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LASSIM -a network inference toolbox for genome-wide mechanistic modeling [USF2, KLF6/COPEB, CBL and HIS1 siRNA]]

ABSTRACT: We present LASSIM, which is a toolbox built to build and infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces the time for the computation to finish.

ORGANISM(S): Homo sapiens

PROVIDER: GSE95508 | GEO | 2017/06/12

SECONDARY ACCESSION(S): PRJNA377298

REPOSITORIES: GEO

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LASSIM -a network inference toolbox for genome-wide mechanistic modeling

Project description:We present LASSIM, which is a toolbox built to build and infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces the time for the computation to finish.

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LASSIM -a network inference toolbox for genome-wide mechanistic modeling [Time-series polarization: CD4+ T cells toward Th2]

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