title: All systems go: launching cell simulation fueled by integrated experimental biology data.
abstract: Biological simulation serves to unify the basic elements of systems biology, namely, model selection, experimentation and model refinement. To select biochemical models for simulation, metabolome analysis can be performed using capillary electrophoresis or liquid chromatography coupled with mass spectrometry. In this manner, selected models can be elaborated with temporal/spatial gene and protein expression data obtained from model organisms such as Escherichia coli. The E. coli single gene deletion mutant library (KO collection) and His-tag/GFP-fusion single open reading frame clone expression library (ASKA) are powerful resources for this task. The integration of parallel experimental datasets into dynamic simulation tools forms the remaining challenge for the systematic analysis and elucidation of biological networks and holds promise for biotechnological applications.
authors.affiliation: Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, 997-0017 Yamagata, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Arita
authors.forename: Martin
authors.initials: M
authors.lastname: Robert
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D002468:Cell Physiological Phenomena; D019295:Computational Biology; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics; D015870:Gene Expression; D015723:Gene Library; D008660:Metabolism; D008954:Models, Biological