Launching ProteoRE infrastructure
IFB is launching a galaxy user-oriented web-based platform for MS-based proteomics data exploration
Du 04-05-2018 au 04-05-2018 à
Date limite d'inscription: Aucune information

What is ProteoRE ?

ProteoRE (Proteomics Research Environment) aims at centrally providing the proteomics community with an online research service enabling biologists/clinicians without programming expertise to annotate and interpret their proteomics data through the Web. ProteoRE is built upon the popular Galaxy framework, providing simple interfaces to tools and online access to computational resources in a collaborative and transparent way.

Website: http://www.proteore.org/

 

ProteoRE version 1.0 content

ProteoRE currently comprises tools (including graphical display) for:

  • Customary data manipulation (e.g. filtering, lists comparison, ID conversion…)
  • Protein list annotation (e.g. information retrieval from public resources - human species)
  • Functional analysis (e.g. GOterms frequencies, enrichment analysis) including graphical representation.
  • Pathway analysis (e.g. Reactome)

This version also includes Galaxy generic tools and some tools from the GalaxyP project that should be of great help for people who want to (re)process their MS-based proteomics data (e.g. peptide/protein identification).


How to use this public ProteoRE instance ?

This public site is meant for academic usage (for commercial usage, please contact us see below). There are currently two ways to work using ProteoRE as a:

  1. Unregistered user: you can start a session by uploading your data (e.g. proteomics identification results in tabular format), then performing your analysis using tools available. Importantly, we inform users that the allocated storage space is limited to 20 Mb and is not conserved between sessions. For frequent use and/or numerous analyses, we highly recommend to create an account (see just below).
  2. Registered user (authentified access): create an account is a right way to keep track and record of your analyses and your workflows. In addition, more storage space is allocated (up to 20 Gb) to registered user. To create an account, please click on "Account registration or login" on the main menu bar (upper part of ProteoRE central panel), click on "registration" and fill in the form. Once submitted, your account is created.

Help and support: contact@proteore.org

 

Tutorials

Tutorial 1. Annotating a protein list identified by LC-MS/MS experiments


Fundings

ProteoRE project is a joint collaboration between the French bioinformatics Institute (IFB) and the proteomics infrastructure ProFI and funded by the French Research Agency (ANR-11-INBS-0013).

People

Lien Nguyen (software engineer), Florence Combes (bioinformatician), Valentin Loux (Bioinformatician , IT Manager), Virginie Brun, Maud Lacombe, Marianne Tardif & Benoit Gilquin (use-case & beta-testing), Yves Vandenbrouck (Project manager)

 

The Galaxy Project is supported in part by NHGRI, NSF, The Huck Institutes of the Life Sciences, The Institute for CyberScience at Penn State, and Johns Hopkins University.


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