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Senior Full Stack Developer
4 months ago
About the team/job
We are currently seeking a talented Senior Full Stack Developer/Data Engineer to join the Human Genomics Team at the EMBL European Bioinformatics Institute (EMBL-EBI). The team provides genome variation and regulation resources as part of the Ensembl project, human variation interpretation services including the DECIPHER platform, and data portals for partners around the world. With underlying infrastructure for these services based on EMBL’s large and long-standing data resources – this is an opportunity to rise to the challenges of ‘big data’ and make contributions that advance the reach and utility of sequence data.
Your role
This is an exciting opportunity to make a significant contribution to development of a new open-source Perturbation Catalogue for harmonised and curated human gene (e.g. CRISPR), variant (e.g. MAVE), and expression (e.g. Perturb-seq) data. This project is funded through the Open Targets consortium, an innovative public-private partnership that uses human genetics and genomics data for systematic drug target identification and prioritisation. The new resource will help to address a fundamental need in the scientific and drug discovery community for a comprehensive resource to understand the impact of modifying genes and proteins.
You will be responsible for support and development of software to handle programmatic access and a portal interface to explore, combine, visualise and access a wealth of perturbation data. This will enable the extension and application of existing algorithms and the design of new computational methods for functional genetics and target identification and prioritisation, offering enhanced statistical power and the capability to work with disease subtypes at a finer granularity. The Perturbation Catalogue will deliver rich community standards, open-source harmonisation and meta-analysis software, gold standard machine learning ready datasets, and a highly customisable public cloud platform with distributed data warehousing technology for cross metadata queries.
You will interact closely with the team’s Biocurator for data coordination into the perturbation data portal, as well as with the wider Human Genomics team. You also will work collaboratively within the Open Targets Perturbation Catalogue project team, alongside scientists, developers and data engineers from EMBL-EBI, Wellcome Sanger Institute, Human Technopole, and industry partners (GSK, Pfizer, Genentech, Sanofi, MSD) to gain their respective expertise and requirements.
You have
- A BSc or MSc in computer science or related fields.
- Expertise in Python, including popular Python libraries: NumPy, Pandas, PySpark and frameworks: Django, Django Rest Framework, FastAPI
- Hands-on experience with both relational (e.g. PostgreSQL) and non-relational databases (e.g. Elasticsearch, Redis).
- Strong experience in data warehousing architecture, big data processing and ETL
- Unix/Linux environments
- GIT and working in collaborative software environments
- 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 developing or maintaining web-based applications (html, css, Javascript frameworks such as Angular, React)
- Cloud (GCP or AWS) and popular cloud Big Data tools - BigQuery, Dataflow, Looker
- Containerisation (Docker or similar) and orchestration (k8s)
- Experience of processing biological archive data
- Tests and CI/CD
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, including spending 2 - 3 days spent working in the office each week.
- 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: This position is a 3 years project based 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.
- EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.
- 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 interview week commencing 5 August 2024
