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

BMC Systems Biology
Pankaj NarangAndrew Michael Lynn

Abstract

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. 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 Gal...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Nov 15, 2002·Nature·Hiroaki Kitano
Sep 4, 2003·Genome Biology·Jennifer L ReedBernhard O Palsson
Oct 29, 2003·Current Opinion in Biotechnology·Kenneth J KauffmanJeremy S Edwards
Dec 4, 2003·Metabolic Engineering·R Mahadevan, C H Schilling
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Mar 15, 2006·BMC Bioinformatics·Robert Urbanczik
May 30, 2006·Bioinformatics·Axel von Kamp, Stefan Schuster
Jun 15, 2006·Briefings in Bioinformatics·Jong Min LeeJason A Papin
Apr 6, 2007·BMC Systems Biology·Steffen KlamtErnst D Gilles
Aug 30, 2007·BMC Bioinformatics·Roland SchwarzThomas Dandekar
Jun 10, 2008·Nature Biotechnology·Adam M Feist, Bernhard Ø Palsson
Jul 1, 2008·BMC Systems Biology·Jeremiah Wright, Andreas Wagner
Mar 17, 2009·Briefings in Bioinformatics·Karthik Raman, Nagasuma Chandra
Mar 10, 2010·Nature Biotechnology·Jeffrey D OrthBernhard Ø Palsson
Apr 21, 2010·BMC Systems Biology·Isabel RochaMiguel Rocha
Apr 30, 2010·BMC Bioinformatics·Jan SchellenbergerBernhard Ø Palsson
Sep 3, 2011·Nature Protocols·Jan SchellenbergerBernhard Ø Palsson
Feb 1, 2012·BMC Systems Biology·Joost BoeleBas Teusink
Aug 4, 2012·BMC Systems Biology·Xueyang FengYinjie J Tang
Nov 8, 2012·Briefings in Bioinformatics·Meiyappan LakshmananDong-Yup Lee
Nov 13, 2012·Briefings in Bioinformatics·Thomas DandekarZeeshan Ahmed
Nov 15, 2013·BMC Systems Biology·Gabriel Gelius-DietrichMartin J Lercher
Jan 1, 2012·Metabolites·Birgitta E EbertLars M Blank

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Citations

Oct 16, 2015·Electrophoresis·Biswapriya B Misra, Justin J J van der Hooft

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Methods Mentioned

BETA
Knock-outs
gene knock-out

Software Mentioned

MetaNET
BiGGSBML Reader
Make Pairs
MATHEMATICA
Reaction knock - out optimizer
Network Information Retriever
MetaNetX
in
MetaNET Metatool
SNA

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