The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June. GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
Authors Lien Nguyen 1* , Maud Lacombe 1 , Sandra Dérozier 2 , Lisa Perus 1 , Olivier Rué 2 , Florence Combes 1 , Christophe Caron 2 , Virginie Brun 1 , Valentin Loux 2 , Yves Vandenbrouck 1 1 : Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université de Grenoble, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) - Grenoble, Centre National de la Recherche Scientifique : FR3425 17, rue des Martyrs 38054 Grenoble cedex 9 - France 2 : Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement (MAIAGE), Institut National de la Recherche Agronomique, Université Paris-Saclay Domaine de Vilvert 78350 Jouy en Josas Cedex - France * : Corresponding author
Abstract Introduction Galaxy is a well-maintained software platform providing simple interfaces to tools and online access to computational resources in a transparent way. Build upon Galaxy, the ProteoRE (Proteomics Research Environment) project is a joint effort between the French proteomics infrastructure (ProFI) and the French bioinformatics Institute (IFB). Its primary aim is to centrally provide the proteomics community with an online research service enabling biologists/clinicians without programming expertise to explore their proteomics data through the Web in a reproducible manner. Methods Starting from proteome software output files (MaxQuant, Proline), various components have been designed driven by expertise and needs from our collaborators. These modules embedded into Galaxy components have been implemented either by reusing tools (from the Galaxy Tool Shed) or by wrapping Bioconductor packages and external code, and further beta-tested.
Results We have set up two use cases scenarios derived from our own research projects to interpret a large proteins identification list and to entail selection of biomarkers candidates based on biochemical criteria. A first ProteoRE instance is now deployed and currently in beta-testing before public release in early 2018.
Conclusions While Galaxy-based tools offers services for primary proteomics data analyses (e.g. MS data conversion, protein database tools, search algorithms), tools focusing on downstream analysis are still lacking. The ProteoRE platform proposes to fill this gap with the hope of promoting proteomics data in the Life Science community.
