GEMSiRV 20130911 – GEnome-scale Metabolic Model Simulation, Reconstruction and Visualization

GEMSiRV 20130911

:: DESCRIPTION

GEMSiRV is a software platform to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.

::DEVELOPER

GEMSiRV team

:: SCREENSHOTS

GEMSiRV

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GEMSiRV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
Liao YC1, Tsai MH, Chen FC, Hsiung CA.

modelBorgifier 1.0 – Comparing and Merging Metabolic Models

modelBorgifier 1.0

:: DESCRIPTION

Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation.

::DEVELOPER

BRAIN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB
  • COBRA Toolbox

:: DOWNLOAD

 modelBorgifier

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1036-8. doi: 10.1093/bioinformatics/btt747. Epub 2013 Dec 25.
Assimilating genome-scale metabolic reconstructions with modelBorgifier.
Sauls JT1, Buescher JM.

FBA-SimVis 1.91 – Dynamic Visualisation of Constraint-based Metabolic Models

FBA-SimVis 1.91

:: DESCRIPTION

FBA-SimVis  (FBASimVis) is a VANTED Add-on for the constraint-based analysis of metabolic models with special focus on the dynamic and visual exploration of metabolic flux data resulting from model analysis.

::DEVELOPER

 Eva Grafahrend-B26elau and members of the groups Plant Bioinformatics and Systems Biology.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 FBA-SimVis

:: MORE INFORMATION

Citation

Eva Grafahrend-Belau1,, Christian Klukas, Björn H. Junker and Falk Schreiber
FBA-SimVis: interactive visualization of constraint-based metabolic models
Bioinformatics (2009) 25 (20): 2755-2757.

MEMOSys 2.1.1 – Metabolic Model System

MEMOSys 2.1.1

:: DESCRIPTION

MEMOSys is a web based bioinformatics platform for the management, storage, and development of metabolic models. It supports the development of new models by providing a built in version control system which offers access to the complete reconstruction history.

::DEVELOPER

the Division of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • Java
  • PostgreSQL

:: DOWNLOAD

 MEMOSys

 :: MORE INFORMATION

Citation

MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data.
Pabinger S, Snajder R, Hardiman T, Willi M, Dander A, Trajanoski Z.
Database (Oxford). 2014 Feb 14;2014:bau004. doi: 10.1093/database/bau004.

MEMOSys: Bioinformatics platform for genome-scale metabolic models.
Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z.
BMC Syst Biol. 2011 Jan 31;5:20. doi: 10.1186/1752-0509-5-20.

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