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MetaPath Online: a web server implementation of the network expansion algorithm, Handorf, T. and Ebenhöh, O., Nucleic Acids Research, 35, Web Server issue: W613-W618 (2007)
Expanding Metabolic Networks: Scopes of Compounds, Robustness and Evolution, Handorf, T., Ebenhöh, O., Heinrich, R., J. Mol. Evol, 61:498-512, (2005)
The synthesizing capacity of metabolic networks (abstract), Handorf, T., Ph.D. Thesis, (2008)For more information on the concept of scopes see:
An integrative approach towards completing genome-scale metabolic networks, Christian, N., May, P., Kempa, S., Handorf, T., Ebenhoeh, O., Mol. BioSyst., DOI: 10.1039/b915913b (2009)
Functional classification of genome-scale metabolic networks., Ebenhöh O., Handorf, T., EURASIP J Bioinform Syst Biol. 2009:570456 (2009)
An environmental perspective on metabolism , Handorf T., Ebenhöh O., Christian N., Kahn D., Journal of Theoretical Biology, 252(3):530-537 (2008)
Biosynthetic Potentials From Species-Specific Metabolic Networks. Basler G., Nikoloski, Z., Ebenhöh, O., Handorf, T., Genome Informatics, 20:135-148 (2008)
Hierarchy of metabolic compounds based on their synthesizing capacity, Handorf, T., Ebenhöh, O., Kahn, D., Heinrich, R., IEE Proc. Systems Biology, 153(5):359-363 (2006)
Evolutionary changes of metabolic networks and their biosynthetic capacities. Ebenhöh, O., Handorf, T., Kahn, D., IEE Proc. Syst. Biol. 153(5):354-358 (2006)
Structural Analysis of Expressed Metabolic Subnetworks. Ebenhöh, O. and Liebermeister, W., Genome Informatics 17(1):163-172 (2006)
A cross species comparison of metabolic network functions. Ebenhöh, O., Handorf, T., Heinrich, R., Genome Informatics 16(1):203-213 (2005)
Structural analysis of expanding networks, Ebenhöh, O., Handorf, Th., Heinrich, R., Genome Informatics Series Vol. 15(1):35-45 (2004)
Modeling mechanistic biological networks: An advanced Boolean approach(preprint), Handorf, T., Klipp, E.,Bioinformatics, accepted, (supplement)The calculations are based on metabolic information obtained from the KEGG database, since it contains very comprehensive pathway information. As the concepts are not bound to a specific database, also other datasets may be provided in future.
The main components of MetaPath Online are written in perl. External programs are used to display the results. The metabolic reaction networks are translated into the "dot" language and layed out by GraphViz. For plotting xmGrace is used.
The reactions sets used in this application can be downloaded here as a documented text file.
