Software Developer at European Bioinformatics Institute (EMBL-EBI) (Hinxton, UK)

Software Developer at European Bioinformatics Institute (EMBL-EBI) (Hinxton, UK)


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Location: Hinxton, UK
Type: Full Time
Created: 2021-08-13 05:00:54

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The Ensembl Software Infrastructure team seeks an enthusiastic Software Developer to join and contribute to the Ensembl project. Ensembl (http://www.ensembl.org/) is one of the leading large-scale bioinformatics projects for genome annotation. Although genome sequencing has advanced tremendously in the past decades, the international scientific community is still trying to understand how genomes operate by collating information on their function, variability and evolutionary history. The Ensembl project imports massive amounts of data from various archives (genome sequences, variation archives, etc), uses them to create summaries (e.g. gene annotations, whole-genome alignments, gene trees, regulatory elements, etc.), then redistributes these freely to researchers across the world.

Your role

The technical challenge resides in modelling the complexity of biological systems in a systematic and programmatically accessible way, while keeping up with the exponential growth of sequencing capacity across the world. These challenges have led us to adopt a hybrid system that includes both relational and non-relational storage solutions, cloud and on premises environments, as well as CI/CD solutions. Ensembl Infrastructure’s mission is to ensure these components remain interoperable.

In this role you will work alongside the existing developers and:

  • Extend Ensembl’s current relational (MySQL) and NoSQL DBMS’s and Perl API to handle new data types/results
  • Maintain the Perl API’s and evolve them using modern technologies and microservices architecture – e.g. Python, Java, gRPC/ProtoBuf, Docker/Singularity, Snakemake/Nextflow
  • Maintain and evolve current Infrastructure team’s products, including Ensembl Hive (workflow manager), GUI-Hive, Xref pipeline, etc
  • Deliver regular presentations of progress to management and colleagues
  • Contribute to develop and improve team’s CI/CD pipelines and procedures
  • Support internal and external users of Ensembl Infrastructure’s pipelines and products, including the delivery of occasional training courses

You have

The ideal candidate will hold a bachelors or higher degree, or have equivalent experience, in Computer Science, Software development and maintenance, Bioinformatics, or related fields.

  • You must have experience in the following:
  • Maintaining a large code base with a database backend.
  • Team software development and/or working in large scientific projects. Advantageous if this was in a genomics context.
  • Good command over Unix like systems
  • Working knowledge of object-oriented Perl in professional context
  • Working knowledge of SQL, preferably MySQL - other RDBMS can be considered
  • Good organisational skills to meet challenging development milestones
  • Good team player
  • Excellent communication and interpersonal skills with senior management, collaborators and other personnel at all levels

You might also have

  • Experience in open-source software development
  • Agile methodology experience, preferably SCRUM
  • Working knowledge of Python in professional context, strongly preferred
  • Working knowledge of git/GitHub/GitLab, highly desirable
  • Working knowledge of workflow/ETL pipeline manager
  • Familiarity with cybersecurity best practices
  • Knowledge of C/C++
  • Experience in or interest in learning Rust or Java
  • Knowledge of HPC systems like LSF
  • Knowledge of working with bioinformatics/biology software systems
  • Ability to work with minimal supervision
  • Ability to work on parallel tasks

Why join us

Do something meaningful At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity. Join a culture of innovation We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.

Enjoy lots of benefits:

  • Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme including 17% employer contribution, death benefit, long-term care, accident-at-work and unemployment insurances
  • Flexible working arrangements
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Generous time off: 30 days annual leave per year, in addition to eight bank holidays
  • Relocation package including installation grant (if applicable)
  • Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
  • Family benefits: On-site 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.
  • For more details please see our employee benefits page.

What else you need to know

  • Contract duration: This position is a 3 year fixed-term contract
  • International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
  • Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities.
  • Job location: 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. Read more about how we are recruiting during the pandemic.
  • Your application: To apply please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date.