Senior Software Developer (commencing immediately) at European Molecular Biology Laboratory (EMBL)

Contract Type: Staff Member

Location: EMBL-EBI, Hinxton near Cambridge, UK

Job Function: Senior Technical Officer (gr. 6-8)

Contract Duration-Length of Time (years/months): 1 year (until grant-end date of 30/10/2023)

Contract Duration-Is this renewable to 9 years?: No

Advertised Grade-Grading: Grade 6 (monthly salary starting at £3,143.06 after tax plus benefits)

About the team/job

We are seeking a senior software developer to join the Archival Infrastructure and Technology Team at the EMBL-European Bioinformatics Institute (EMBL- EBI). The team develops services and provides technology to support the activities of EMBL-EBI’s molecular archives, including data submission, storage, validation, coordination and presentation. With underlying infrastructure for these services based around the European Nucleotide Archive – one of life science’s largest and longest standing data resources – this is an exciting opportunity to rise to the challenges of ‘big data’ and make contributions that advance the reach and utility of sequence data.

The successful candidate must be able to commence immediately due to the project/grant. 

Your role

This is an opportunity to make a significant contribution to EMBL-EBI’s COVID-19 scientific response. The European COVID-19 Data Platform comprises two components: the SARS-CoV-2 Data Hubs for the management and analysis of outbreak sequence data, and the COVID-19 Portal (www.covid19dataportal.org/) that will enable researchers to upload, access and visualise COVID-19 related reference data and specialist datasets. The European COVID-19 Data Platform is supported by a number of grants, including VEO, ReCoDID, ELIXIR-CONVERGE and BY-COVID.

As part of the EMBL-EBI COVID-19 task force, you will be part of the team that coordinates and develops automated workflows to process SARS-CoV-2 datasets. Adapting and developing innovative workflows to process and present COVID-19 data held across EMBL-EBI archives and the wider scientific community. You will also contribute to the Google and OpenStack cloud HPC workflow platforms that automate the analysis of incoming COVID-19 data.

You will design and extend workflows, including investigating and selecting appropriate technologies, to meet the data processing and presentation needs of the projects. You will work with teams from across EMBL-EBI and collaborate with expert scientists across Europe to provide innovative services.

You have

You should have a university degree in the computer sciences or life sciences and have minimum 3 years’ experience as a full time software developer with the following experience:

  • Experience with developing and maintaining bioinformatic pipelines
  • Proficiency in CI/CD principle and practice, including design, implementation, testing, maintenance, version control and deployment
  • Proficiency in programming languages: Bash, Python, Java / Groovy, SQL
  • Proficiency in Linux administration via command line
  • Experience with HPC workflow engines such as LSF & Slurm
  • Experience with workflow platforms such as Nextflow & Airflow
  • Experience with containerisation (Docker or similar) and orchestration
  • Experience with RESTful APIs
  • Experience with database connectivity and schema design for Relational and noSQL databases
  • Willingness to learn new skills as the project requires
  • Self-motivated and capable of working both independently and as part of a team
  • Excellent communication, interpersonal and English language skills

You might also have

  • Experience with Kubernetes
  • Experience with Phylogenetics
  • Experience with pathogen sequence data and/or multi-omics methods
  • Experience with Jupyter ipython notebooks
  • Experience with Cloud deployment on GCP and OpenStack
  • Prior experience working in a multidisciplinary scientific environment.
  • Experience in the design and management of biomolecular data resources
  • Experience in the data curation process
  • Experience dealing with an international audience of scientists

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, 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 required)
  • 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, 10 days of 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: The position is for 1 year initially for the grant-limited duration specified above, but there is possibility for extending a year further depending on funding. The successful candidate must be able to start immediately, latest by October 2022. 
  • 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, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you.
  • How to apply: 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. Applications will be reviewed on a rolling-basis, early application is advised. 


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