOSys is a platform for genome-scale metabolic models.

Facile supports SBML

(19 Jul. '11) Facile is a command line tool that generates networks in SBML, XPP, MATLAB and other formats.

PRISM 4.0 released

(3 Jul. '11) PRISM 4.0 is a probabilistic model checker that supports SBML input.

MatCont 4.1 supports SBML

(29 Jun. '11) MatCont is a MATLAB package for studying parameterized continuous and discrete dynamical systems.

iPathways 1.1 released

(15 Jun. '11) iPathways is an iPhone/iPad app for browsing map diagrams created in CellDesigner.

STEPS supports SBML

(13 Jun. '11) STEPS can do stochastic simulation of reaction-diffusion systems in arbitrary 3D geometries.

Systrip supports SBML

(1 Jun. '11) Systrip is a new, open-source, visual environment for analyzing time-series data from biological networks.

BioUML reads CellDesigner

(13 May '11) BioUML workbench 0.9.2 will support reading CellDesigner diagrams and displaying them in SBGN format.

SGMP exports SBML

(26 Apr.'11) The UCSD Signaling Gateway Molecule pages now support SBML!

BioModels Database rel. 19

(15 Apr.'11) BioModels Database release 19 features 69 new models!

SBML-PET-MPI 1.1 released

(29 Mar.'11) SBML-PET-API is a parallel parameter estimation tool for SBML models.

SBML Harvester 0.2

(21 Mar.'11) Creates an ontology-based representation of SBML models, for verification and querying.

SED-ML v1.1 released

(29 Mar.'11) The version 1.1 specification for SED-ML is now available!

ONDEX released

(21 Mar.'11) ONDEX is a data integration platform enabling diverse data sets to be linked and visualized.

SBW 2.8.2 Released

(18 Mar.'11) SBW has an updated JDesigner, improved SBML event handling, and SBGN-ML and SED-ML 1.1 support.

SBML2LaTeX release 0.9.8

(8 Mar.'11) SBML2LaTeX is now a pure Java program. Version 0.9.8 offers new features + SBML Level 3 support.

Metannogen

(8 Mar.'11) Metannogen assists you or a team in manually annotating SBML files.

SBGN-ML and libSBGN!

(6 Feb.'11) The LibSBGN project has released a specification for SBGN-ML as well as LibSBGN Java and LibSBGN C++.

BRENDA supports SBML!

(26 Jan.'11) BRENDA is a well-known comprehensive enzyme information system. It now supports output in SBML.

BioSyS 1.0 released

(20 Jan.'11) BioSyS performs distributed simulations using grid computing systems and offers many analysis features.

ProMoT 0.8.3 released

(19 Jan.'11) ProMoT lets you model and simulate complex biological systems. The new version has improved SBML support.

SurreyFBA supports SBML

(11 Jan.'11) SurreyFBA performs constraint-based simulations and network map visualization, and can import SBML.

Cain 1.6 released

(25 Dec.'10) Cain is an application for stochastic simulations. This new version adds improved support for SBML.

PINT 1.1 supports SBML

(20 Dec.'10) PINT can integrate SBML files from different sources and explore phenotypic outcomes implied by particular conditions.

Omix 1.4 supports SBML

(16 Nov.'10) Omix is an editor for metabolic network diagrams and a customizable, scriptable visualization framework.

Snoopy 1.01 released

(16 Nov.'10) Snoopy is a graphical tool for working with biomolecular networks as Petri nets.

Reactome redesigned

(3 Nov.'10) The new version of the Reactome open-source, manually curated pathway database features many updates.

FASIMU 2.2.0

(26 Oct.'10) FASIMU is a free simulation and analysis framework for FBA offering a range of new computational methods.

iBioSim 1.5 released

(9 Oct.'10) The latest release of

iBioSim supports SBML Level 3 Version 1 and includes many enhancements.

COPASI 4.6.33 released

(7 Oct.'10) This development release of COPASI supports SBML Level 3 Version 1 and includes many enhancements.

BioModels Database rel. 18

(1 Oct.'10) The latest release of BioModels Database adds 157 new models, new conversions for Octave and BioPAX, and more.

Cain 1.5 released

(26 Sep.'10) Cain is an application for stochastic simulations. This new version adds support for events.

