Download Microme Software

Our FTP site hosts some software which can be used by external users to access and analyse various elements of the Microme data set.


Reaction Matrix

We provide a Perl script and accompanying data designed to allow users to analyse the spread of inferred reactions using the large Microme data set (reaction matrix): find pathways in genomes specified by their parent node in taxonomy, reactions in RhEA involved in these pathways, and the genes assigned to UniProt proteins associated with these reactions.

 

Genome-scale functional characterization of a species


We provide a software package that performs the following functionalities:

  • find an optimal media (OM) for a given organism - an OM is the media in terms of uptake reactions that still enables maximal growth rate (the latter refers to the limit growth rate obtained at rich media)
  • fing a minimal media for a given organism, when the organism is forced to grow at list X% of its maximal biomass
  • given an organism, find essential genes, i.e. whose knock-out results in zero growth
  • similarly, find essential gene pairs; the percentage of essential genes and gene pairs provides a measure of the network's genetic robustness


Biolog

The Phenotype MicroArray (OmniLog®) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. The phenotypic reaction of single-celled organisms and animal cell cultures to up to 2,000 environmental challenges can be recorded on sets of 96-well microtiter plates.

One of our project members, DSMZ – German Collection of Microorganisms and Cell Cultures in Braunschweig, has developed an application-oriented software package for the analysis of Biolog high-throughput phenotypic data. The opm (OmniLog Phenotype MicroArray) package, which is based on the free software environment R, allows comprehensive statistical analyses on quantitative data of energy production curves and a better graphic presentation.

Read More


Web Services

We provide a set of web services example clients, developed in different languages, for exploring the data provided by some partners of the project.

Name Server Language Description
ReactomeWSClient.jar Reactome Java

Examples of querying the bacterial Reactome repository using the WS Java API
reactome_ws_client_example.pl Reactome Perl

Export pathway diagrams to SVG/BioPax and other simple examples

infer-operons_client.pl*

 RSAT/NeAT Perl Predict operons for a given organism (either restricted to a list of query genes, or applied to all genomes of the genome)

microcyc-webserviceclient-1.0-20120319-1410-project.zip**

  Microscope Java Java template project (Eclipse) showing how to query the MicroCyc repository

get-gpr-genoscope.pl

  Microscope Perl Retrieve the list of GPRs

get-organisms-genoscope.pl

 Microscope Perl Get the list of supported organisms

supported-organisms-genoscope.py

 Microscope Python Get the list of supported organisms
gene-ec-genoscope.py Microscope Python Get the list of genes, the taxonnomic ID and the species name of the specified organism and EC number of GPR
metabolic-network-genoscope.py Microscope Python Get the list of reactions and compounds, the list of arcs (list of compounds involved in each reaction)

(*) For other, more comprehensive examples of querying RSAT/NeAT, go to http://rsat.ulb.ac.be/rsat/ws_clients.html

(**) The project is also available at http://www.genoscope.cns.fr/microme/microcyc-wsc/index.html