Inception Call G5 – Available positions

  • Candidate information

  • Keywords

  • PhD

  • Publication records

  • Application summary

  • Selected publications

  • Selected publications

  • Upload your complete application document

  • In a single file (pdf, 1.5 spacing, 25MB max):
    · Description of past and present research activities (4 pages)
    · Proposed research project (6 pages)
    · Detailed CV and full publication list
    · Three scientists from whom letters of recommendation can be sought
    · The names of scientists with a potential conflict of interest
  • Accepted file types: pdf.

News – IFB Projects – Developement of innovative bioinformatics services for life sciences

Thirty nine projects have been submitted to IFB, sixteen have been accepted. Five of those accepted projects imply the C3BI.

Enhancing the CRISPRdb database and related services: CRISPR-Cas++

Leader : D. Gautheret (psud) Partners :

  • eBio, I2BC, Orsay (1 group + PF) 5 pers
  • Institut Pasteur, Paris (2 groups + PF)
  • Bilille bioinformatics platform, Université Lille 1 pers

Description :

CRISPRs are genetic loci present in bacteria and archaea which, associated to cas genes, provide defense against foreign sequences. The CRISPR-Cas system is a highly successful biotechnology tool and CRISPR sequences are used in genotyping pathogenic bacteria. The CRISPR database and services developed at I2BC are leading international resources for CRISPR sequence analysis. These resources now need to be strengthened and new tools and services should be added to meet growing user demands. This proposal is a collaboration between a senior member of the initial CRISPRdb team, two labs with strong expertise in cas gene sequence analysis and bacterial genotyping, and three bioinformatics platforms providing engineering support. The project is divided in two parts. First we will improve the existing CRISPR tools in terms of database structure, search engines and interfaces and develop a standalone version of the CRISPR finding tool to support large scale analyzes. Second, we will incorporate new features: a Cas sequence database and analysis tool and a bacterial genotyping tool. Involving key players such as Institut Pasteur and the French Bioinformatics Institute (that will host the future web site) should provide a strong foundation to this new CRISPR-Cas resource and promotes its international status.

Duration : 2 years

ARIA for hybrid structure determination on the cloud

Leader : B. Bardiaux (bis, pasteur) Partners:

  • Pasteur (6 pers)


Protein structure determination is crucial for understanding protein function, as it paves the way to the discovery of new drugs and of new approaches to control pathological biological processes. The recent advances in structural biology now allow collecting structural information from a variety of techniques at various resolutions. Integration of such heterogeneous data to determine hybrid structure is currently a computational challenge in molecular modelling, both in term of computing efficiency and availability of bioinformatics tools. The widely used ARIA software developed at Institut Pasteur [258 citations, Rieping W et al.(2007)] has proven very efficient in automatically determining protein structures from NMR data. In this project, we will expand the repertoire of input data types that can be used with ARIA for hybrid structure determination. In parallel, it is necessary to bridge the data analysis modules of ARIA with other relevant structure generation engines to be able to analyse the data types. To ultimately provide a perfectly transparent service to the end user, we will design a web-interface for ARIA and make hybridARIA freely available for the scientific community, notably through the cloud deployed by IFB.

Duration : 2 ans

Leader : S. Cohen-boulakia (lri- psud) Partners :

  • IGS (3 pers)
  • LRI (1 pers)
  • Institut Pasteur (4 pers)
  • LIRMM (2pers)

Description :

With 50,000 data analysis per month and more than 1,500 citations (google scholar), the phylogenetic analysis pipeline [1898 citations, Dereeper A et al.(2008)] is one of the most visible French IT resources both at the national and international levels. Phylogenetic analysis is performed by chaining (selected) programs together. Today, users’ needs have evolved; they can use for teaching, inducing possibly hundreds of users at the same time, or employ it in batch mode leading to the submission of large amount of requests to the same server. Those practises have led to several engorgements of our servers. In this project, we thus plan to increase the robustness of The originality of the new version of lies in considering a scientific workflow environment (Galaxy) coupled with a web interface allowing visualization and interaction with phylogenetic objects. More precisely, this project will provide (i) a large set of phylogenetic analysis bricks and for each brick, access to diverse programs, all encapsulated into Galaxy thus making the system able to deal with large groups of users and/or large sets of data, (ii) a set of optimized, robust and expressive workflows extending the basic phylogenetic workflow to various and rich contexts of phylogenetic analyses, (iii) an easy-to-install environment equipped with a new visualization layer, on top of the Galaxy system, and dedicated to phylogenetic analyse

Duration : 2 years

Provide ready to use Galaxy analyses environment for LiFe Sciences communities

Leader : O. Inizan (URGI) Partners:

