Meta-All 1.2 – Store and Access Information about Metabolic Pathways

Meta-All 1.2

:: 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

  Meta-All

:: 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.

TrackSM 1.00 – Associate Chemical Compound to Known Metabolic Pathway

TrackSM 1.00

:: 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

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

 TrackSM

:: 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.

SensiPath 2.1.1 – Computer-aided Design of Sensing-enabling Metabolic Pathways

SensiPath 2.1.1

:: 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

  • Web browser

:: DOWNLOAD

 SensiPath

:: 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.

Desharky – Computational Design of Metabolic Pathways in E. coli.

Desharky

:: DESCRIPTION

DESHARKY is a Monte Carlo algorithm that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism together with its impact in the cellular context by using mathematical models of the cell resources and metabolism.

::DEVELOPER

Jaramillo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 DESHARKY

 :: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 1;24(21):2554-6. doi: 10.1093/bioinformatics/btn471. Epub 2008 Sep 5.
DESHARKY: automatic design of metabolic pathways for optimal cell growth.
Rodrigo G1, Carrera J, Prather KJ, Jaramillo A.

MetaPath 0.83 – Comparative Analysis of Metabolic Pathways in Metagenomics

MetaPath 0.83

:: 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

Bo Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MetaPath

:: MORE INFORMATION

Citation:

Liu B, Pop M:
Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets.
Lect Notes Comput Sci 2010, 6053: 101-112

Metabolome Searcher – Metabolite Identification and Metabolic Pathway Mapping

Metabolome Searcher

:: DESCRIPTION

Metabolome Searcher, a web-based tool, facilitates putative compound identification of MS output based on genome-restricted metabolic capability.

::DEVELOPER

Metabolome Searcher team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

 NO

:: MORE INFORMATION

Citation

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction.
Dhanasekaran AR, Pearson JL, Ganesan B, Weimer BC.
BMC Bioinformatics. 2015 Feb 25;16(1):62.

M-path – Navigating a Potential Metabolic Pathway

M-path

:: DESCRIPTION

M-path calculates random combinations of a wide variety of reactions to list potential metabolic routes from initial to target compounds efficiently, which could be a heuristic approach in designing potential metabolic pathways in practical applications.

::DEVELOPER

Michihiro Araki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

M-path: A Compass for Navigating Potential Metabolic Pathways.
Araki M, Cox RS 3rd, Makiguchi H, Ogawa T, Taniguchi T, Miyaoku K, Nakatsui M, Hara KY, Kondo A.
Bioinformatics. 2014 Nov 13. pii: btu750.

PathWave 2.1 – Discovering Patterns of Differentially Regulated Enzymes in Metabolic Pathways

PathWave 2.1

:: DESCRIPTION

PathWave enables the user to easily analyse gene expression data considering the topology of metabolic pathways as provided by KEGG.

::DEVELOPER

EILSLABS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • R package

:: DOWNLOAD

 PathWave

:: MORE INFORMATION

Citation

BMC Syst Biol. 2014 May 16;8:56. doi: 10.1186/1752-0509-8-56.
Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling.
Piro RM, Wiesberg S, Schramm G, Rebel N, Oswald M, Eils R, Reinelt G, König R

Bioinformatics. 2010 May 1;26(9):1225-31. doi: 10.1093/bioinformatics/btq113. Epub 2010 Mar 24.
PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways.
Schramm G, Wiesberg S, Diessl N, Kranz AL, Sagulenko V, Oswald M, Reinelt G, Westermann F, Eils R, König R.

MapMan 3.6.0RC1 – Displays large datasets onto Diagrams of Metabolic Pathways

MapMan 3.6.0RC1

:: 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, Golm, Germany.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MapMan

:: 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.

ReTrace 1.03 – Infers Branching Metabolic Pathways

ReTrace 1.03

:: DESCRIPTION

ReTrace is a computational method for inferring branching pathways in genome-scale metabolic networks.

::DEVELOPER

Esa Pitkänen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Python

:: DOWNLOAD

 ReTrace

:: 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.