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- Title
Software for systems biology: from tools to integrated platforms.
- Authors
Ghosh, Samik; Matsuoka, Yukiko; Asai, Yoshiyuki; Hsin, Kun-Yi; Kitano, Hiroaki
- 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.
- Subjects
SYSTEMS biology; BIOLOGICAL systems; BIOINFORMATICS software; SIMULATION methods &; models; ELECTRONIC data processing software; COMPUTER software; COMPUTER simulation; BIOLOGICAL models; RESEARCH; RESEARCH methodology; MEDICAL cooperation; EVALUATION research; BIOINFORMATICS; COMPARATIVE studies; SYSTEM integration; DATA mining
- Publication
Nature Reviews Genetics, 2011, Vol 12, Issue 12, p821
- ISSN
1471-0056
- Publication type
journal article
- DOI
10.1038/nrg3096