23/03/2019

Bioinformatician – Cloud-based proteomics data pipelines


  • ORGANISATION/COMPANY
    European Molecular Biology Laboratory (EMBL)
  • RESEARCH FIELD
    Biological sciences
    Computer science
  • RESEARCHER PROFILE
    First Stage Researcher (R1)
    Recognised Researcher (R2)
    Established Researcher (R3)
    Leading Researcher (R4)
  • APPLICATION DEADLINE
    21/04/2019 23:59 - Europe/Brussels
  • LOCATION
    United Kingdom › Hinxton, Cambridge
  • TYPE OF CONTRACT
    Other
  • JOB STATUS
    Other

About the team/job

We are seeking an enthusiastic Bioinformatician to join the Proteomics Team, working on the PRIDE project at the European Bioinformatics Institute (EMBL-EBI). The team is responsible of the maintenance and further development of the PRIDE database and related tools and resources. PRIDE is a world-leading international proteomics database, a founding member of the ProteomeXchange Consortium that is capturing large-scale mass spectrometry (MS)-based proteomics data from the scientific community and currently managing hundreds of TBs of data.

Your role

The post holder will be responsible of the further development and deployment of proteomics open data analysis pipelines (using various open source tools and frameworks, such as e.g. nexflow and Docker, etc), within the EMBL-EBI “Embassy Cloud” infrastructure. The post holder is also expected build an architecture to run the different pipelines using public datasets, with the objective of disseminating proteomics data to other EMBL-EBI resources (e.g. UniProt, Ensembl and Expression Atlas). These activities are part of running BBSRC and Wellcome Trust grants. The post holder may also have to contribute to other tasks related to the maintenance and development of the services and tools offered by the team. There is also the opportunity to contribute to training activities, if this is desired by the post-holder.

Responsibilities:

    • Further development and deployment of open proteomics data analysis pipelines in the cloud, within the EMBL-EBI “Embassy Cloud”.
    • Use this infrastructure to run the analysis of public proteomics datasets.
    • Collaborate with other EMBL-EBI Services teams to disseminate and integrate proteomics data into their resources.
    • Collaborate with the EMBL-EBI Software Development and Operations team, in making the pipelines available to external researchers.
    • Contribute to reports and publications.
    • Participate in meetings with internal and external collaborators.

You have

You must have a degree in computer science or bioinformatics and be able to demonstrate a minimum of 3 years’ experience in software development and/or bioinformatics data analysis, ideally with some knowledge of cloud technologies.

You must be able to demonstrate at least 3 years’ working experience in a suitable programming language such as Java, C++ or Python. Working experience in bioinformatics is essential, and more concretely, skills in computational proteomics would be highly advantageous.

The candidate should ideally have some experience with cloud technologies, such as e.g. OpenStack, Docker, and Kubernetes.

Applicants will work in a highly international, team-oriented environment and collaborate closely with external partners. Excellent communication skills are essential. The ability to work independently, under time pressure, and the dedication to communicate openly are necessary skills.

You must be able to demonstrate at least two years’ working experience in a suitable programming language such as Java, C++ or Python. In addition:

  • Good understanding of code versioning tools, such as Git.
  • Knowledge of cloud technologies such as e.g. Docker, Kubernetes and nextflow.
  • Good understanding of technologies such as JSON, XML and relational databases.

 

You might also have

Experience in software development in computational proteomics would be highly advantageous.

Why join us

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 22 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.

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.

What else you need to know

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.

Map Information

Job Work Location Personal Assistance locations
Work location(s)
1 position(s) available at
European Molecular Biology Laboratory (EMBL)
United Kingdom
Hinxton, Cambridge

EURAXESS offer ID: 392810
Posting organisation offer ID: 682971

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