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Software Engineer/ Bioinformatician- UniRules

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

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. For more information about pay and benefits click here.

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

The EMBL-EBI Sequence Families Team, led by Rob Finn, is responsible for a number of world-leading protein family annotation resources, including Pfam and InterPro. Pfam is a database of protein families, represented by multiple sequence alignments and profile hidden Markov models (HMMs). InterPro is a resource that classifies protein sequences into families, and predicts the presence of functionally important domains and sites. It does this by incorporating protein signatures from 13 different specialist international member databases, including Pfam.
There is an opportunity for a bioinformatician/software developer to join the team to work on the integration of the TreeGrafter software within the InterPro production pipeline, as well as into InterProScan, a tool which facilitates predictions of features on novel protein sequences. You will be working on the UniRules Project. Your role

  • Evaluate different approaches to scaling the TreeGrafter software within InterProScan
  • Develop a new component for TreeGrafter analysis within InterProScan
  • Determine how best to propagate annotations generated within the InterPro pipeline to backend data stores
  • Work with UniProtKB to enable the expansion of the UniRule system to take advantage of the tree-based annotations
  • Support the InterPro team in the intergration of TreeGrafter-based annotations with internal annotation tools
  • Develop training materials to support the execution and interpretation of TreeGrafter results
Requirements

You haveMasters level or equivalent qualification/experience in computational, biological or related scientific discipline.

The ideal candidate would have worked within a professional environment for two or more years, building and running analysis pipelines, and contributing to their development as part of a team effort.

  • Strong scripting skills in Python and/or Java, although other languages would be considered for the right candidate
  • Familiarity with software version control (e.g. GitHub)
  • Experience in relational database querying, basic schema design and optimization (e.g. MySQL, PostgreSQL)
  • Experience working with phylogenetic trees
  • Knowledge of sequence analysis and associated tools
  • Attention to detail and ability to problem solve when problems arise
  • Experience in Unix/Linux

The candidate will need to be able to work independently, as well as interact with the rest of the development team. Good communication skills and attention to detail are essential, as is the ability to work to deadlines.The successful candidate will function as a bridge between InterPro staff and other project stakeholders, via regular meetings and videoconferencing. The primary direction for the pipeline development and data analysis will come from team leader and/or line manager. Other requirements may also come from other team members and the consortium. The postholder will also be required to interact with members of other teams at EMBL-EBI.You might also have

  • Experience working with protein family data
  • Familiarity with compute cluster job schedulers (e.g. LSF, Oracle grid engine)
  • Background in evaluating software through the construction of appropriate benchmarking tests
  • Experience with Perl 
  • Knowledge of using RAxML
  • Understanding of software development cycle
  • Knowledge of workflows (e.g. Snakemake, Galaxy or Common Workflow Language)
How to Apply

To view a copy of the full job description please click here

To apply please submit a covering letter and CV through our online system. Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.

This position is limited to the project duration specified.

Applications will close at 23:00 GMT on the date listed above.

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 over 27 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

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