About this job
The PDX Finder team harmonises, analyses and helps disseminate the rich Omic and phenotypical data from Patient derived Xenograft (PDX) cancer models to advance cancer research by adhering to the Findable, Accessible, Interoperable, Reusable (FAIR) data principles. PDX models are engineered to propagate human cancers and are increasingly being used in clinical research to test new chemotherapeutic regimes and study drug resistance mechanisms. The PDX Finder integrates PDX-related data from multiple sources and leverages EMBL-EBI’s resources that store genomic and transcriptomic data.
You will have an exciting opportunity to design and develop new interfaces to explore one of the fundamental problems of biology - how do our genes contribute to cancer?
Your roleYou’ll be part of a multi-disciplinary team to ingest, store, present and query semantically annotated data. This project presents an interesting challenge for the presentation of complex biological data to users in intuitive, visually appealing ways.
You will be developing a web interface, integrating a range of new search and query features that focus on cancer and associated Omics data. You’ll be expected to be involved in soliciting user feedback and will need to be responsive to evolving requirements.
You’ll be working within Mouse Informatics at EMBL-EBI alongside developers, bioinformaticians and ontologists that make up the wider Samples, Phenotypes and Ontologies Team (SPOT). As part of your day to day job, you’ll be collaborating with the team, who have a range of expertise in semantics, data analytics, image analysis and 3D image display. You’ll also be interacting with other groups at EMBL-EBI and external collaborators, both within the UK and internationally, to improve our websites.
- BSc/MSc in Computer Science, Software Engineering or Bioinformatics or relevant field, or equivalent experience.
- Experience with user interface design and development
- Experience in full stack software engineering practises and development cycle including design, implementation, testing, version control and deployment
- Experience or willingness to learn Apache Spark
- Developing and interacting with RESTful APIs and Graph QL APIs
- Experience or willingness to learn Containerisation (Docker) and container orchestration (Kubernetes)
- Excellent communication skills for effective collaboration within the team and with our partners in other countries and institutions
- Ability to work independently while also interacting in a team environment
You might also have
- Experience in working in an agile development environment
- Experience in data harmonisation
- Experience of Solr, Lucene or ElasticSearch
- Experience with Python
- Familiarity with SQL databases
- Experience with semantic web technologies such as OWL, RDF or SPARQL
- Experience in using ontologies and data harmonization
- Experience in data wrangling and bioinformatics
Life at European Bioinformatics Institute (EMBL-EBI)
About European Bioinformatics Institute (EMBL-EBI)
EMBL-EBI is a worldwide leader in bioinformatics. 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 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 picturesque South Cambridgeshire countryside, our 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 including:
- 30 days of annual leave + bank holidays
- Competitive salaries and allowances (non-resident / family / child)
- Comprehensive international health insurance for yourself + dependents
- Visa exemption for international candidates
- Flexible working and remote onboarding
- Access to exceptional technical infrastructure
- Subsidised gym and cafeteria + free shuttle bus
- On-site nursery + child sick leave days
- Paid career development and training
- Casual dress code