BioUML Workbench 0.9.0a

(24 Sep.'10) The newest release of BioUML adds tons of new features and updates.

JigCell 7.1.0 released

(13 Sep.'10) JigCell is a Java-based model development tool and ODE-based simulator. Among other things, it supports SBML Events.

PRISM 3.3

(10 Aug.'10) PRISM is a probabilistic model checker. The new release supports SBML.

MetNetMaker 0.9.9

(9 Aug.'10) MetNetMaker creates metabolic networks from KEGG LIGAND for FBA in the COBRA toolbox.

CRdata.org Announced!

(3 Aug.'10) CRdata.org is a free, open-source, cloud-based simulation, analysis and sharing system for R, Bioconductor and SBML users.

SBW 2.8.1 Released

(31 Jul.'10) SBW now supports SBML Level 3 Core (Final Candidate 1), and has an improved Simulation Tool and other updates.

COPASI 4.6 Released

(22 Jul.'10) The new stable release of COPASI adds support for events, new stochastic algorithms, and SBML L2v4.

CellDesigner 4.1!

(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.

Cain 1.4 released!

(31 May.'10) Cain is a stochastic simulator with highly efficient implementations of many methods.

SBW 2.8.0 released!

(10 May.'10) SBW is a component-based application framework. The update improves support for simulation of SBML models and Windows 7 support.

CBO workshop @ ICSB

(2 May.'10) There will be a Cell Behavior Ontology (CBO) and Standards for Multicellular Model Specification workshop @ ICSB 2010.

CompuCell3D & SBW workshop

(2 May.'10) Workshop on "Developing multi-scale, multi-cell developmental and biomedical simulations with CompuCell3D and SBW" in August.

BioModels Database rel. 17

(27 Apr.'10) The latest release of BioModels Database adds 20 new models and many software improvements.

sbmltidy released

(23 Apr.'10) sbmltidy is a simple script to run tidy to reformat an SBML file.

SBMLsqueezer 1.3 released

(3 Apr.'10) SBMLsqueezer generates rate laws from SBML reactions based on SBO annotations.

New MIASE website

(10 Feb.'10) The MIASE effort has a new website, connected to BioModels.net.

BioModels release 16

(26 Jan.'10) The latest release of the BioModels Database features over 450 total models.

Cain 1.2 released!

(1 Jan.'10) Cain is a stochastic simulator with highly efficient implementations of many methods.

BioUML Web Edition

(30 Nov.'09) BioUML, the Java-based modeling platform, now has a web edition.

BioMet Toolbox

(29 Oct.'09) BioMet Toolbox is a web-based toolbox for analyzing genome-scale models.

modelMaGe v. 1.0beta

(27 Oct.'09) modelMaGe can generate models and fit models to data.

CycSim supports SBML

(27 Oct.'09) CycSim is a pathway genome simulator supporting constraint-based models of metabolism.

New TEDDY release

(19 Oct.'09) TEDDY is an ontology for describing behaviors & other aspects of dynamical systems.

Antimony 1.3 released

(18 Oct.'09) Antimony is a human-readable model definition language and accompanying editor.

Reactome seeks feedback

(23 Sep.'09) The Reactome project is seeking feedback.

BridgeDb released

(17 Sep.'09) BridgeDB is a library for finding and manipulating identifiers. It supports MIRIAM URIs.

DOTcvpSB supports SBML

(12 Sep.'09) DOTcvpSB is a MATLAB-based dynamic optimization tool for models.

MetExplore supports SBML

(8 Sep.'09) MetExplore is a web system to help map metabolomics experiments onto metabolic networks.

BioModels Database rel. 15

(2 Sep.'09) BioModels Database, a free database of published models, now contains 231 curated and 198 uncurated models.

CellDesigner 4.1 beta

(28 Aug.'09) CellDesigner is a modeling tool with a GUI. This release adds SBML L2v4, SABIO-RK, SBGN and other support.

BioUML 0.8.6 Released!

(28 Aug.'09) BioUML is a Java-based integrated workbench for systems biology. This release adds many powerful new features.

MFO 2 released

(19 Aug.'09) Model Format OWL (MFO) is an expression of SBML in OWL. It now supports all constructs in SBML.

