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RACIPE: A computational tool for Modeling Gene Regulatory Circuits using Randomization

By Bin Huang, Dongya Jia, Jingchen Feng, Herbert Levine, José N. Onuchic, Mingyang Lu

Posted 27 Oct 2017
bioRxiv DOI: 10.1101/210419 (published DOI: 10.1186/s12918-018-0594-6)

Motivation: One of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental data and/or educated guesses, which can be time-consuming and error-prone, especially for large networks. Results: We present a computational tool based on our newly developed method named random circuit perturbation (RACIPE), to explore the robust dynamical features of gene regulatory circuits without the requirement of detailed kinetic parameters. RACIPE generates an ensemble of circuit models with distinct random parameters and uniquely identifies robust dynamical properties by statistical analysis. Here, we discuss software implementation and illustrate the usage of RACIPE on coupled toggle-switch circuits and a published circuit of B-lymphopoiesis. We expect RACIPE to contribute to a more comprehensive and unbiased understanding of gene regulatory mechanisms. Availability: RACIPE is a free open source software distributed under (Apache 2.0) license and can be downloaded from GitHub (https://github.com/simonhb1990/RACIPE-1.0).

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