Developer/Bioinformatician
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years (Renewable up to 9 years)
Grading: Grade 5 or 6 (starting at £2,738 or £3,063 per month after tax) + other paid benefits
Closing Date: 4 December 2020
Reference Number: EBI01724
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 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. We also translate existing data into the context of new reference structures, such as the pangenome, reanalysing data on those structures as needed.

Your role

This varied role offers opportunities in data management, analysis and development work.

Development work is divided between work on our data management and sharing infrastructure, and analysis pipeline development. We maintain 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 at EMBL-EBI. Our analysis pipelines focus on read alignment and variant calling.

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.

This role presents an opportunity for the right candidate to increase the range of technologies that they work with. Our current technologies include Python, Perl, MySQL, Kubernetes, Elasticsearch and Javascript, with pipelines implemented in Nextflow and eHive. 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).

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 could include:
  • Maintaining and developing our data portal and website infrastructure;
  • Maintaining and building data management and analysis pipelines for a range of environments (i.e. local compute clusters, AWS or GCP);
  • 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.

You will be familiar with common bioinformatics tools such as BWA and specifications such as SAM and VCF.

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 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 an advantage.

Existing knowledge of Perl or Python will be a strong advantage and familiarity with Javascript or AngularJS will be an advantage

Experience of developing analysis pipelines will be a strong advantage.

Familiarity with resources such as ENA and Ensembl will be a strong advantage.

Why join us

EMBL-EBI is a worldwide leader in bioinformatics. We encourage personal and professional development and are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work.

Surrounded by beautiful South Cambridgeshire countryside, our state-of-the-art Campus provides employees with a relaxed atmosphere where the pursuit of scientific discovery and meaningful work, underpin every role. In addition, our employees have access to a wide range of benefits including:
  • 30 days annual leave per year plus 8 bank holidays
  • Flexible work arrangements
  • Unique pension scheme including 17% employer contribution
  • Annual salary review
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Death benefit, long-term care, accident at work and unemployment insurances
  • Relocation package including installation grant (if required)
  • On-site library and subsidised on-site gym and cafeteria
  • Casual dress code
  • Free shuttle bus to and from Campus
  • Extensive sports and social club activities (run on campus and remotely)
  • Family benefits: Onsite nursery, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
  • Benefits for non UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance

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 sponsorship information will be discussed in more depth with applicants selected for interview. 3 year staff member contract renewable up to 9 years of service

This role is based in Hinxton, UK and you will be required to relocate once it is safe to do so if you are currently based abroad. More info on how we are recruiting in this period is available on our page: Recruitment and Onboarding during Covid19.