Web-based kinetic modelling using JWS Online
Bioinformatics
CellML2SBML: conversion of CellML into SBML
Bioinformatics
SBMLToolbox: an SBML toolbox for MATLAB users
Bioinformatics
Supporting the SBML layout extension
Bioinformatics
SBW - a modular framework for systems biology
Proceedings of the 38th conference on Winter simulation
Modelling cellular processes using membrane systems with peripheral and integral proteins
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins
Electronic Notes in Theoretical Computer Science (ENTCS)
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The complexity of biological systems is at times made worse by the diversity of ways in which they are described: the organic evolution of the science over many years has led to a myriad of conventions. This confusion is reflected by the in-silico representation of biological models, where many different computational paradigms and formalisms are used in a variety of software tools. The Systems Biology Markup Language (SBML) is an attempt to overcome this issue and aims to simplify the exchange of information by imposing a standardized way of representing models. The success of the idea is attested to by the fact that more than 110 software tools currently support SBML in one form or another. This work focuses on the translation of the Cyto-Sim simulation language (based on a discrete stochastic implementation of P systems) to SBML. We consider the issues both from the point of view of the employed software architecture and from that of the mapping between the features of the Cyto-Sim language and those of SBML.