Job Description
Are you a highly motivated full stack software engineer with imaging experience who wants to join an exciting international consortium to help build a comprehensive catalogue of phenotype images relevant to human health? Do you have the motivation to develop new skills in the latest machine learning/deep learning algorithms and infrastructure for imaging applications? If so, this position is for you!
The IMPC is a G7 recognised global research infrastructure that coordinates the production and phenotyping of thousands of new mutant mouse strains to better understand human health. Over the last five years, we have made 20,000 new gene-phenotype associations from 26 million data points including 300,000 images from diverse modalities such as micro-CT, X-ray, histopathology, fundus microscopy and electrocardiograms.
As part of an exciting new phase, we are relaunching the www.mousephenotype.org portal with an emphasis on data visualisation and tooling to support machine learning. This opportunity will enable you to apply your imaging analysis and archiving skills to resources that play a crucial role into research with human genetic diseases and aging. Your primary responsibilities will be to support and extend existing image archiving pipelines, and work closely with the others within IMPC resource to find new ways to leverage the currently richly annotated image resource as a training dataset to automate image annotation for the future.
You’ll be working within Mouse Informatics at EBI alongside a diverse and international team of developers, bioinformaticians and ontologists that make up the wider Samples, Phenotypes, and Ontologies (SPOT) team. You will collaborate closely with the team, who have a range of expertise in semantics, data analytics, and web technologies. You will also be collaborating with other groups at EMBL-EBI and external collaborators, both within the UK and internationally. 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. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 23 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world. For further information please visit www.ebi.ac.uk For further information about the International Mouse Phenotyping Consortium, visit www.mousephenotype.org
Qualifications and Experience
You will be qualified to degree level in either computer sciences or bioinformatics:
- Experience with imaging software platforms (e.g. OMERO)
- Practical knowledge of machine learning/deep learning algorithms for detecting and classifying objects in 2D and 3D medical images.
- Willing to manage and further develop existing image archiving pipeline and implement new automation and container technologies
- Solid working knowledge of a systems / scripting language (BASH, Python, etc.)
- Working knowledge of a server side programming language (we use Java)
- Willing to learn, Java software project management tools, i.e. Maven, Nexus, etc.
- Superb communication skills
- Ability to work independently while also interacting in a team environment
Additionally, these qualifications would be considered desirable:
- Involvement with model organism databases
- Working knowledge, or eager to learn, modern deployment strategies – Docker, Kubernetes, etc.
- Familiarity with indexing and database technologies (e.g. SolR, Lucene, ElasticSearch, MySQL, Neo4J)
- Interacting with RESTful APIs
- Experience with the Java Spring framework family of technologies
- Working knowledge of version control, git and github in particular
Benefits
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.
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.
Application Instructions
To apply please submit a covering letter and CV, with two referees, through our online system.
Additional Information
Applications are welcome from all nationalities - 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 GMT on the date listed above.