Parent pages: SBML.org / News

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.

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.

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.