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  • MetaboSim: Metabolic pathway simulation - Summary

    All categories :: bioinformatics software development :: MetaboSim: Metabolic pathway simulation

    In Contrast to low-level Petri Nets (Place/Transition nets), Coloured Petri nets (CPN) belong to the high level nets. The idea of CPN is to overcome some limitations of low level Petri nets by adding of higher programming languages.

    License: GNU General Public License

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    Project admins: [Photo] Raghunadha Reddy Burri

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    Module name: metabolism
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    Project Homepage
    Submitted by Raghunadha Reddy Burri; posted on Friday, September 19, 2003


    Hi Friends,
    My Project Homepage ( was Started (18th Sep), If you have interest in Simulation of Metabolic Paths using CPN, your most welcome.
    • -Raghu
    Systems Biology Markup Language (SBML) Specification Level 1
    Submitted by Raghunadha Reddy Burri; posted on Tuesday, September 16, 2003 (1 comment)


    "a description language for simulations in systems biology. SBML is oriented towards representing biochemical networks common in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. The motivations for developing SBML stem from the current inability to exchange models between simulation/analysis tools. SBML Level 1 is meant to support non-spatial biochemical models and the kinds of operations that are possible in existing analysis/simulation tools. The primary specification document uses a simple UML-based notation to describe the data structures and presents a first-pass XML Schema; a secondary supporting document explains the 'SCHUCS' UML-based notation. SBML Level 1 is the result of merging modeling-language features from the following simulation systems: BioSpice, DBSolve, E-Cell, Gepasi, Jarnac, StochSim, and Virtual Cell. SBML was developed with the help of the authors of these packages; as a result of being based on actual working simulation software, it is a practical and functional description language. The team's goal in creating SBML has been to provide an open standard that will enable simulation software to exchange models."

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