:: DESCRIPTION
SemGen is an experimental software tool for automating the modular composition and decomposition of biosimulation models.
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Citation
J Biomed Inform. 2011 Feb;44(1):146-54. doi: 10.1016/j.jbi.2010.06.007. Epub 2010 Jun 30.
Multiple ontologies in action: composite annotations for biosimulation models.
Gennari JH, Neal ML, Galdzicki M, Cook DL.
:: DESCRIPTION
TF-finder can be successfully used to infer novel transcription factors (TFs) involved a biological process of interest using publicly available gene expression data and known positive genes from existing knowledge bases.
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N/A
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Citation
BMC Bioinformatics. 2010 Aug 12;11:425. doi: 10.1186/1471-2105-11-425.
TF-finder: a software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base.
Cui X1, Wang T, Chen HS, Busov V, Wei H.
:: DESCRIPTION
The SPiM (Stochastic Pi Machine) is a programming language for designing and simulating computer models of biological processes. The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. The language features a simple graphical notation for modelling a range of biological systems, and can be used to model large systems incrementally, by directly composing simpler models of subsystems.
The SPiM Player is a graphical interface to SPiM
::DEVELOPER
Andrew Phillips, Luca Cardelli, Matthew Lakin, Filippo Polo, Microsoft Research.
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N/A
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:: DOWNLOAD
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:: DESCRIPTION
The PNK (Petri Net Kernel) 2e is a software environment for the modeling and simulation of biological processes. It was developed as part of a M.Sc. project at the University of Edinburgh, UK. The software uses Stochastic Petri Nets (SPNs), a graphical representation of Markov Jump Processes.
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:: DOWNLOAD
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