GEMINI – Gene Expression and Metabolism Integrated for Network Inference

GEMINI

:: DESCRIPTION

GEMINI produces a regulatory network that is simultaneously consistent with observed gene knockout phenotypes, gene expression data, and the corresponding metabolic network.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Matlab

:: DOWNLOAD

GEMINI

:: MORE INFORMATION

PROM – Probabilistic Regulation of Metabolism

PROM

:: DESCRIPTION

The PROM algorithm represents the successful integration of a genome scale transcriptional regulatory network with a biochemically detailed metabolic network, bridging two important classes of systems biology models that have rarely been combined quantitatively.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Matlab

:: DOWNLOAD

PROM

:: MORE INFORMATION

Citation

A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism).
Simeonidis E, Chandrasekaran S, Price ND.
Methods Mol Biol. 2013;985:103-12.

BioMet Toolbox 2.0 – Genome-wide analysis of Metabolism and Omics data

BioMet Toolbox 2.0

:: DESCRIPTION

The BioMet ToolBox is a web-based resource for exploiting the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, powered by RAVEN, gene set analysis and basic microarray analysis using PIANO, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, V?remo L, Nookaew I, Nielsen J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371.

XenoSite – Metabolism Prediction Web Server

XenoSite

:: DESCRIPTION

XenoSite Web provides prediction web services for small molecule biochemistry. XenoSite Web can be used by medicinal chemists and biologists to make predictions about the human in vivo metabolism of small molecules.

::DEVELOPER

S Joshua Swamidass

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

XenoSite-Server: A Web-Available Site of Metabolism Prediction Tool.
Matlock MK, Hughes TB, Swamidass SJ.
Bioinformatics. 2014 Nov 18. pii: btu761.