Community
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.
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| SBToolbox2 version 2.0(6 Jun.'08) The latest version of SBToolbox adds GUIs, new optimization methods, and new sensitivity analysis methods. |
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| Cell Illustrator 4.0(14 May.'08) BioBase has released version 4.0 of Cell Illustrator. It supports importing SBML. |
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| COPASI user workshop(23 Apr.'08) The COPASI team will hold a 3-day workshop July 22–24, 2008, at the VBI in Virginia. |
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| Computational Cell Biology course(22 Apr.'08) The application deadline for the 3-week intensive computational cell biology course at CSHL is April 30. |
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| 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. |
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| 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. |
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| SBToolbox2 version 1.1(21 Mar.'08) The latest version of SBToolbox adds support for several SBML constructs such as delays and "fast" reactions. |
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| 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. |
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| PottersWheel 1.5 released(27 Jan.'08) PottersWheel is a multi-experiment fitting toolbox that supports SBML. The new version includes identifiability analysis. |
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| SBToolbox2 released(18 Jan.'08) The rewritten SBToolbox and companion add-on package (SBPD) offer powerful features for biological modeling in MATLAB. |
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| PhysioLab Modeler supports SBML(10 Jan.'08) Entelos's PhysioLab Modeler, a powerful whole-organism simulation and analysis system, now imports and exports SBML. |
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| SIGNALIGN supports SBML(9 Jan.'08) SIGNALIGN is a new tool for alignment and prediction of biochemical pathways. It supports input in SBML format. |
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| BiologicalNetworks supports SBML(27 Nov. '07) BiologicalNetworks provides visualization and analysis services and an information management framework for PathSys, an integrated data resource. |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| Genetdes supports SBML(5 Jul. '07) The new software package Genetdes automatically designs transcriptional networks with desired behaviors. It reads and writes SBML. |
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| RMBNToolbox(25 Jun. '07) A new MATLAB-based toolbox for generating random models for biochemical networks, the RMBNToolbox, is now available. It supports SBML. |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| SBO online services(15 Jan. '07) The Systems Biology Ontology (SBO) has an updated browser and now provides web services, OWL export and more. |
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| 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. |
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| 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. |
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| PottersWheel supports SBML(4 Oct. '06) PottersWheel 1.2 beta, a MATLAB systems biology toolbox, supports model creation, fitting data, and designing new experiments. |
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| Cyto-Sim Announced(21 Jul. '06) Cyto-Sim is a simulator for compartmental models containing membranes with peripheral and integral proteins. |
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| 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. |
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| JSim supports SBML(8 May '06) JSim is a Java-based simulation system for building and analyzing quantitative models. |
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| 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. |
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| 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. |
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| 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. |
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| COPASI RC1(21 Feb. '06) COPASI is a biochemical modeling software package and successor to the popular Gepasi. It supports SBML. |
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| 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. |
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| 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. |
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| 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. |
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| 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). |
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| BioModels Database paper published!(9 Jan. '06) The first paper about BioModels Database has been published in Nucleic Acids Research v. 34, D689-D691. |