Job:Bioinformatician position at EMBL, Heidelberg, Germany (3 * 3 years)
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6.8 years ago
cha.girardot ▴ 10

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).

EMBL is seeking a highly motivated (bio)informatician to work in the Genome Biology Computational Support (GBCS) group. The position involves the maintenance and development of emBASE, an EMBL-wide web-based application dedicated to the management of *omics data (in particular NGS data) produced by the different EMBL groups. The successful applicant will also maintain tools and scientific libraries on unix-based servers, develop analysis pipeline in Galaxy and/or using workflow management systems (e.g. snakemake), and help managing our Galaxy server. Ideally, the candidate is able to conduct data analysis (in particular NGS data using e.g. R/bioconductor) and has some experience with docker and cloud-based technologies. The successful applicant is in charge of supporting users on a daily basis, assembling training materials (e.g. writing of wiki-based documentation/how-to) and organizing tutorials

Qualifications and Experience

Applicants should have an appropriate university degree in computer science or bioinformatics (master degree with 3+ years of experience or PhD).

Extensive experience in web application development/deployment with Python/Django, javascript, AJAX, web/REST API development (and associated collaborative tools i.e. git, IDEs...) is a must. Experience in unix server administration, database administration/design and PHP programming are highly desirable. Analysis of large datasets, prior experience with NGS datasets management/analysis, R/bioconductor scripting, Java programming and some practical experience with docker, VM provisioning (e.g. vagrant, puppet, CHEF...) or cloud computing are definite advantages.

The successful applicant will have demonstrated experience using standard software development tools (SCMs, unit/db testing, design patterns, database design, code versioning systems, agile development notions...). (S)he will be organized (documentation and communication is an important aspect of the job), open-minded, able to work on different projects in parallel, proactive (problem solving skills are essential) and have a user-oriented spirit. The candidate should be able to work independently and also interact well within a team environment. A working knowledge of English is a must.

An initial contract of 3 years will be offered. This might be renewed twice (i.e. up to 9 years).

Application Instructions

Please apply online through

Questions/Enquiries can be addressed to Charles Girardot (


GBCS website:

python NGS RNA-Seq R ChIP-Seq • 2.4k views

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