SBW 2.7.10 released

(19 Aug.'09) SBW is a component-based application framework. The update improves support for SBML "events" & the proposed layout/render extension.

SBGN Level 1 published!

(7 Aug.'09) SBGN (The Systems Biology Graphical Notation) is a visual notation for diagrams in systems biology.

Cain 1.0 released

(29 Jul.'09) Cain is a stochastic simulator with highly efficient implementations of many methods.

BioModels Database rel. 14

(16 Jun.'09) BioModels Database, a free database of published models, now contains 216 curated and 196 uncurated models.

MCSim supports SBML

(25 Apr.'09) GNU MCSim lets you design statistical or simulation models & perform Bayesian inference.

Pathway Tools workshop

(24 Apr.'09) Tutorial & workshop on SRI's Pathway Tools and BioCyc database in August '09.

Cain 0.12 released

(23 Apr.'09) Cain is a stochastic simulator with highly efficient implementations of many methods.

DSMTS & SBML shorthand

(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.

BioModels Database rel. 13

(25 Mar.'09) BioModels Database, a free database of published models, now contains 211 curated and 124 uncurated models.

Cain 0.10 released

(16 Mar.'09) Cain is a stochastic simulator implementing many methods, including tau-leaping.

ByoDyn 5.3 released

(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.

SBW 2.7.9 released

(3 Mar.'09) The Systems Biology Workbench is a component-based application framework. New features include improved simulator and auto-layout performance.

BioModels Database mirror @ Caltech

(26 Feb.'09) BioModels Database, a free, public resource, now has a mirror site at Caltech for better load balancing.

New version of SABIO-RK

(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.

New version of SBO

(13 Dec.'08) The latest update of the Systems Biology Ontology sports an updated interfaces and new vocabulary branches.

BioUML version 0.8.4

(13 Dec.'08) The latest BioUML has architectural improvements, parameter fitting, and new database interfaces.

BioModels Database 12th release

(3 Dec.'08) BioModels Database, a free, public resource, now contains 208 curated and 85 uncurated models, totalling over 34 000 reactions.

Cain 0.7.1

(20 Nov.'08) Cain is an optimized stochastic simulator implementing many methods, including tau-leaping.

SynBioSS 1.0.1

(3 Nov.'08) SynBioSS is a suite for generating and simulating synthetic biological networks.

GNA 6

(1 Nov.'08) GNA models and simulates qualitative genetic regulatory networks. It supports SBML.

ConsensusPathDB

(27 Oct.'08) ConsensusPathDB contains human pathways of metabolisms, signal transduction and gene regulation.

VCell 4.5 & 4.6 beta!

(18 Sep.'08) The latest stable (4.5) and beta (4.6) versions of the Virtual Cell are now available.

SBMLeditor 1.3.3 released

(9 Sep.'08) The new release of SBMLeditor, an XML editor for SBML files, fixes bugs and uses libSBML 3.0.2.

SBGN Level 1 Process Diagrams

(23 Aug. '08) The specification for Process Diagrams in the Systems Biology Graphical Notation (SBGN) is now available.

BioModels Database 11th Release

(21 Aug. '08) BioModels Database is a public resource containing published mathematical models of biological interest.

COPASI 4.4.27 (dev) released

(20 Aug.'08) The latest COPASI adds MIRIAM support and bug fixes.

iBioSim 1.0 released

(19 Aug.'08) iBioSim is a tool for analyzing and designing genetic circuit models. It features virtually complete support for all of SBML L2v3.

SBW 2.7.8 released

(18 Aug.'08) The Systems Biology Workbench is a component-based application framework. The new release adds many exciting across-the-board feature enhancements.

SBMLeditor 1.3.2 released

(5 Jul.'08) SBMLeditor is an XML editor for SBML files. The new release fixes some bugs and adds updates for MIRIAM.

CellDesigner 4.0 released

(4 Aug.'08) CellDesigner is a popular biochemical network modeling tool with a powerful graphical interface.

SYCAMORE released

(11 Jul.'08) SYCAMORE is a web-based system providing access to software for modeling, viewing and simulating biochemical systems.

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.

physiolabModeler.php PhysioLab Modeler supports SBML

(10 Jan.'08) Entelos's physiolabModeler.php 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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