Scientific Programmer - European Nucleotide Archive EMBL

Location: EBI - Hinxton near Cambridge, UK

Staff Category: Staff Member

Contract Duration: 3 years

Grading: 6

Closing Date: 16 May 2012

Reference number: EBI_00172

Job Description

We are looking to recruit an experienced Scientific Programmer to join the European Nucleotide Archive (ENA) Team at the European Bioinformatics Institute (EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.

The EBI is Europe's leading provider of information services to biological researchers in academia and industry. An integral part of this service is the archiving of nucleotide sequences into the Sequence Read Archive (SRA), one of the world’s largest and fastest growing scientific databases. The SRA currently contains more than 175 trillion sequenced base pairs, equivalent to tens of thousands of human genomes. The SRA provides an exciting opportunity for candidates looking to work with extremely large databases, data processing pipelines and data compression algorithms.

We are currently recruiting a Scientific Programmer to maintain and improve SRA’s data validation, transformation and compression pipelines. SRA accepts data submissions in a variety of formats including platform-specific and cross-platform formats (e.g. Fastq, BAM and VCF). The main responsibilities of the post holder are the development and operation of SRA’s data processing pipelines and the development of lossless and lossy compression algorithms within the CRAM framework. The candidate will be expected to familiarize themselves with most common sequence read, alignment and variation data formats and to create and extend data processing pipelines and databases to process and manage these data.

The EBI is part of the European Molecular Biology Laboratory (EMBL) and is Europe's largest provider of information services to biological researchers in academia and industry.

For further information please visit www.ebi.ac.uk

Qualifications and Experience

The ideal applicant should hold a university degree in computer sciences, mathematics or life sciences and have several years experience in software development. A strong command of Java is essential together with a good understanding of common data structures and algorithms. Detailed knowledge of relational databases and programming methodologies is highly desirable.

Excellent communication, interpersonal and English skills are essential for working productively alone as well as part of a team. Other desirable skills include contributions to open-source projects, knowledge of next generation sequencing technologies and file formats, familiarity with compression algorithms, experience with high-throughput pipeline development and practical experience with C/C++.

Application Instructions

Please apply online through www.embl.org/jobs

Additional Information

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

Note that special visa requirements apply to employees from non EU countries working at EMBL-EBI in the UK. The period of work does not qualify them for the Highly Skilled Migrants Programme.

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