Tools

BioDiVinE 2.0

BioDiVinE 2.0

BioDiVinE 2.0 is an ongoing project aiming at the creation of a tool for the robustness analysis of stochastic biochemical systems.

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BioDiVinE 1.0

BioDiVinE 1.0 is a tool set created for verifying properties of biochemical systems given as a system of ordinary differential equations.

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Esther

Esther| Esther is an online interface to multiple tools, among others Parsybone, for analysis of discrete multi-valued models. Esther provides user-friendly interface for model creation, dynamical simulation connected with LTL model checking and result analysis.

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Parsybone

Parsybone is a CLI based tool for synthesis of discrete kinetic parameters in gene regulatory networks and for their further analysis.

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Parasim

Parasim Parasim is a tool for robustness analysis. Given a SBML model, a property and perturbation set, it computes the robustness of the model over the perturbation set with respect to the property. A perturbation set consists of intervals over model parameters and initial variable values. Properties are entered in the form of signal temporal logic formulae.

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Genesim

GeNeSim is a web based GUI for managing models of biological interaction networks given either as Qualitative models defined by Piece-wise Linear Differential Equations (PLDEs) or Quantitative models defined by Multiaffine Ordinary Differential Equations (MODEs). These models are intended for analysis using the BioDiVinE 1.0 tool.

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BCS generator

BCSgen Biochemical Space language software tool (BSCgen) serves for interpreting BCSL models as transition systems and translating rule-based models to reactions-based models.

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