Welcome to GINsim

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GINsim (Gene Interaction Network simulation) is a software tool for the design and analysis of qualitative dynamical models of genetic regulatory networks.

Recent developments in functional genomics have generated large amounts of data on gene expression and on the underlying regulatory mechanisms. This has resulted in the progressive mapping of complex regulatory networks. As these networks usually include numerous intertwined feedback circuits, gaining an understanding of their spatio-temporal behaviour defies the intuition. Formal modelling approaches become a necessary complement to experimental tools. As precise information on molecular mechanisms and the value of kinetic parameters are currently difficult to establish, qualitative methods offer a highly attractive approach to model and analyse essential properties of genetic regulatory networks.

Logical modelling formalism

GINsim consists of a simulator of qualitative models of genetic regulatory networks based on a discrete, logical formalism.

GINsim allows the user to specify a model of a genetic regulatory network in term of asynchronous, multivalued logical functions, and to simulate and/or analyse its qualitative dynamical behaviour.

Citing GINsim

If you use GINsim, please cite it the following publication.

Logical modelling and analysis of cellular regulatory networks with GINsim 3.0. A. Naldi, C. Hernandez, W. Abou-Jaoudé, P. Monteiro, C. Chaouiya, D. Thieffry. Frontiers in Physiology 9:646 (2018).

Main features

Model editor

Build qualitative models in a graphical interface.

GINsim

The regulatory graph represent interactions between biological entities.

Logical rules define the dynamical behaviour of each component.

Annotations keep track of the underlying knowledge.

Apply perturbations to account for mutants or alternative hypothesis.

Reduce complex models by hiding intermediate components.

Dynamical analysis

STG

Visualize simulation results as state transition graphs.

The non-deterministic trajectories represent alternative cell fates.

Efficient identification of some dynamical properties, up to complex models.

Fixed points and trap spaces are attractors of the system.

Functional circuits highlight key interactions in the model.

Interoperability

CoLoMoTo

GINsim can load and export models from the SBML qual format, enabling to share them with other software tools. Its integration in the CoLoMoTo notebook enables the definition of complex, reproducible anlysis workflows.

  • Efficient reachability analysis using pint,
  • Complex reachability analysis using the NuSMV model checker,
  • Quantification of reachability probabilities using MaBoSS,
  • 2D modelling of a cellular tissue using Epilog.

The people behind GINsim

Claudine

Claudine Chaouiya

Project coordination

Pedro

Pedro Tiago Monteiro

Software development

Aurelien

Aurélien Naldi

Software development

Denis

Denis Thieffry

Project coordination

Please send your comments, questions or suggestions to the public user group GINsim Users at ginsim-users@googlegroups.com. Specific questions can also be adressed to the GINsim team at support@ginsim.org.

Former contributors

The GINsim logo was designed by Mauricio Guzman.

GINsim is currently hosted at the IGC. It was previously hosted at the TAGC, Université de la Méditerranée.