  • INRA-URGI (1 pers)
  • CNRS-ABiMS (1 pers)
  • Institut Curie (1pers)
  • IRD-soutgreen (1 pers)
  • INRA-Genotoul (1 pers)
  • INRA-Migale (1pers)
  • INRA-PFEM (1pers)
  • INIRIA-Genouest (1 pers)
  • Institut Pasteur (1pers)

Description :

With virtualization technologies the way we consider accessibility and reproducibility (A/R) in computing science has shifted. From the classical approach where A/R was possible through bioinformatics tools distribution, we are now ready to use appliances available on marketplaces hosted in a cloud. Such appliances represent an important shift because not only tools are accessible for reproducibility, but also all the components contributing to the environment of analysis. As virtualization and cloud computing technologies will expand, we expect that the ability to build such containers and to deploy them on heterogeneous infrastructures (desktop, cloud, medium infrastructure hosted in a lab) will become a major topic for the activity consisting in providing services to scientists. On the other hand, the galaxy platform meets a great success in several scientific communities and becomes an important layer of environments dedicated to biological analysis. In this project, we plan to provide ready-to-use Galaxy-environments for analysis to several scientific communities. This project will be organized around two axes. In the first axe, partners from several scientific communities will design representative use cases. In the second axe, use cases will be implemented as containers and made accessible on the IFB cloud infrastructure. We expect that the technical solutions and expertise developed during the project will be re-usable and useful for wider scientific communities, specially for the european life science community: ELIXIR.

Duration : 2 years


Leader : D. Vallenet (genoscope) Partners:

  • LABGeM: (4 pers)
  • Institut Pasteur: (1pers)

Description :

MicroScope [269 citations, Vallenet D. et al.(2006)] is an integrated platform to support microbial genomes (re)annotation and comparative analysis. The current project aims at designing a version of the MicroScope platform using Cloud technologies to progressively switch into a Software as a Service (SaaS) distribution mode. This technical evolution will require several adaptations of the current architecture in: (i) the integration of the MicroScope components in a single appliance (ii) the adaptation of workflows for dynamic provisioning of cluster workers (iii) the setup of a service providing and handling the update of the required reference databanks for the different MicroScope instances. Additional functionalities will also be developed: (i) user interfaces for data and workflow management (ii) a central repository of MicroScope genomes to allow users to share their data within the community of microbiologist. The main purpose of the project is to provide biologists with an on-demand MicroScope solution without any requirement of specific computational skills and with minimal user support. Furthermore, it should increase the flexibility in scale and cost for the needs of computation and storage to face the challenge of Big Data in genomics. These technological developments will be made in collaboration between the CEA/Genoscope (LABGeM), the Pasteur Institute (C3BI/CIB) and the Institut Français de Bioinformatique (IFB), and could be the starting point of a new ELIXIR pilot project ( in the domain of microbial genomics.

Duration : 2 ans

Training – Session d’hiver : programmation et scripting – 11 February 2016

EVENT : C3BI Training – Programmation & Scripting

Ecole Du C3BI : Session d’hiver : programmation et scripting

From : 11/02/2015

To : 25/02/2015

Objectif de la formation : Ce cours s’adresse à toute personne du campus souhaitant acquérir des bases de la programmation et du scripting utiles à la bioinformatique et ayant du mal à trouver du temps pour se former tout le long de l’année.
Pré-requis :Aptitude à travailler onze jours en continu en informatique et avoir des besoins confirmés par des projets en cours ou à venir.

Cette formation n’est accessible qu’aux personnes de l’Institut Pasteur, retrouvez les modalités d’inscription sur le site intranet de Pasteur.

Trainings – Leishield Training Course on Next Generation Sequencing

EVENT : C3BI Training – NGS Data Analysis

Leishield – Training Course on Next Generation Sequencing

Organizing Committee & Module coordinators : Fatma Z. Guerfali, Antonio V. Borderia,  Marie-Agnès Dillies, Christophe Malabat, from Institut Pasteur Tunis & C3BI

Date : from 30/11/2015 to 04/12/2015

Location : Pacific room – CIS (22), Institut Pasteur, Paris

The primary aim of this course was to provide a basic understanding of the Leishmania genome, NGS technology and analysis tools, and to develop a basic pipeline for the students to start working on their data. This first pipeline will help to standardize all analysis done in the consortium and should facilitate a posterior paper publication. This pipeline will evolve in the context of a collaboration between the Leishield partners and the C3BI, taking into account the difficulties to analyze and interpret the sequence data generated, and the specific needs of each Consortium node. A future Workshop will be organized in June 2016 to tackle all these questions, and to have a follow-up on the analysis.


The secondary aim of this course was to have a first contact between the C3BI and Leishield in order to establish a future collaboration. This course provided to the teachers and students, fertile ground to work together and exchange ideas.


Available Positions – C3BI 2016 – Job Application

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 and