title: The executable pathway to biological networks.
abstract: As time goes by, it becomes more and more apparent that the puzzles of life involve more and more molecular pieces that fit together in increasingly complex ways. Genomics and Proteomics technologies nowadays, produce reliable and quantitative data that could potentially reveal all the molecular pieces of a particular puzzle. However, this is akin to the opening of Pandora's box; and we are now facing the problem of integrating this vast amount of data with its incredible complexity into some coherent whole. With the aid of engineering methods designed to build and analyze computerized man-made systems, a new emerging field called 'Executable Biology' aims to create computer programmes that put together the pieces in ways that allows capturing their dynamicity and ultimately elucidating how molecular function generates cellular function. This review aspires to highlight the main features characterizing these kinds of executable models and what makes them uniquely qualified to reason about and analyze biological networks.
authors.affiliation: Microsoft Research Cambridge, 7 JJ Thomson Ave., Cambridge, UK. jasmin.fisher@microsoft.com
authors.forename: Jasmin
authors.initials: J
authors.lastname: Fisher
authors.forename: Nir
authors.initials: N
authors.lastname: Piterman
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D003198:Computer Simulation; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology*; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000502:physiology*; D008954:Models, Biological; D015233:Models, Statistical; D016571:Neural Networks, Computer; D015398:Signal Transduction / Q000502:physiology*; D012984:Software