Scientific Programmer

European Bioinformatics Institute - European Molecular Biology Laboratory (EMBL-EBI)
Job Location
Wellcome Trust Genome Campus
CB10 1SD
United Kingdom
Grade 5 - monthly starting salary at £2,387.20 free of UK income tax

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. We provide a dynamic, international working environment and have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute.

EMBL-EBI staff also enjoy excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment set in 55 acres of parkland.


The initial contract is for a period of three years with the possibility of a fixed-term extension.

Job Description

Job Description

We are seeking to recruit an enthusiastic developer to work as a Scientific Programmer on the eHive production system. You will join the Vertebrate Genomics Ensembl team at the European Bioinformatics Institute (EMBL-EBI), which is located on the Wellcome Trust Genome Campus near Cambridge in the UK.

Ensembl ( is one of the most successful large-scale bioinformatics projects and one of the leading projects for genome annotation. Ensembl is importing massive amounts of data from various archives (genome sequences, variation archives, etc) and is also creating new resources (gene annotation, whole-genome alignments, gene trees, annotation of regulatory elements, etc). Most of those production workflows (worth 250 CPU years in 2014) are driven by the eHive system. eHive is a task manager that keeps track of all jobs to be performed within a pipeline, and schedules them in the appropriate order. It works above the job-scheduling system (Platform LSF, Grid Engine, etc).

We are looking for someone who will be involved in adding a Remote Procedure Call (RPC) system to eHive. The aim is to allow job execution on a remote compute cluster, via a predefined interface, whilst maintaining the concurrent abilities of eHive pipelines. This would allow us to expose some of the Ensembl tools as components that users can add to their own pipelines.

Your primary tasks will be to design and implement a RPC system in eHive in collaboration with the current eHive developer. In particular and in addition to the above, this role will involve: 

  • Efficient control flow transfer between eHive pipelines: develop a method to efficiently track remote jobs;

  • Efficient data transfer between eHive pipelines: develop an interface for transferring parameters and data between pipelines;

  • Efficient Transfer of Events Back to the Calling Pipeline: develop a method for transferring events (for example job failure) back to the calling pipeline;

  • Outreach activities: engage with collaborators and potential users, for example by holding workshops.

The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry. We are part of EMBL, Europe’s flagship laboratory for the life sciences.


You will hold an MSc in Computer Science or Bioinformatics, and should have previous experience of working in a production software environment and organising tasks to fit defined release cycles. 

Experience of working in a UNIX/Linux environment, a minimum of 2 years’ experience of Perl programming and programming in other languages would be highly advantageous.

A high proficiency in object-oriented Perl and shell scripting is essential. You will be expected to be comfortable working in a Unix environment and with relational databases.

In addition you will:

  • Be self-motivated and capable of working both independently and within a closely interacting team of scientists in an international academic environment;

  • Be comfortable with detail-orientated work and project deadlines;

  • Enjoy the challenges and excitement associated with working in a fast moving field;

  •  It's essential that you have excellent English communication skills, both written and oral, and  interpersonal skills.

Experience in the following fields would be beneficial but not essential:

  • Compute grid engines (such as Platform LSF) 

  • Standards of the Open Grid Forum (e.g. GridRPC, DRMAA)

  • Network protocols

  • Inter-process communication

  • Version control systems, especially Git.

How to Apply

We welcome applications irrespective of gender and appointment will be based on merit alone. Applications are welcome from all nationalities. Visa information will be discussed in more depth with applicants selected for interview.


Please apply online through

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