Software for systems biology: from tools to integrated platforms

被引：173

作者：

Ghosh, Samik ^{[1
]}

Matsuoka, Yukiko ^{[1
,2
]}

Asai, Yoshiyuki ^{[3
]}

Hsin, Kun-Yi ^{[3
]}

Kitano, Hiroaki ^{[1
,3
,4
]}

机构：

[1] Syst Biol Inst, Minato Ku, Tokyo 1080071, Japan

[2] JST ERATO Kawaoka Infect Induced Host Response Pr, Minato Ku, Tokyo 1088639, Japan

[3] Okinawa Inst Sci & Technol, Kunigami, Okinawa 9040412, Japan

[4] Sony Comp Sci Labs Inc, Shinagawa Ku, Tokyo 1410022, Japan

来源：

NATURE REVIEWS GENETICS | 2011年 / 12卷 / 12期

基金：

日本科学技术振兴机构; 日本学术振兴会;

关键词：

MINIMUM INFORMATION; GENE-EXPRESSION; TRANSCRIPTIONAL REGULATION; COMMUNITY APPROACH; MARKUP LANGUAGE; NETWORK MOTIFS; PATHWAY; RECONSTRUCTION; STANDARDS; MAP;

D O I：

10.1038/nrg3096

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：821 / 832

页数：12

共 111 条

[51] PathText: a text mining integrator for biological pathway visualizations [J].