:: DESCRIPTION
PathRanker is an R-package for extraction and analysis of the most active metabolic pathways through gene expression data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Sep 1;26(17):2128-35. doi: 10.1093/bioinformatics/btq344. Epub 2010 Jun 29.
Mining metabolic pathways through gene expression.
Hancock T1, Takigawa I, Mamitsuka H.
:: DESCRIPTION
ReTrace is a computational method for inferring branching pathways in genome-scale metabolic networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Syst Biol. 2009 Oct 29;3:103. doi: 10.1186/1752-0509-3-103.
Inferring branching pathways in genome-scale metabolic networks.
Pitkänen E1, Jouhten P, Rousu J.
:: DESCRIPTION
GLAMM (The Genome-Linked Application for Metabolic Maps) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. We use Microbes Online as the first of what will ultimately be multiple sources for metabolic reconstruction and pathway data, including custom, user-uploadable networks.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
John T. Bates; Dylan Chivian; Adam P. Arkin
GLAMM: Genome-Linked Application for Metabolic Maps
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr433
:: DESCRIPTION
MetaPath can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Liu B, Pop M:
Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets.
Lect Notes Comput Sci 2010, 6053: 101-112
:: DESCRIPTION
PathwayAnalyser is a software for systems biologists who want to perform flux based analyses and simulations on SBML Models. PA affords FBA as well as interfacing with Taylor software for high precision simulations of ODEs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SensiPath will help you design Sensing-Enabling Metabolic Pathways (SEMP) for synthetic biology applications in prokaryotes.
::DEVELOPER
Jean-Loup Faulon’s group at Micalis.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
SensiPath: computer-aided design of sensing-enabling metabolic pathways.
Delépine B, Libis V, Carbonell P, Faulon JL.
Nucleic Acids Res. 2016 Apr 22. pii: gkw305.
:: DESCRIPTION
MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.
::DEVELOPER
Max Planck Institute for Molecular Plant Physiology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY and M Stitt (2004)
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Plant J. 37(6):914-39.
:: DESCRIPTION
Meta-All is a software that allows to store and access information about metabolic pathways, including reaction kinetics, detailed locations, environmental circumstances and taxonomic information.
::DEVELOPER
Life Science Informatics – Prof. Dr. Falk Schreiber
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S. Weise, I. Grosse, C. Klukas, D. Koschuetzki, U. Scholz, F. Schreiber and B.H. Junker.
Meta-All: a system for managing metabolic pathway information.
BMC Bioinformatics, 7:e465, 2006.
:: DESCRIPTION
TrackSM is a cheminformatics tool which designs to associate a chemical compound to a known metabolic pathway based on molecular structure matching techniques.
::DEVELOPER
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Chem Inf Model. 2015 Mar 23;55(3):709-18. doi: 10.1021/ci500517v.
Metabolic pathway predictions for metabolomics: a molecular structure matching approach.
Hamdalla MA1, Rajasekaran S, Grant DF, Măndoiu II.
:: DESCRIPTION
kMech is a comprehensive collection of single and multiple substrate enzyme reactions and regulatory mechanisms that extends Cellerator function for the mathematical modeling of enzyme reactions.
::DEVELOPER
Institute for Genomics and Bioinformatics, University of California
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2005 Mar;21(6):774-80. Epub 2004 Oct 27.
An enzyme mechanism language for the mathematical modeling of metabolic pathways.
Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW.
