BMC Syst Biol. 2012 Aug 02;6:94. doi: 10.1186/1752-0509-6-94.
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.
BMC systems biology
Xueyang Feng, You Xu, Yixin Chen, Yinjie J Tang
Affiliations
Affiliations
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO 63130, USA. [email protected]
PMID: 22857267
PMCID: PMC3447728 DOI: 10.1186/1752-0509-6-94
Abstract
BACKGROUND: Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results.
RESULTS: We have developed a semi-automatic, web-based platform (MicrobesFlux) for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites) of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes) and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language). Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions) for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production.
CONCLUSION: MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG database. Our system facilitates users to reconstruct metabolic networks of organisms based on experimental information. Through human-computer interaction, MicrobesFlux provides users with reasonable predictions of microbial metabolism via flux balance analysis. This prototype platform can be a springboard for advanced and broad-scope modeling of complex biological systems by integrating other "omics" data or 13 C- metabolic flux analysis results. MicrobesFlux is available at http://tanglab.engineering.wustl.edu/static/MicrobesFlux.html and will be continuously improved based on feedback from users.
References
- Nat Protoc. 2010 Jan;5(1):93-121 - PubMed
- BMC Syst Biol. 2011 Feb 15;5:28 - PubMed
- Nat Biotechnol. 2008 Oct;26(10):1155-60 - PubMed
- Biophys J. 2002 Sep;83(3):1331-40 - PubMed
- BMC Syst Biol. 2010 Mar 22;4:31 - PubMed
- Mol Syst Biol. 2006;2:2006.0004 - PubMed
- Appl Environ Microbiol. 2009 Aug;75(15):5001-8 - PubMed
- Appl Environ Microbiol. 1994 Oct;60(10):3724-31 - PubMed
- BMC Syst Biol. 2010 Apr 19;4:45 - PubMed
- Nat Biotechnol. 2010 Sep;28(9):977-82 - PubMed
- Genome Biol. 2003;4(9):R54 - PubMed
- Nat Biotechnol. 2010 Dec;28(12):1279-85 - PubMed
- BMC Syst Biol. 2011 Jul 21;5:116 - PubMed
- PLoS Comput Biol. 2009 Feb;5(2):e1000285 - PubMed
- Microb Cell Fact. 2009 May 01;8:25 - PubMed
- PLoS Comput Biol. 2012 Feb;8(2):e1002376 - PubMed
- PLoS One. 2011;6(7):e21784 - PubMed
- Appl Microbiol Biotechnol. 2008 Oct;80(5):849-62 - PubMed
- Bioresour Technol. 2011 Oct;102(20):9586-92 - PubMed
- Appl Environ Microbiol. 2011 Nov;77(22):7998-8008 - PubMed
- Proc Natl Acad Sci U S A. 2000 May 9;97(10):5528-33 - PubMed
- Mol Syst Biol. 2007;3:121 - PubMed
- Nat Protoc. 2007;2(3):727-38 - PubMed
- Bioinformatics. 2009 Nov 1;25(21):2850-2 - PubMed
- BMC Syst Biol. 2012 Jan 30;6:8 - PubMed
- Mol Syst Biol. 2011 Aug 02;7:518 - PubMed
- J Biol Chem. 2007 Sep 28;282(39):28791-28799 - PubMed
- Genome Res. 2003 Feb;13(2):244-53 - PubMed
- Genome Res. 2004 Jul;14(7):1298-309 - PubMed
- IET Syst Biol. 2009 May;3(3):167-79 - PubMed
- Genome Biol. 2009;10(6):R69 - PubMed
- Nat Rev Microbiol. 2011 Jan;9(1):39-50 - PubMed
- Nucleic Acids Res. 2010 Jul;38(Web Server issue):W144-9 - PubMed
MeSH terms
Publication Types