Systems Biology Workbench
TinkerCell
SBML2MATLAB
Software Libraries
Systems Biology Workbench (SBW)
SBW is a simple framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. Many biological modeling and simulation tools are a part of SBW, including JDesigner and Jarnac.
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Screenshot of JDesigner
Screenshot of Jarnac
TinkerCell
TinkerCell is a Computer-Aided Design software tool for Synthetic Biology. It combines visual interface with programming API (Python, Octave, C, Ruby) and allows users to share their code with each other via a central repository.
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SBML2MATLAB
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The SBML2MATLAB translator program will convert an SBML file into a MATLAB function. These translated models can also import model information (parameters, species, etc) into MATLAB. MatlabTranslator depends on NOMLib, a simple C based API for libSBML, used for reading information from SBML. NOMLib can be built as a separate library for use in other programs.
Software Libraries
libSBML
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LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications.
COPASI API
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C interface to the Copasi C++ library. This library can be used to read and write Systems Biology Markup Language (SBML) files and simulate them using deterministic or stochastic simulation. Additional analysis, such as computing eigenvalues and steady states, can also be performed. The models can also be constructed using C function calls such as cCreateSpecies(…) and cCreateReaction(…). Antimony scripts can also be used to load models. The structural library is also included within this library for analyzing the stoichiometry matrix.
NOMLib
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The NOMLib exposes the SBW SBML Api. This API is a simple C based API that we feel is easier to use.
libStruct
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The structural analysis library is a C/C++ portable software library for analyzing the structural properties of stoichiometric networks.
LibSEDML
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This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.