CIB Team – CDD Job application

CDD en Bioinformatique au sein de la Cellule Informatique pour la Biologie

Le CIB (Cellule Informatique pour la Biologie) est une composante majeure du nouveau centre de Bioinformatique, de Biostatistiques et de Biologie intégrative (C3BI) de l’Institut Pasteur. Son rôle est de répondre aux besoins informatiques des scientifiques du campus par le développement, la mise à disposition et le déploiement d’outils bioinformatique. Son pôle “Intégration Web et Développement Logiciel” recrute un Ingénieur (Bio-)Informatique dans le cadre d’un CDD (6 mois, du 01 novembre au 15 mai 2015). → Vous assurerez, en collaboration avec le reste de l’équipe de la plate-forme Galaxy de l’Institut Pasteur: L’évolution de celle-ci (mises à jour, modifications de la configuration) Le développement et la maintenance d’interfaces pour des outils bioinformatique Le support et la formation aux utilisateurs → Vous participerez aussi à l’étude de faisabilité de la mise en place d’un serveur public Galaxy.

Compétences requises

De formation BAC+5, type Master Informatique/Bioinformatique, vous maitrisez le langage de programmation Python ainsi qu’au moins un logiciel de gestion de versions. Vous avez des connaissances des formats XML, JSON et de préférence, une première expérience de Galaxy. Maîtrise de l’anglais (lu et écrit). Esprit d’équipe, ouverture d’esprit et autonomie sont des qualités recherchées.   English version below

Support engineer for Galaxy at the CIB in the Institut Pasteur

The CIB (Informatics cell for Biology) is a major component of the new Institut Pasteur Center of Bioinformatics, Biostatistics and Integrative Biology. Its role is to fulfill the scientific computational needs of the campus with software implementation, bioinformatics software providing and/or their deployment. Its group “Web Integration and Software Development group” is hiring an (Bio-)informatics engineer for a 6 month contract (from November 1st to May 15th 2015) In collaboration with the rest of Institut Pasteur’s Galaxy Team, he will insure:
  • The evolution of our Galaxy instance (updates, configuration modifications, …)
  • The implementation and the maintenance of Galaxy tools
  • The support and training for Galaxy users
→ He will also participate in the study of the possibility to create a public Galaxy instance hosted in the Institut Pasteur. The engineer has to be familiar with Python, as well as a versioning tool such as git, or svn, … He will have working knowledge of XML, Json formats. Previous experience on Galaxy is a plus. An open mind, autonomy and teamwork skills are mandatory for this position. Proficiency in written and spoken English as well as minimal notions of French (for support and training tasks) are required. If interested, send your application to olivia.doppelt@pasteur.fr and herve.menager@pasteur.fr

C3BI News – REGATE, REGISTRATION OF GALAXY TOOLS IN ELIXIR

ReGaTE is a software component enabling the automated publication of Galaxy tools into the ELIXIR Tools and Data Services Registry

Upcoming Events : C3BI News – Galaxy Community Conference 2015

Date : 6-8th July 2015 Location : The Sainsbury Laboratory, Norwich, UK

REGATE, REGISTRATION OF GALAXY TOOLS IN ELIXIR

Olivia Doppelt-Azeroual1, Fabien Mareuil1, Eric Deveaud1, Matus Kalas2, Hervé Menager1 1 Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France 2 Computational Biology Unit, University of Bergen, Norway ReGaTE is a software component enabling the automated publication of Galaxy tools and workflows into the ELIXIR Tools and Data Services Registry (https://elixir-registry.cbs.dtu.dk/#/). This registry is a web portal for the exploration of bioinformatics resources, such as software packages, web services, websites, or reference databases. Through a dedicated interface, its users can search and locate relevant tools and data resources, and bioinformatics resource providers can enhance the visibility of their services. The registration of resources in the registry can be performed either manually, by filling a form on a web user interface, and providing the required description elements, or automatically by using the registry API. ReGaTE uses the BioBlend API and the Registry API to completely automate the registration of the tools installed on any given Galaxy portal. Central to the development of this tool is the mapping of the Galaxy datatype system to the EDAM Ontology. EDAM provides a controlled vocabulary for the description of scientific topics, software operations, types of data and data formats and it is used to describe the contents of the ELIXIR Registry. This mapping enables the automation of the registration of Galaxy tools by describing the format of their input and output data in the controlled vocabulary of the registry. This mapping is being developed in collaboration with members of the Galaxy team, the EDAM ontology and the Common Workflow Language project. ReGaTE is available at http://github.com/bioinfo-center-pasteur-fr/ReGaTE

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