About the team/job
We are looking for an experienced Bioinformatician to join us in the exciting role of developing a phylogenetic annotation procedure in one of the world’s leading scientific resources, the Universal Protein resource (UniProt) at the EMBL-European Bioinformatics Institute (EBI) located on the Wellcome Genome Campus near Cambridge in the UK.
The successful candidate will have the wonderful opportunity of working with scientists in the UniProt and Gene Ontology (GO) groups at EMBL-EBI and University of Southern California, respectively. S(he) will be working in the integration of the phylogenetic tree-based annotations from the GO Phylogenetic Annotation project with the rule-based automatic annotation system (UniRule) developed by UniProt. S(he) will be based in a multidisciplinary team within the Protein Function group and will respond to the Protein Function development Team Leader at EMBL-EBI.
The Protein Function development team maintains bioinformatics infrastructure of the world leading Universal Protein Resource (UniProt), Gene Ontology Annotation and Enzyme resource. This is a very dynamic and interdisciplinary team comprising talented and enthusiastic software engineers and bioinformaticians working closely together with the biocurators in these resources. The UniProt resource is one of the most internationally used protein databases serving a large and diverse research community in genomics, proteins and proteomics.
The EBI is a world-leading bioinformatics centre providing biological data to the scientific community, with expertise in data storage, analysis and representation. The Universal Protein Resource (UniProt) provides a central resource on protein information and a solid set of services and computational analysis of protein data. UniProt is produced by the UniProt Consortium – a collaboration between the EBI, the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB).
The post holder will be working in developing computational methods for annotation of proteins based on phylogenetic trees approaches. This is a dynamic, challenging environment, provides an excellent opportunity to handle, organise and annotate large-scale complex biological data; observe emerging trends and methods from forefront and be part of working within an international environment.
- Collaborate with the project scientists in the scientific design and development of the project
- Develop formats for conversion of the rule-based system UniRule into evolutionary models
- Analyse and evaluate project software for phylogenetic tree-based annotation of proteins with functional annotations
- Develop software a new pipeline for phylogenetic tree-based annotation in UniProt
- Assist Software engineers in the team in the development of the annotation pipeline within the database production
- A degree in a Biological and/or Computational science
- At least 2 years of working experience in developing software in Bioinformatics or Computational Biology, ideally in the field of evolutionary biology
- Strong programming skills in Python, Java or Scala
- Familiarity with standard development tools (VCS, CI, etc)
- Experience in relational database querying (e.g. MySQL, PostgreSQL)
- Familiarity with Unix command line
- Attention to detail and ability to solve scientific problems
- Work independently or with minimal supervision
- Excellent communication and interpersonal skills
- Enthusiastic to learn and help the scientific community
You might also have
- Knowledge/experience of proteomics and genomics
- Knowledge of UniProtKB, InterPro, Ensembl, ENA, RefSeq would be very valuable
- Familiarity working with computing cluster such as LSF or SGE
- Understanding/experience with widely used biological file formats, methods and tools
- Experience using team collaboration tools: Git, Jira, Confluence
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. 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 over 27 member states and two associate member states. 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.
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.
Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. 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.