Bioinformatics Developer

1000scholars; Hinxton; On-site; GBP 39,000 - 43,000; Full time

Job summary

EMBL-EBI - European Bioinformatics Institute in Hinxton, United Kingdom, is seeking a Bioinformatics Developer to join the DECIPHER team. You will work with two software developers and a project lead to make research data available for clinical use, applying your bioinformatics knowledge to assessment, data integration, and reformatting tasks.

The role offers opportunities to gain clinical genomics insight and web development skills while contributing to a platform used for rare disease research

Qualifications

• Bachelor's (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.

Responsibilities

• Investigating, assessing and integrating molecular biology and phenotypic data 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 EMBL-EBI groups and external collaborators to understand resources and integration opportunities.
• Bringing bioinformatics expertise to the DECIPHER team and representing the project at meetings.

Skills

Python

R

Node.js

UNIX/Linux

Genomics data

PostgreSQL

JavaScript

Git

Education

Bachelor's degree

Higher degree

Tools

Ensembl VEP

PostgreSQL

VS Code

Job description

Bioinformatics Developer

EMBL-EBI - European Bioinformatics Institute

Hinxton, United Kingdom

GBP 3,452.05 or GBP 3,861.91 per month net

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 utilises 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 utilise 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.