Senior Bioinformatician, Project Lead

Organization
EMBL-EBI
Job Location
EMBL-EBI Wellcome Genome Campus
Hinxton
Cambridge
Cambridgeshire
CB10 1SD
United Kingdom
Salary
Competitive
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.

Job Description

We are looking for a highly motivated Senior Bioinformatician, Project Lead to help lead the ingest support team; assisting in building tools for and providing front line support on the Data Coordination Platform (DCP) for the Human Cell Atlas project (HCA). You will work at EMBL-EBI located on the Wellcome Genome Campus, near Cambridge, in the UK.


Do you want to work as part of the HCA project to define comprehensive reference maps of all human cells? The HCA is using single cell gene expression techniques as the basis for both understanding human health and understanding different disease mechanisms. We are building and supporting the tools which will be used by the HCA. For more information about the HCA project click here.


We will deliver simple, open and direct access to all HCA data across many cloud based systems and as part of this team you will have great opportunities to engage with the data generators, project users and our collaborators from the University of California, Santa Cruz (UCSC), the Broad Institute and the funders the Chan Zuckerberg Initiative (CZI) to build the DCP. 

The DCP will include:

  • An ingestion interface enabling users to validate and submit data
  • A query API to discover the HCA data
  • Containerized analysis pipelines
  • Interactive portals for visualisation and analysis.

 

These services will help facilitate scientific discovery based the reference maps of human cells produced by the HCA.

As project leader for the Ingest support team you would be responsible for:

  • Leading human facing support for the Ingest service
  • Ensuring the Ingest support team communicates well internally and with our collaborators
  • Managing members of the Ingest support team and ensuring they complete their tasks on time
  • Monitoring the Ingest support team and participating in their appraisals
  • Helping with general staff assessment
  • Helping with screening and interviewing new staff

You would also work with the rest of the team to support the Ingest service. You tasks would include:

  • Designing and extending services to ensure the HCA is collecting high quality metadata to support and enable discovery and integration operations on its data
  • Supporting the data flow into the HCA and EMBL-EBI archives from project contributors
  • Collaborating with expert biologists and external collaborators to define and extend the minimum standards for the various HCA data types
  • Working with biologists and other collaborators to define requirements for HCA services
  • Working closely with collaborators at UCSC to coordinate data flow for the HCA
  • Running training courses on how to submit data to the HCA project
  • Working with other teams across EMBL-EBI to deliver our components of the HCA Data Coordination Platform

 

Representing the team and the institute at HCA project meetings and international scientific conferences.

Requirements

You should hold an MSc, PhD or have equivalent experience in Computer Science, Bioinformatics, Genetics or related fields including evidence of your ability to write, understand and maintain complex code. Typically people in this role have four or more years of experience in the domain.

You should have several years experience in object-oriented programming, and in developing software in a primarily Unix-based environment. You should be familiar with development tools such as Git and JIRA. Knowledge of Perl is useful as this is the primary programming language of the team. Experience in developing computationally efficient solutions for running complex data flows and familiarity with both relational databases and document stores would be an advantage.


Do you love working in a team to support users to provide high quality, well described data? As the project lead for this team you will need to interact with users of the system, training them and providing ongoing support while they use the HCA Ingest service, and ensure the whole team delivers on this aim. You will also gather requirements from these users to inform new features in the system and help us improve the service we offer. Experience ensuring data flows smoothly in large scientific collaborations and assisting other team members to meet their targets will be considered an advantage.

How to Apply

To apply please submit a covering letter and CV, with two referees, through our online system at: http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=55817&aid=15470

About Our Organization

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 22 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.

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