title: From a biological hypothesis to the construction of a mathematical model.
abstract: Mathematical models serve to explain complex biological phenomena and provide predictions that can be tested experimentally. They can provide plausible scenarios of a complex biological behavior when intuition is not sufficient anymore. The process from a biological hypothesis to a mathematical model might be challenging for biologists that are not familiar with mathematical modeling. In this chapter we discuss a possible workflow that describes the steps to be taken starting from a biological hypothesis on a biochemical cellular mechanism to the construction of a mathematical model using the appropriate formalism. An important part of this workflow is formalization of biological knowledge, which can be facilitated by existing tools and standards developed by the systems biology community. This chapter aims at introducing modeling to experts in molecular biology that would like to convert their hypotheses into mathematical models.
authors.affiliation: Institut Curie, Paris, France.
authors.forename: David
authors.initials: D
authors.lastname: Cohen
authors.forename: Inna
authors.initials: I
authors.lastname: Kuperstein
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
authors.forename: Andrei
authors.initials: A
authors.lastname: Zinovyev
authors.forename: Laurence
authors.initials: L
authors.lastname: Calzone
mesh_terms: D018797:Cell Cycle Proteins / Q000235:genetics* / Q000378:metabolism; D003196:Computer Graphics; D003198:Computer Simulation; D030541:Databases, Genetic; D050687:E2F1 Transcription Factor / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D006801:Humans; D007700:Kinetics; D008954:Models, Biological; D016160:Retinoblastoma Protein / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology
chemical_list: D018797:Cell Cycle Proteins; D050687:E2F1 Transcription Factor; C493753:E2F1 protein, human; D016160:Retinoblastoma Protein