rasmodel.org

Welcome to the RAS executable model! — Ras model 0.1 documentation

The RAS Executable Model. Welcome to the RAS executable model! Welcome to the RAS executable model! If you are new to this project, please read the overview. Returning visitors can jump right into the model. The codebase for the RAS executable model (REM) is currently undergoing updates and further development; expect the next incremental release of REM in late Spring, 2016. REM is constructed automatically using a newly developed software system, the Integrated Dynamical Reasoning Assembler ( INDRA.

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Welcome to the RAS executable model! — Ras model 0.1 documentation | rasmodel.org Reviews

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The RAS Executable Model. Welcome to the RAS executable model! Welcome to the RAS executable model! If you are new to this project, please read the overview. Returning visitors can jump right into the model. The codebase for the RAS executable model (REM) is currently undergoing updates and further development; expect the next incremental release of REM in late Spring, 2016. REM is constructed automatically using a newly developed software system, the Integrated Dynamical Reasoning Assembler ( INDRA.

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4 model analysis

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Welcome to the RAS executable model! — Ras model 0.1 documentation | rasmodel.org Reviews

https://rasmodel.org

The RAS Executable Model. Welcome to the RAS executable model! Welcome to the RAS executable model! If you are new to this project, please read the overview. Returning visitors can jump right into the model. The codebase for the RAS executable model (REM) is currently undergoing updates and further development; expect the next incremental release of REM in late Spring, 2016. REM is constructed automatically using a newly developed software system, the Integrated Dynamical Reasoning Assembler ( INDRA.

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rasmodel.org

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The RAS Executable Model (REM) — Ras model 0.1 documentation

http://rasmodel.org/components/index.html

The RAS Executable Model. The RAS Executable Model (REM). The RAS Executable Model (REM). Ras proteins are GTPases. Ras binds GTP and GDP. Ras converts GTP to GDP. Oncogenic Ras mutants have reduced GTP binding and GTPase activity. Post-translational modifications of the C-terminus. Ras regulation by GEFs. Identities of Ras-specific GEFs. Rates of GEF activation. Specificity of RASGRF1 for Ras isoforms. Ras regulation by RasGAPs. RasGAPs for the Ras subfamily. Mechanism of accelerating hydrolysis.

2

Ras proteins are GTPases — Ras model 0.1 documentation

http://rasmodel.org/components/ras/ras_gtpase.html

The RAS Executable Model. Ras proteins are GTPases. Ras binds GTP and GDP. Ras converts GTP to GDP. Oncogenic Ras mutants have reduced GTP binding and GTPase activity. Post-translational modifications of the C-terminus. Ras regulation by GEFs. Ras regulation by RasGAPs. The RAS Executable Model (REM). Ras proteins are GTPases. Ras proteins are GTPases. For a diagram of the primary structure of Ras, see http:/ www.ncbi.nlm.nih.gov/pmc/articles/PMC3915522/figure/F1/. The sites are as follows:. The three fu...

3

Overview — Ras model 0.1 documentation

http://rasmodel.org/intro.html

A “literate” model. The RAS Executable Model. The Ras Executable Model (REM) is a model of the signaling pathway of the Ras family proteins (K-RAS, N-RAS, H-RAS), including their regulators and effectors, at a biochemical level of detail. It is a rule-based model. REM consists of three interlinked levels. Model components. Consist of PySB modules that implement pathway mechanisms. A model scenario. And manual development by a team of modelers. By the Sorger Lab. Resource for improving reading algorithms.

4

Model analysis — Ras model 0.1 documentation

http://rasmodel.org/experiments/index.html

The RAS Executable Model. Ras binding to GTP and GDP. KRAS mutant MAPK signaling. Ras binding to GTP and GDP. KRAS mutant MAPK signaling. Provided by Read the Docs.

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References — Ras model 0.1 documentation

http://rasmodel.org/references.html

The RAS Executable Model. Barbacid M. ras genes. Annu Rev Biochem. 1987;56:779-827. Review. PMID:. Scolnick EM, Papageorge AG, Shih TY. Guanine nucleotide-binding activity as an assay for src protein of rat-derived murine sarcoma viruses. Proceedings of the National Academy of Sciences of the United States of America. 1979;76(10):5355-5359. PMID:. Nature. 1980 Oct 23;287(5784):686-91. PMID:. Proceedings of the National Academy of Sciences of the United States of America, 81(22), 6924 6928. PMID:. Sweet R...

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Welcome to the RAS executable model! — Ras model 0.1 documentation

The RAS Executable Model. Welcome to the RAS executable model! Welcome to the RAS executable model! If you are new to this project, please read the overview. Returning visitors can jump right into the model. The codebase for the RAS executable model (REM) is currently undergoing updates and further development; expect the next incremental release of REM in late Spring, 2016. REM is constructed automatically using a newly developed software system, the Integrated Dynamical Reasoning Assembler ( INDRA.

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