Job:Java Bioinformatics Software Engineer/Scientist
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10.2 years ago
geoff.barton ▴ 10

Job Description

We seek a skilled Java software engineer to help enhance and extend a widely used open-source system for the visualization and analysis of biological data. You will have an interest in open source software development, and some experience in creating software that can be used to explore and analyse complex data.

This job is within Jalview ( development team, which is part of the Barton Group at the University of Dundee ( in the new research Division of Computational Biology which will occupy one floor of the new CTIR building ( from March 2013. Jalview is an open source program for the creation, editing and analysis of multiple sequence alignments, and is used by tens of thousands of researchers, educators and students worldwide. You will work closely with the rest of the team to advance the Jalview ecosystem by extending and improving its visualization and analysis capabilities, user interface, and software architecture as well as supporting existing versions, identifying and fixing bugs. You will also help develop new features and service clients in collaboration with researchers in Dundee, EMBL-EBI and elsewhere.

Skills & Requirements

We are looking for someone with:

  • A degree, masters or Ph.D. in computer science, bioinformatics or related area, or equivalent industry experience.
  • At least two years experience developing and supporting Java software.
  • Demonstrated ability to apply good software engineering practice (version control, documentation, test-driven development)
  • Good written, visual, oral, and online communication skills
  • Awareness of web resources relevant to biomedical researchers (e.g. ENSEMBL, ENA, Interpro, TCGA, COSMIC, wwwPDB and GO).
  • Basic knowledge of the principles of user-centric design as applied to interactive scientific software
  • Good understanding of algorithms and data models for space and time efficient analysis of very large datasets
  • Strong self-motivation and ability to learn new skills as needed.

You’ll have technical knowledge of:

  • JAVA GUI development in Swing, AWT, SWT
  • Web service technologies – e.g. HTTP & HTTPS authentication, REST & Interoperable SOAP, XML schema design, JSON & other container formats.

Ideally, you’ll also know about:

  • Application and service development in Java using OSGi
  • Fundamental principles for web application development
  • Java/Javascript intercommunication and Javascript API development
  • High-level web application frameworks such as J2EE
  • Community driven open source practice (e.g. the Apache Way).

About University of Dundee

The University of Dundee, College of Life Sciences (CLS) is one of Europe’s leading life sciences research centres. It ranked equal 5th in the UK in the most recent RAE in terms of percentage of world leading researchers. It is a highly dynamic department with staff of over 50 different nationalities organized in 90 research groups and housed in a complex of three buildings that are interlinked on every floor, so allowing for easy interaction and collaboration. CLS regularly appears in the top 3 in polls of best place to work as voted by readers of The Scientist magazine. Consistent with this, it provides a supportive working environment with particularly vibrant Post- Doc and Ph.D. associations. Since 2001, annual research income has been £23 million p.a.. According to Thomson Scientific, in terms of citations per paper (1995-2005), Dundee was overall top in Europe in the category “Biology and Biochemistry” and overall second in Europe in the category “Molecular Biology and Genetics”. The College has state-of-the art infrastructure and facilities in computing, imaging and proteomics, provided to all through dedicated research service facilities. In January 2013 Geoff Barton formed the new Research Division in Computational Biology. The new Division currently includes groups in bioinformatics as well as Biophysical modelling and Imaging. The new division will be housed from March 2014 on a dedicated floor of the new £26 million Centre for Translational and Interdisciplinary Research that is linked at every floor into the existing CLS complex.

The origins of the University of Dundee go back to 1881, with the founding of University College, Dundee. The College then had a 70-year relationship with the University of St Andrews before it became an independent institution in 1967. It is now a firmly established university, with a world-class reputation in teaching and research.

Academic Strengths

Dundee students enjoy the benefits of studying at a university consistently placed in the UK top 10 for graduate employment. As well as this, Dundee was shortlisted for the Sunday Times University of the Year 2008 and also came second in Scotland in the National Student Survey 2008.

The majority of the University’s research activity is conducted in departments graded 4, 5 or 5 and over half of this research takes place in departments graded 5 or 5 (indicating research of international excellence). Earnings from research place the University third in Scotland and particular strengths include biochemistry, engineering, mathematics, law, computing, art & design, and accountancy & finance.

The campus boasts state-of-the-art teaching facilities, library, accommodation, sports and social areas. This helps to create a sense of community and a relaxed, friendly atmosphere.


Dundee is a campus university situated in the heart of a thriving city. The city of Dundee has a population of 150,000 and is very university-orientated, with excellent cultural, social, sporting and shopping facilities.

The city enjoys a spectacular scenic location on the estuary of the River Tay on the east coast of Scotland, with the Highlands to the north and St Andrews and Edinburgh to the south. All of Scotland’s major tourist and historic sites are within easy reach and the major cities of Glasgow and Edinburgh are just a 1 hour train journey away.

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