Genomics

Dataset Information

37

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


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. Overall design: Refer to individual Series

INSTRUMENT(S): Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)

SUBMITTER: Danuta Gawel  

PROVIDER: GSE60683 | GEO | 2017-06-12

SECONDARY ACCESSION(S): GSE65880PRJNA259237 GSE60681 GSE95508

REPOSITORIES: GEO

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Publications


Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-line  ...[more]

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