Bioinformatics Developer

European Bioinformatics Institute; Cambridge; Hybrid; GBP 54,000 - 67,000; Full time

Benefits offered by this job

Hybrid working

Pension scheme

Private medical insurance

30 days annual leave

Relocation package

On-site gym and facilities

Job summary

European Bioinformatics Institute in Cambridge seeks a Bioinformatics Developer to maintain and extend DECIPHER, a platform for rare-disease data sharing and variant interpretation. You will work with two software developers and a project lead to make research data usable in clinical settings.

You will gain experience in clinical genomics and web development while collaborating with clinical groups and other DECIPHER stakeholders to deliver high-quality tools.

Qualifications

• Bachelor's degree in biological, clinical or computational sciences.
• Higher degree or equivalent in bioinformatics or computational sciences.
• Experience with bioinformatics tools and data analysis.
• Experience designing and using large relational databases, ideally PostgreSQL.
• Proficiency in R and Python for data manipulation and analysis.
• Familiarity with UNIX/Linux environments and JavaScript development.

Responsibilities

• Integrate molecular biology and phenotypic data from public resources.
• Deploy bioinformatics tools within the DECIPHER environment.
• Design and test data structures and interfaces for genomic information.
• Support DECIPHER users by responding to bug reports and requests.
• Translate stakeholder requirements into feature specifications.
• Perform ad hoc analyses to investigate data issues and aid decisions.
• Collaborate with EMBL-EBI groups and external partners on integration.
• Represent the DECIPHER project in internal and external meetings.

Skills

Bioinformatics

Python

R

JavaScript

Unix/Linux

PostgreSQL

Education

Bachelor's degree in biological, clinical or computational sciences

Higher degree or equivalent in bioinformatics or computational sciences

Tools

Node.js

PostgreSQL

Job description

About the team

We are seeking a skilled and highly motivated Bioinformatics Developer to join the Human Genomics Team at EMBL-EBI and contribute to the maintenance and development of the DECIPHER platform. DECIPHER is a global data sharing platform that fuels rare disease discovery and enables patient diagnosis. This is an exciting opportunity to join an innovative multi-disciplinary team dedicated to providing tools to assist in the interpretation of genetic variation and the responsible sharing of clinical data for patient benefit.

DECIPHER aggregates information from open data resources such as gnomAD and UniProt and utilizes bioinformatics tools such as the Ensembl Variant Effect Predictor (VEP) to create detailed variant annotations. These are presented in user friendly visualisations to help clinical experts interpret likely disease-associated variants identified in their patients.

Clinical centres can share variants and summary phenotype information from their patients through DECIPHER, enabling matching with other patients with similar conditions and collaboration between clinicians for patient benefit. With the help of DECIPHER, many thousands of patients now have a diagnosis and hundreds of papers are published every year improving understanding of rare diseases. By joining this project you will be playing an important role in advancing rare disease research, diagnosis, and discovery for genomic health.

Your role

As the Bioinformatics Developer in the DECIPHER team, you will work alongside two software developers, a support specialist and the project leader to make the latest research data available for use in clinical settings. You will utilize your bioinformatics knowledge in assessment of resources, discussions with data producers and data analysis, reformatting, and integration tasks. This role offers the exciting opportunity to gain knowledge of clinical genomics and improved web development skills while creating tools to facilitate genomic medicine. You will see the real world impact of your work through interactions with our clinical collaborators and other DECIPHER stakeholders.

This role can be offered on a full-time or a part-time basis at 80% of full-time hours.

Your primary responsibilities will include:

• Investigating, assessing and integrating molecular biology and phenotypic data in varying formats from public resources


• Deploying bioinformatics tools in the DECIPHER environment and analysing genomic data


• Designing, testing, implementing data structures and user interfaces to represent information relating to the human genome and genetic disorders.


• Supporting DECIPHER users by responding to bug reports and requests for support or new features


• Working with stakeholders to understand and translate their requirements into feature specifications


• Performing ad hoc analyses to investigate potential data issues and support decision making


• Liaising with other groups at EMBL-EBI and external collaborators to understand the resources they have created and how they could integrate with DECIPHER


• Bringing bioinformatics expertise to the DECIPHER team and representing the DECIPHER project at internal and external meetings

You have

• Bachelors (or equivalent) degree in biological, clinical or computational sciences


• Higher degree or equivalent experience in bioinformatics, software engineering or computational sciences


• Experience of bioinformatics standards, tools and resources, preferably those relevant to variant annotation


• Experience of creating methods to manage and process genomics data


• Experience designing and utilising large-scale relational databases, preferably with PostgreSQL.


• Proficiency in a language used for data manipulation and analysis such as R and Python.


• Familiarity with software development in JavaScript (preferably Node.js or browser-based).


• Proficiency working in a UNIX/Linux environment.


• Excellent attention to detail and the ability to deliver a high-quality product to agreed deadlines.


• Good communication and interpersonal skills and the ability to work closely with colleagues, giving and receiving constructive feedback


• A professional and helpful manner when responding to support requests

You may also have

• Experience of collaborating on development projects and working with colleagues from different disciplines.


• Experience of working with and interpreting genomic/ molecular biology datasets


• Experience in developing reactive, data-driven web applications in JavaScript frameworks such as Vue, React, or Angular.


• Proficiency working in a HPC bioinformatics environment.


• Experience of working with clinical data and/or ontologies


• Experience of training people to use web tools or supporting users seeking assistance through a helpdesk system

Hybrid Working

At EMBL-EBI, we are pleased to offer hybrid working options for all our employees, with an expectation that you will be on site at least two days a week, with Thursday being our "team day".

Contract length: 2 years grant based contract

Salary: Grade 5 or 6 monthly salary from £3,452.05 or £3,861.91 after tax plus generous benefits and financial allowances based on personal circumstances. Excluding personal pension and insurance contributions.

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. Watch this video to see how EMBL-EBI makes an impact.

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 hybrid working patterns


• 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 public 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.

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.


• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.


• Diversity and inclusion: At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.