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GINsim | Qualitative analysis of regulatory networks: a computational tool based on a discrete formal framework

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks. General information on modelling and analysis of genetic regulatory networks can be found in [1]. GINsim consists of a simulator of qualitative models of genetic regulatory networks based on a discrete, logical formalism. GINsim is OS independent (Linux, Mac OS 10.3 , Windows). Feel free to grab it at the downloads. Section and please contact us. With your comments or suggestions.

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GINsim | Qualitative analysis of regulatory networks: a computational tool based on a discrete formal framework | ginsim.org Reviews

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GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks. General information on modelling and analysis of genetic regulatory networks can be found in [1]. GINsim consists of a simulator of qualitative models of genetic regulatory networks based on a discrete, logical formalism. GINsim is OS independent (Linux, Mac OS 10.3 , Windows). Feel free to grab it at the downloads. Section and please contact us. With your comments or suggestions.

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3 documentation

4 model repository

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6 publications

7 companion tools

8 contacts

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10 references

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GINsim | Qualitative analysis of regulatory networks: a computational tool based on a discrete formal framework | ginsim.org Reviews

https://ginsim.org

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks. General information on modelling and analysis of genetic regulatory networks can be found in [1]. GINsim consists of a simulator of qualitative models of genetic regulatory networks based on a discrete, logical formalism. GINsim is OS independent (Linux, Mac OS 10.3 , Windows). Feel free to grab it at the downloads. Section and please contact us. With your comments or suggestions.

INTERNAL PAGES

ginsim.org

1

Modeling and simulation of genetic regulatory systems: a literature review. | GINsim

http://www.ginsim.org/node/13

Raquo; Modeling and simulation of genetic regulatory systems: a literature review. Modeling and simulation of genetic regulatory systems: a literature review. Modeling and simulation of genetic regulatory systems: a literature review. J Comput. Biol.

2

Biblio | GINsim

http://www.ginsim.org/biblio/author/10

De Jong, Hidde. 2002 Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 9(1):67-103.

3

Companion Tools | GINsim

http://www.ginsim.org/companion_tools

Raquo; Companion Tools. EpiLog is a tool which makes use of LogicalModel to implement a cellular automata, defining a convenient framework for the qualitative modelling of epithelium pattern formation. You can obtain more information at http:/ epilog-tool.org. LogicalModel is a tool for the manipulation of multi-valued logical models. It provides a set of core interfaces for the interoperability between different logical modelling tools (such as GINsim and EpiLog).

4

Biblio | GINsim

http://www.ginsim.org/biblio/author/6

In Press. Qualitative dynamical modelling can formally explain mesoderm specification and predict novel developmental phenotypes. 2015 Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS computational biology. 11(8):e1004426. 2014 Computational modeling of the main signaling pathways involved in mast cell activation. Current topics in microbiology and immunology. 382:69-93. 2013 Logical modelling of Drosophila signalling pathways. Molecular bioSystems. 9(9):2248-58.

5

Downloads | GINsim

http://www.ginsim.org/downloads

File with dependencies included:. GINsim-2.9.4-with-deps.jar. File without dependencies included:. GINsim-2.9.4.jar. Library bundle zip file:. GINsim-2.9.4-lib.zip. ChangeLog-2.9.4.txt. GINsim-v2.9.4.tgz. GINsim-2.3.1.jar. ChangeLog-2.3.1.txt. You can grab the nightly build at http:/ ginsim.org/dev. Starting with version 2.9.3, GINsim is freely available under the terms of GPLv3 license ( view full GNU GPL v3.0 license. Older versions are freely available for academic use. Java -jar GINsim-version.jar.

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pedromonteiro.org

Pedro T. Monteiro

http://www.pedromonteiro.org/software.html

Pedro T. Monteiro. Work in progress in collaboration with Pedro L. Varela, Camila Veludo, Adrien Fauré and Claudine Chaouiya, at Instituto Gulbenkian de Ciência, Yamaguchi University and INESC-ID. GINsim 2.9.3. Work done in collaboration with Aurélien Naldi, Lionel Spinelli, Nuno Mendes, Denis Thieffry and Claudine Chaouiya, at Instituto Gulbenkian de Ciência, École Normale Supérieure, Université de Lausanne and INESC-ID. Work done at IGC, Oeiras. Http:/ www.phyloviz.net/wiki/. The PHYLOViZ DataStats mod...

epilog-tool.org

Companion Tools | EpiLog

http://www.epilog-tool.org/companion_tools

Raquo; Companion Tools. GINsim is a computer tool for the modeling and simulation of genetic regulatory networks, based on the discrete logical formalism. You can obtain more information at http:/ GINsim.org. LogicalModel is a tool for the manipulation of multi-valued logical models. It provides a set of core interfaces for the interoperability between different logical modelling tools (such as GINsim and EpiLog). You can get it at https:/ github.com/colomoto/logicalmodel. Page by Dr. Radut.

pedromonteiro.org

Pedro T. Monteiro

http://www.pedromonteiro.org/index.html

Pedro T. Monteiro. With a FCT Investigator grant. Rua Alves Redol 9. P-1000-029 Lisboa, Portugal. 351) 21 3100 320. I belong to http:/ CoLoMoTo.org. Consortium for Logical Models and Tools), a consortium of research groups interested in logical modelling. The consortium works on the definition of standards for model representation and interchange (especially the SBML qual format), and on the comparison of methods, models and tools. In this context, I am currently involved on the development of:. Database...

biomodels.caltech.edu

BioModels Database (Caltech mirror)

http://biomodels.caltech.edu/path2models

Path2Models is a branch of BioModels Database dedicated to hosting models automatically generated from pathway resources, such as KEGG. Models from this branch are classified in 3 distinct categories:. Whole genome metabolism models. One can also browse those models by organism:. List of all organisms. The following search will only look for models coming from the path2models project:. Help about the search. Will be used to combine them. Double quotes ( ". The colon character ( :. Archives of all models.

quantitative.caltech.edu

BioModels Database (Caltech mirror)

http://quantitative.caltech.edu/path2models

Path2Models is a branch of BioModels Database dedicated to hosting models automatically generated from pathway resources, such as KEGG. Models from this branch are classified in 3 distinct categories:. Whole genome metabolism models. One can also browse those models by organism:. List of all organisms. The following search will only look for models coming from the path2models project:. Help about the search. Will be used to combine them. Double quotes ( ". The colon character ( :. Archives of all models.

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GINsim | Qualitative analysis of regulatory networks: a computational tool based on a discrete formal framework

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks. General information on modelling and analysis of genetic regulatory networks can be found in [1]. GINsim consists of a simulator of qualitative models of genetic regulatory networks based on a discrete, logical formalism. GINsim is OS independent (Linux, Mac OS 10.3 , Windows). Feel free to grab it at the downloads. Section and please contact us. With your comments or suggestions.

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