SBML

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. The systems biology markup language (SBML) a medium for representation and exchange of biochemical network models. Bioinformatics 2003 19 524-31. 

SBML [200, 201] The Systems Biology Markup Language http //www. sbml.org/... 

JDesigner ERATO project—Caltech Win32 application, which allows one to draw a biochemical network and export the network in the form of SBML (http //sbw. kgi.edu/sofiware/jdesigner.htm)... 

The modeling software used for our purposes should allow an easy model exchange with other software and scientists within BioSim. Therefore, this evaluation is restricted to software allowing the import and export of standard model files like SBML [71] and CellML [72]. Moreover, the software should be freely available to academic users in order to allow international free access to the respective models and simulation results. 

With these boundary conditions in mind, one can distinguish between SBML-and CellML-compatible software. 

A list of SBML-compatible software is available at littp //sbml.org/index.psp. With the minimal requirements mentioned above, we consider the following packages best suited Cellware, Copasi, Ecell, SBW, JigCell, JSim, XPPAUT, Virtual Cell (Vcell). 

However, CellML models can be converted to SBML via a freely available tool (http //sbml.org/software/cellml2sbml/) and thus be available for the above described software. 

Both Copasi and XPP comply with the SBML standard for exchange of biochemical models. The SBML-based PharmBiosim approach combines the above simulation-based strategy with the application of algorithms based on continuation and bifurcation analysis from applied mathematics. 

Using the modeling platform Copasi, the reaction network was encoded in the language SBML and the elementary flux modes were calculated, i.e. minimum sets... 

SBML (Hucka et al. 2003) is a machine-readable format for describing qualitative and quantitative models of biochemical networks that use MathML for the specification of mathematical formulas. It defines a subset of the language to be used in the SBML, using a widely applicable standard, without the need to implement all features of the MathML specification. The excellent documentation provided for SBML provides an example worth following (http //sbml.org/ documents/). 

The SBML homepage (http //sbml.org) provides an impressive list of software implementing the notation. The site offers downloads of software libraries that enable easy incorporation to several programming languages (C, C++, Java, Python) as well as mathematics packages (Matlab, Mathematica), and this accessibility has significantly contributed to its success. 

Pathway Tools can export PGDBs into several different file formats that are described at http //bioinformatics.ai.sri.com/ ptools/flatfile-format.html. These formats include column-delimited tables, SBML (see http //sbml.org/), BioPAX (see http //biopax.org/), Genbank, FASTA, and attribute-value. 

SBML http // sbml.org/Main Page For models of biological processes... 

Bois FY (2009) GNU MCSim Bayesian statistical inference for SBML-coded systems biology models. Bioinformatics 25 1453-1454... 

Software platform System Biology Workbench and System Biology Mark-Up Language (SBML)... 

The Systems Biology Markup Language (SBML, http //sbml.org) is a widely used standard for annotating a reaction network with dynamics and biology-specific semantics. It is applicable to static and dynamic models of, for example, cell-signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. An SBML document contains a detailed specification of a biochemical model (e.g., the initial quantities for the entities, kinetic laws for the reactions, etc.). 

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