About the team/job
As a Bioinformatics Developer in our PDCM Team, 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?
The PDCM Finder team is looking for a Bioinformatics Developer to help extend an existing cancer model platform (www.pdxfinder.org). Our team harmonises, analyses and disseminates rich omic and phenotypic data from Patient Derived Xenograft (PDX), organoid, and cancer cell line models to produce a unified catalog of cancer research materials and data. These resources advance cancer research by enabling researchers to find and obtain relevant data and models. We adhere to the Findable, Accessible, Interoperable, Reusable (FAIR) data principles in order to maximize the availability and reach of cancer research models to the wider scientific community.
PDX, organoids and cell line models are used to investigate human cancers and are increasingly being used in clinical research to test new chemotherapeutic regimes and study drug resistance mechanisms. The PDCM Finder integrates cancer model data from multiple international sources and leverages EMBL-EBI’s resources that store genomic and transcriptomic data.
You’ll be part of the Samples, Phenotypes and Ontologies Team (SPOT) at EMBL-EBI alongside developers, bioinformaticians and ontologists. This project presents an interesting opportunity for the presentation of complex biological data to users in intuitive, visually appealing ways. You will be helping to extend the metadata of PDCM Finder to cell lines and organoids models and managing the data for the world’s largest open PDX model catalog.
You’ll be involved in soliciting user feedback and will need to be responsive to evolving requirements. As part of your day to day job, you’ll be working in an agile team with expertise in software design and engineering, semantics, data science, image analysis and 3D image display.
You’ll also interact with other groups at EMBL-EBI and external collaborators, both within the UK and internationally, to improve our websites.
- Demonstrated skill set and experience in working in Bioinformatics ideally in a production or relevant research background
- Proficiency with at least one programming language (e.g. Python, Java) applied in a bioinformatics context (preferably cancer biology) Experience in full stack software engineering practises and development cycle including design, implementation, testing, version control and deployment
- Knowledge of human genetics, next-generation sequencing methods, variant calling pipelines and annotation tools.
- Experience or willingness to learn Apache Spark
- You are proficient in using a command line UNIX/Linux environment
- 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 maintaining integrity and integrating heterogenous omic datasets and catalogue metadata
- Experience or willingness to learn Containerisation (Docker) and container orchestration (Kubernetes)
- Familiarity with SQL databases
- Experience with semantic web technologies such as OWL, RDF or SPARQL
- Experience in using ontologies and data harmonization
- Experience of cancer research
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, 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 year fixed-term project limited contract with an anticipated completion date of 31/08/2025.
- 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.
- How to apply: To apply please submit a cover letter and a CV through our online system. As part of the recruitment process, there will be a technical test and interviews are likely to be held on DD MM. We aim to provide a response within two weeks after the closing date: 31 October 2021
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