title: Software for systems biology: from tools to integrated platforms.
abstract: Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review describes the types of software tools that are required at different stages of systems biology research and the current options that are available for systems biology researchers. We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform.
authors: The Systems Biology Institute, Minato, Tokyo, Japan. ghosh@sbi.jp
authors: Samik
authors: S
authors: Ghosh
authors: Yukiko
authors: Y
authors: Matsuoka
authors: Yoshiyuki
authors: Y
authors: Asai
authors: Kun-Yi
authors: KY
authors: Hsin
authors: Hiroaki
authors: H
authors: Kitano
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D057225:Data Mining; D006801:Humans; D008954:Models, Biological; D012984:Software; D049490:Systems Biology; D018511:Systems Integration