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Celiku_Friedenberg_2022 -- Probabilistic Model Checking of Cancer Metabolism

ABSTRACT: We provide a model of glycolysis and TCA cycle in cancers in which IDH is encountered both in its wild type form as well as mutated and capable of catalyzing an onco-metabolite. The model is constructed using the Probabilistic Symbolic Model Checker (PRISM,https://www.prismmodelchecker.org/) specification language, and properties are specified using a temporal-property specification language. The reaction rates are instantiated using both experimentally derived metabolic flux rate data (under normoxia and hypoxia conditions) as well as derived through a combination of these experimental rates and relative enzyme activity levels estimated using mRNA expression data from patient samples. We provide shell scripts for invoking the freely-available automatic model checker for reasoning about the specified properties.

SUBMITTER: Orieta Celiku  

PROVIDER: MODEL2207180001 | BioModels | 2022-07-18

REPOSITORIES: BioModels

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Dataset's files

Source:
Action DRS
MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5.sh Other
MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_gln_varied.sh Other
MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_gluc_varied.sh Other
MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_nut_varied_cumulative.sh Other
MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_nut_varied_saturation.sh Other
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