Software Developer - Human Cell Atlas
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 2 years
Grading: 5-6 (monthly salary starting at £2,738.29 or £3,063.41 after tax)
Closing Date: 9 August 2020
Reference Number: EBI01653
We are looking for a software developer to join the Archive Infrastructure and Technology team (AIT). You will help deliver software infrastructure that can support sharing the vast and diverse data collection efforts for the Human Cell Atlas project.   

The HCA is a cutting-edge initiative using recent technological advances that allows us to measure and observe individual human cells at scale. Labs all over the world are collecting vast volumes of data that will help us to understand health and disease better. As part of this team, you will support the HCA community sharing this data and increasing our understanding of human biology.

You will be building services that make single-cell data Findable, Accessible, Interoperable and Reproducible (FAIR), as part of the Data Coordination Platform (HCA-DCP) for the HCA community.  We deliver services that biologists and bioinformaticians in labs all over the world use to submit datasets to the DCP, uploading terabytes of data at a time. This is big data, but the hardest challenge we face is variability, not volume, as we support submitters to accurately describe their experiments using our tools. As part of our team, you will have the chance to engage with our collaborators from the Broad Institute and the University of California Santa Cruz.  

Your role

You will have technical aptitude and the ability to pick up new skills quickly.  You should be adaptable, enthusiastic and value-focused, as these are traits we look for in all our team members. Existing experience with the technologies we use is useful, but a willingness to learn and versatility in approach is key.

We follow agile principles in our approach to development and operations, focusing on our user needs when prioritizing work to be done. You will be part of a cross-functional team where software developers and bioinformaticians work together to understand the needs of the HCA scientists and deliver and run services to meet those needs.

The HCA ingestion services we deliver are deployed in the cloud (AWS and Google Compute Platform). They are predominantly built using Angular 2+, Spring Boot and MongoDB, so you’ll need some Java and Javascript, but we use a lot of Python to manage our data processing pipelines. We like Docker, Kubernetes and Helm for managing our deployments, but in general, we value people who can use the right tool for the right job.

As part of your day to day job, you can expect to interact with other groups at EMBL-EBI as well as our external collaborators to improve the submission of data to the HCA-DCP. All of our software is built and published using continuous integration/deployment and version control, and you should be confident in making your code open source.

This position is a fantastic opportunity to gain hands-on experience, working on a high-profile project with major scientific impact in a world-leading bioinformatics institute.  

You have

  • Bachelors or higher degree in computer science, software engineering or bioinformatics, or demonstrated software development experience.
  • A willingness to help with all parts of the software cycle from architecture and design to running the release process.
  • Experience with at least one of Java, Python and Javascript and a willingness to learn others.
  • Demonstrated aptitude for learning new technologies, processes and domains on the job but with the pragmatism and resourcefulness needed to get work done.
  • A desire to apply your software development skills to solving the biggest problems your users have
  • Willingness to help with all parts of the software cycle from architecture and design to running the release process.
  • Good verbal and written communication skills.

You might also have

  • Worked with scientific or biological data in the past.
  • A keen interest in agile development.
  • Been part of collaborative projects involving the development of new software, and especially if coding was shared between team members
  • Experience of working on open-source projects interacting with users and other developers.
  • Experience with technologies and programming techniques such as Angular2+, Node.js, Spring, REST, RabbitMQ, Docker and Kubernetes.
  • A degree of DevOps experience.  
  • Willingness to take initiative within a software development team and work autonomously on tasks within a software project. 

Why join us

At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. 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 are located on the Wellcome Genome Campus near Cambridge in the UK, and our 850 staff are engineers, technicians, scientists and other professionals from all over the world.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits click here.

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

What else you need to know

To view a copy of the full job description please click here

To apply please submit a covering letter and CV through our online system. We have adapted our recruitment processes to ensure the safety of our staff and our candidates, you can read more on what you can expect here. We are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work. We proudly employ people from over 70 countries and strongly encourage applications from talented individuals regardless of gender, culture or background. Visa information will be discussed in more depth with applicants selected for interview. EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone. This position is limited to the project duration specified. Applications will close at 23:00 BST on the date listed above.