Job Description
Software Development and Engineering
Hinxton, UK
In this job
Your role
You have
You might also have
Why join us
What else you need to know
More about EMBL-EBI
We are looking for an experienced Bioinformatician Developer to join the GWAS Catalog development team within the Samples, Phenotypes and Ontologies team.
You’ll be working on the GWAS Catalog Summary Statistics Infrastructure, and you’ll have the opportunity to influence the design and development of the system to meet future challenges in this exciting era of genomic science.
The Samples, Phenotypes and Ontologies team is a diverse team of developers, curators and bioinformaticians. The GWAS Catalog is a manually curated, high-quality repository of all published genome-wide association studies and has been running since 2008. It is considered the “go-to” resource for looking up findings relating human genotype to phenotype associations.
Our tech stack includes:
Python
Docker
Kubernetes
HPC (High Performance Compute clusters)
A biological background or experience working in a bioinformatics environment is essential for this role.
Your role
As bioinformatician developer, your main responsibilities will include developing and maintaining the GWAS Catalog Summary Statistics data management tools using a variety of frameworks and technologies, including Python, Docker, Kubernetes, HDF5, NextFlow, Java, and other web development frameworks. You will also collaborate with the data content generation team to prioritise scientific requirements and ensure a user-centric approach.
You will:
Contribute to the development of:
GWAS SumStats App, used for managing summary statistics data upload using RabbitMQ, Celery Workers in a Flask App
GWAS SumStats Harmonization pipeline, for bringing variants to a desired genome assembly and harmonising them to match variants in reference data
GWAS SumStats Tools, a simple toolkit for validation, processing, and formatting sumstats data.
Develop ETL pipelines, back-end databases, and Rest APIs to provide search functionality for Harmonized GWAS Summary Statistics Data
Manage data release pipelines, including preparation of reports and documentation
Collaborate with external researchers to manage the eQTL Catalogue, a database of expression and splicing QTLs recomputed from public datasets.
Work as part of a team that follows the Agile model of software development involving sprints in which user requirements are prioritised via issue tracking software. a cross-functional team using various technologies to process semantically annotated big data
Understand the role of ontologies and semantic web technologies to develop applications capable of semantically enriching the raw GWAS data by annotation to ontologies.
We value teamwork and as part of the team you will:
Collaborate with the data content team to analyse and understand requirements, determine computational strategies, and create scalable solutions
Support users and actively participate in team meetings
Present your work at internal project meetings & external conferences, as well as provide training on submission and access to the GWAS Catalog
Detailed job description can be found here.
Closing date: 31 July 2023
Contract duration: 2 years
Grading: Grade 5 (monthly salary starting at £3,090 after tax) other paid benefits
Reference number: EBI02140
You have
Postgraduate degree in life sciences or bioinformatics or computational biology, or computer science
Production experience with at least one programming (e.g Python, Java) applied in a bioinformatics context and working with SQL and/or NoSQL Databases
Understanding of statistical methods of complex disease genetics such as GWAS, whole genome/exome sequencing analyses, identification and QC of variants
You are proficient in using a command line UNIX/Linux environment
Familiarity with Devops, docker, Kubernetes
Willingness to learn new languages and excited about finding the right tool for the right problem.
Skilled in breaking down problems, documenting issue statements, estimating efforts and working to deadlines while delivering a high-quality product.
Excellent communication and organisation skills
Ability to work collaboratively and inclusively with a range of stakeholders
You might also have
Experience working with:
High Performance Computing (HPC) clusters
Terabyte data, and high-performance data transfers using Globus
workflow Management systems such as Snakemake, or Nextflow for managing reproducible and scalable data-driven computational pipelines
Familiarity with:
RabbitMQ or similar technologies and running asynchronous tasks with Celery
Git version control systems, and CI/CD tools such as Travis, or Bamboo, or Gitlab-CI
static Code analysis tools such as Sonarcube, Codacy, Pylint
Java technologies, and web design and development experience
Prior experience working with ontologies or semantic web technologies
Familiarity creating user-friendly tools and APIs in a production microservices environment
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
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 benefit page.
Developers at EMBL-EBI
What it is like to be a developer at EMBL-EBI?
Since my first day at EMBL-EBI, I have cherished how friendly, helpful and talented everyone is. I particularly like the lively exchange of knowledge on campus.
Anja Thormann, Software Developer, Variation team
What else you need to know
Contract duration: This position is an approximately 2 year fixed-term contract, grant-limited with an estimated contract end date of 09/2025.
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.
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 provide a response within two weeks after the closing date.
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