Project Leader

Job Location
EMBL-EBI Wellcome Trust Genome Campus Hinxton
CB10 1SD
United Kingdom

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 have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

Job Description

EMBL-EBI seeks an enthusiastic software project manager to lead our software development and informatics efforts supporting manual genome annotation within the GENCODE project. 

GENCODE seeks to annotate all evidence-based features in the human and mouse genomes with high accuracy and then release these annotations for the greatest possible benefit to biomedical research and genome interpretation. Given how intensively reference genomes are used by hundreds of thousands of biologists and clinicians across the world, it is imperative that the annotation error rate is brought down as close to zero as possible.

A unique aspect of the GENCODE approach is manual comparison of the final gene annotation with supporting evidence. This process involves expert human curators viewing experimental data, the results of automated algorithms and other information to create the final gene annotations.

Supporting the work are four developers that provide these curators with specialised tools to visualise the data, report errors and correct annotations. You will help lead this group and the development of these tools, in particular:

  • Develop and maintain the existing MySQL backend and its Perl API;
  • Develop and maintain the existing C++ GUI, ZMap;
  • Ensure these two components communicate seamlessly;
  • Migrate this infrastructure from the Sanger Institute to EMBL-EBI;
  • Ensure compatibility between the GENCODE backend and Ensembl;
  • Add new features to the system, in support of the GENCODE curators;
  • Plan and execute the creation of new and replacement software tool components as required.

Within EMBL-EBI, you will work within the greater Ensembl project as part of the Genome Analysis team (led by Daniel Zerbino) and collaborate closely with the Ensembl HAVANA curation team (led by Adam Frankish).


An ideal candidate has:

  • PhD or MSc in Computational, Physical or Biological Sciences or equivalent experience in a computational research or software engineering environment
  • 5+ years experience of developing high-quality or production software in Perl, MySQL or C++
  • Experience of communicating and working with expert technical users (e.g. in a science community)
  • Experience in working in large scientific projects, especially in the field of genomics, would be strongly preferred

We welcome applications from scientists interested in moving from a full-time research position to an R&D/production role.

You must have experience with software development and be fully fluent with one or more of the following technologies:

  • Perl
  • MySQL
  • C++
  • Web technologies
  • Git


Although the job has a clear technical component, the key attributes sought are the ability to work in a team, and to communicate both biological and computational ideas to biologists and programmers (orally and in writing) to help define the direction of the project. GENCODE encompasses approximately 20 people, and the Project Leader will have to be organized in order to meet our regular deadlines, reports and procedures.

How to Apply

To apply please submit a covering letter and CV, with two referees, through our online system.

About Our Organization

At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 23 member states and two associate member states and proud to be an equal-opportunity employer. Our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

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