Tag: Metabolic Network

COBRA Toolbox 3.0.6 / COBRApy 0.17.1 – MATLAB Scripts for Constraint-based Modeling of Metabolic Networks

COBRA Toolbox 3.0.6 / COBRApy 0.17.1

:: DESCRIPTION

COBRA Toolbox (COnstraint-Based Reconstruction and Analysis Toolbox) is a software package running in the MATLAB environment which allows for quantitative prediction of cellular behavior using a constraint-based approach.

COBRApy is a package for constraints-based modeling of biological networks

::DEVELOPER

COBRA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

COBRA Toolbox , COBRApy

:: MORE INFORMATION

Citation:

Becker, S. et al.,
“Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox”,
Nat. Protoc 2, 727-738 (2007).

PITUFO – Find minimal sets of Precursors of Target Compounds in a Metabolic Network

PITUFO

:: DESCRIPTION

PITUFO is a java software to find minimal sets of precursors of target compounds in a metabolic network.

::DEVELOPER

Ludovic Cottret

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Java

:: DOWNLOAD

 PITUFO

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2010 Sep 2;6(9). pii: e1000904. doi: 10.1371/journal.pcbi.1000904.
Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.
Cottret L, Milreu PV, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF.

MOTUS 1.1.3 – Motif search in Metabolic Networks

MOTUS 1.1.3

:: DESCRIPTION

Motus is a tool for searching and inferring reaction motifs in metabolic networks.
A metabolic network is modelled as an undirected graph. Nodes (reactions) are labelled with EC numbers (code of 4 numbers expressing the chemistry of a reaction).
A reaction motif is defined as a set of (partial) EC numbers. An occurrence of the motif in the network is a set of nodes (reactions) which is connected and labelled by EC numbers that are similar to the ones of the motif.

 MOTUS Online Version

::DEVELOPER

Vincent Lacroix

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MOTUS

:: MORE INFORMATION

Citation

V. Lacroix, C. G. Fernandes, and M.-F. Sagot.
Motif search in graphs: Application to metabolic networks.
Transactions in Computational Biology and Bioinformatics, vol. 3, pages 360-368, 2006.

MetaNetSam 1.1 – Metabolic Network Sampling

MetaNetSam 1.1

:: DESCRIPTION

MetaNetSam is an application for sampling subnetworks from metabolic networks.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE

:: DOWNLOAD

 MetaNetSam

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2013;9(3):e1002981. doi: 10.1371/journal.pcbi.1002981. Epub 2013 Mar 21.
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.
Jiao D1, Ye Y, Tang H.

MetNetMaker 1.6.2 – Creation of Novel Metabolic Networks in SBML format

MetNetMaker 1.6.2

:: DESCRIPTION

MetNetMaker is the only free software designed solely to create metabolic networks based on the KEGG LIGAND database ready for Flux-Balance Analysis in the COBRA toolbox.MetNetMaker helps with creating a Metabolic Network by keeping track of the details, like naming conventions, cellular compartments and network subdivisions so that FBA-ready networks in SBML format can be created by anyone familiar basic concepts of metabolism.

::DEVELOPER

Tom Forth.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MetNetMaker

:: MORE INFORMATION

Citation

Forth,T. et al. (2010)
MetNetMaker: A free and open-source tool for the creation of novel metabolic networks in SBML format.
Bioinformatics (2010) 26 (18): 2352-2353.

FFCA 1.01 – Feasibility-based Flux Coupling Analysis of Metabolic Networks

FFCA 1.01

:: DESCRIPTION

FFCA is a Matlab based tool for flux coupling analysis. An LP solver should be installed separately and made “visible” from within Matlab. FFCA currently supports the usage of Linprog, Clp, Lindo and Glpk.

::DEVELOPER

Prof. Dr. Alexander Bockmayr

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Linux

:: DOWNLOAD

 FFCA

:: MORE INFORMATION

Citation

L. David, S.-A. Marashi, A.Larhlimi, B. Mieth, A. Bockmayr.
“FFCA: a feasibility-based method for flux coupling analysis of metabolic networks“,
BMC Bioinformatics 2011, 12:236.

yasimSBML 1.0.1 – Simulate Metabolic Network depending on the Flux Distribution

yasimSBML 1.0.1

:: DESCRIPTION

yasimSBML ( (Yet another simulator of SBML)) implements a simple method to simulate metabolic network depending on the flux distribution.

::DEVELOPER

yasimSBML Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 yasimSBML 

:: MORE INFORMATION

MetAnnoGen – Metabolic Network Annotation

MetAnnoGen

:: DESCRIPTION

The MetAnnoGen facilitates the reconstruction of metabolic networks. It is an information system to collect and manage data from different databases and scientific literature in order to generate a metabolic network of biochemical reactions that can be subjected to further computational analyses.

::DEVELOPER

Dr. Christoph Gille

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 MetAnnoGen

:: MORE INFORMATION

Citation

Metannogen: annotation of biological reaction networks.
Gille C, Hübner K, Hoppe A, Holzhütter HG.
Bioinformatics. 2011 Oct 1;27(19):2763-4. Epub 2011 Aug 8.

ExPA 050216 – Extreme Pathway Analysis for Metabolic Networks

ExPA 050216

:: DESCRIPTION

ExPa (extreme pathways analysis) , a generating set for all possible steady state flux maps in a biochemical reaction network, can be computed from the stoichiometric matrix, an incidence-like matrix reflecting the network topology. ExPa compute these pathways.

::DEVELOPER

Bernhard Palsson

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

ExPA

:: MORE INFORMATION

Citation:

Bell, S.L. and Palsson, B.Ø., “A Program for Calculating Extreme Pathways in Biochemical Reaction Networks“, Bioinformatics, in press (2004).

Metaboflux 2.0.6 – Predict Flux Distribution in Metabolic Networks

Metaboflux 2.0.6

:: DESCRIPTION

Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model. Metaboflux aims to provide a complete environnement to study the interaction and
constraints of a metabolic network.

::DEVELOPER

Metaboflux Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Metaboflux

:: MORE INFORMATION