Developer/Bioinformatician
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: Grade 5 or 6 (starting at £2,738 or £3,063 per month after tax)
Closing Date: 3 September 2020
Reference Number: EBI01668
We are looking for a versatile Developer/Bioinformatician who cares about open access to scientific data and putting FAIR principles into practice while working with one of the most valuable and high-profile data collections in genomics.

This is an opportunity to contribute to the ongoing development and sharing of resources initially established by the 1000 Genomes Project (https://www.internationalgenome.org), a foundational project in human genomics. The International Genome Sample Resource (IGSR), based at the European Bioinformatics Institute (EMBL-EBI), builds on the 1000 Genomes Project, maintaining and expanding its openly consented reference resources, which are heavily used by the scientific community. This expansion is further driven via the Human Genome Structural Variation Consortium (HGSVC) and the Human Pangenome Reference Consortium (HPRC). We are seeking to recruit an experienced and highly motivated Developer/Bioinformatician to join this effort.

As researchers generate new data on new and existing openly consented human samples, we are working to integrate data sets, including data from new technologies, into the existing resources, actively collaborating with researchers and providing data coordination for their work.

Your role

This varied role offers opportunities in both development and data management.

The development focus of the role is on our data management and sharing infrastructure, which includes a website (https://www.internationalgenome.org), data portal (https://www.internationalgenome.org/data-portal/sample), tracking database (which records information on the >500,000 files on our FTP site), and processes interacting programmatically with other data resources and systems (i.e. the archive object store) at EMBL-EBI. This role presents an opportunity for the right candidate to increase the range of technologies that they work with. Current technologies used by the project include AngularJS, Javascript, Typescript, Elasticsearch, MySQL and a predominantly Perl code base for archival activities, which is increasingly moving to Python. Tasks are specified and tracked in JIRA and code is in publicly accessible GitHub repositories (https://github.com/igsr, https://github.com/EMBL-EBI-GCA).

In data management, the postholder will interact with labs around the world, which are using leading edge sequencing technologies, and collaborate with colleagues in the archive and technical teams at EMBL-EBI, while working as part of a small team of dedicated project staff. This work ensures that data, and all necessary metadata, are shared with the wider scientific community.

Excellent communication skills, high levels of attention to detail, a strong user and service focus, and an ability to deliver technically sound solutions, meeting specification, are essential.

Your primary responsibilities will include:
  • Maintaining and developing our data portal and website infrastructure;
  • Maintaining and building pipelines and infrastructure capable of supporting archiving and distribution of data via multiple platforms, such as the project FTP site and Clouds managed by collaborators (i.e. AWS and AnVIL);
  • Developing archiving strategies for novel data types and performing data coordination tasks, working proactively with data generation labs and transferring files to our public FTP site;
  • Extracting data and metadata from the archives;
  • Integrating new data and metadata with our existing resources in a user-friendly way;
  • Developing and maintaining tools that assist users in accessing the data;
  • Liaising with members of Ensembl, other groups at EMBL-EBI and collaborators worldwide;
  • Supporting our users, delivering training and presenting at conferences.

You have

You should have a bachelors degree and either a higher degree or equivalent experience in genetics, biological or computational sciences.

You will have experience of working in a production development environment, working on a shared codebase, meeting specifications and working to deadlines. You will also have experience of working collaboratively in a scientific environment, demonstrating an ability for clear and accurate technical communication.

You will be comfortable working in a UNIX/Linux environment and have extensive and demonstrable programming experience, preferably using OOP. In addition, you will demonstrate a willingness to learn the range of technologies used by the project and new technologies as needed. You will have experience of RDBMS, preferably with MySQL.

We are seeking highly motivated candidates with excellent communication and interpersonal skills. You must have curiosity, initiative and a willingness to learn. You will work both independently and as part of a closely interacting team of international scientists. Skill in delivering a high-quality product, with excellent attention to detail, is essential as is a focus on meeting the needs of our users and collaborators. Flexibility and a willingness to adapt to support delivery of project goals, including in analysis and outreach activities, is also required.

You might also have

You might also have a research degree (PhD or MRes).

Experience of managing, archiving and presenting genomics data in a user-friendly manner, compliant with the FAIR principles will be a strong advantage.

Existing knowledge of Perl and/or AngularJS will be a strong advantage and familiarity with either Python or TypeScript will be an advantage.

Familiarity with common bioinformatics tools such as BWA and specifications such as SAM and VCF will be a strong advantage, as would a familiarity with resources such as ENA and Ensembl.

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 over 27 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 850 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.