User:Hbdesiato/List of systems biology modeling tools

Systems Biology is the systematic study of complex interactions in biological systems and offers the chance to predict the outcome of not well understood or unknown processes. Appropriate computational models are develeoped to explore in silico behavior under conditions which might be difficult to realize in vivo or in vitro with existing experimental techniques.

Existing software help to model and simulate biological systems...

COPASI
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GEPASI
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GeNGe
description: The GEne Network GEnerator (GeNGe) is a web application for the generation and analysis of gene regulatory networks (GRNs) providing different simulation steps with interactive user interfaces. An arbitrary number of networks and simulation data can be generated to provide for instance benchmark data for reverse engineering applications. Furthermore, GeNGe offers features for the topological characterization of GRNs. The simulation results can be used to define critical network nodes and suitable candidates for perturbation experiments and thus guide future experimental work.

type: web-based

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costs: free for academic useres

homepage: http://genge.molgen.mpg.de

PyBioS
description: PyBioS is a system for the modeling and simulation of cellular processes. PyBioS acts as a model repository and supports the generation of large models based on publicly available information like data of the Reactome database. An ODE-system of a model can be generated automatically based on pre- or user-defined kinetic laws and used for subsequent simulation of time course series and further analysis of the dynamic behavior of the underlying system. The forward-modeling approach supports the formulation of hypotheses, e.g. for in silico knock-out experiments or time series.

type: web-based

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costs: free for acadamic users (requires registration)

homepage: http://pybios.molgen.mpg.de

SynBioSS
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SynTRen
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