MetaNET - a web-accessible interactive platform for biological metabolic network analysis

BMC Systems Biology

Open Source Drug Discovery Consortium²  Andrew Michael Lynn²  Anmol Jaywant Hemrom¹  Shawez Khan²  Pankaj Narang² 

[1] School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India;The Open Source Drug Discovery (OSDD) Consortium, Council of Scientific and Industrial Research, Anusandhan Bhavan, 2 Rafi Marg, New Delhi 110001, India

关键词: Perturbation analysis;    in silico gene knock-out;    Systems biology;    Metabolic network;    Flux balance analysis;   

Others  :  1091345
DOI  :  10.1186/s12918-014-0130-2

 received in 2014-07-16, accepted in 2014-11-12,  发布年份 2014

【 摘 要 】

Background

Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug targets and optimize metabolic throughput at a systemic level. While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality. We have developed MetaNET, an open source user-friendly platform-independent and web-accessible resource consisting of several pre-defined workflows for metabolic network analysis.

Result

MetaNET is a web-accessible platform that incorporates a range of functions which can be combined to produce different simulations related to metabolic networks. These include (i) optimization of an objective function for wild type strain, gene/catalyst/reaction knock-out/knock-down analysis using flux balance analysis. (ii) flux variability analysis (iii) chemical species participation (iv) cycles and extreme paths identification and (v) choke point reaction analysis to facilitate identification of potential drug targets. The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components. Pre-defined workflows are available for common processes, and an exhaustive list of over 50 functions are provided for user defined workflows.

Conclusion

MetaNET, available at http://metanet.osdd.net webcite, provides a user-friendly rich interface allowing the analysis of genome-scale metabolic networks under various genetic and environmental conditions. The framework permits the storage of previous results, the ability to repeat analysis and share results with other users over the internet as well as run different tools simultaneously using pre-defined workflows, and user-created custom workflows.

【 授权许可】

   
2014 Narang et al.; licensee BioMed Central Ltd.

【 图 表 】

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