Difference between revisions of "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: | 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: | ||
| − | + | * 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) | |
| + | |||
| + | -Insert how to set it up. | ||
Revision as of 03:37, 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)
- ↑ 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
- ↑ http://www.mybiosoftware.com/bnpbn-toolbox-toolbox-boolean-networks-probabilistic-boolean-networks.html
- ↑ https://github.com/boaguilar/multicell_boolean_networks
