Difference between revisions of "Boolean Networks"
From Biocellion
m (Shinwook moved page Boolean networks to Boolean Networks) |
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− | + | First proposed by Stuart Kauffman<ref>Kauffman, S. A. (1969). "Metabolic stability and epigenesis in randomly constructed genetic nets". Journal of Theoretical Biology. 22 (3): 437–467. doi:10.1016/0022-5193(69)90015-0. PMID 5803332</ref>, Boolean Network (BN) is a way to model the dynamics of Gene Regulatory Networks. A Boolean Network is comprised of gene states and their corresponding input (update) functions. Each gene takes on the value of either 1 or 0 (ON or OFF), and the state of the gene is the realization of inputs from the previous time step. In a general case of Random Boolean Networks, | |
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+ | Following the convention of BN/PBN Toolbox (Lähdesmäki & Shmulevich)<ref>http://www.mybiosoftware.com/bnpbn-toolbox-toolbox-boolean-networks-probabilistic-boolean-networks.html</ref>, we have developed a general framework for implementing [https://github.com/boaguilar/multicell_boolean_networks Multicell Boolean Networks]<ref>https://github.com/boaguilar/multicell_boolean_networks</ref> in Biocellion. In Multicell Boolean Networks, the user is able to implement up to two different Boolean Networks for specified cells. It requires users to input 5 parameter file: | ||
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+ | # Cell Location File (i.e. pcc_qwang_phi0.12.txt) | ||
+ | # NV File (i.e. pcc_qwang_.nv) | ||
+ | # Truth Table File (i.e. pcc_qwang.tt) | ||
+ | # varF File (i.e. pcc_qwang.varf) | ||
+ | # Initial State File (i.e. pcc_qwang_phi0.12.st) |
Revision as of 03:36, 4 March 2017
First proposed by Stuart Kauffman[1], Boolean Network (BN) is a way to model the dynamics of Gene Regulatory Networks. A Boolean Network is comprised of gene states and their corresponding input (update) functions. Each gene takes on the value of either 1 or 0 (ON or OFF), and the state of the gene is the realization of inputs from the previous time step. In a general case of Random Boolean Networks,
Following the convention of BN/PBN Toolbox (Lähdesmäki & Shmulevich)[2], we have developed a general framework for implementing Multicell Boolean Networks[3] in Biocellion. In Multicell Boolean Networks, the user is able to implement up to two different Boolean Networks for specified cells. It requires users to input 5 parameter file:
- Cell Location File (i.e. pcc_qwang_phi0.12.txt)
- NV File (i.e. pcc_qwang_.nv)
- Truth Table File (i.e. pcc_qwang.tt)
- varF File (i.e. pcc_qwang.varf)
- Initial State File (i.e. pcc_qwang_phi0.12.st)