Job description

Job summary

We are looking to recruit two experienced bioinformatics software developers to work on a Wellcome Trust funded project (i) to develop and benchmark novel protein modelling algorithms using machine learning and then (ii) to disseminate their use to the community via web-site development. The successful candidates will undertake research work to further develop and disseminate the following popular biomedical resources: (i) The Missense3D portal ( http://www.sbg.bio.ic.ac.uk/~missense3d/  ) that predicts the damaging effect of genetic variants by providing a 3D structure-based analysis. Missense3D is a popular resource for the genetic community with over 8000 users in 2022 and >200 citations since its launch in 2019. (ii) The Phyre portal ( http://www.sbg.bio.ic.ac.uk/~phyre2/ ) that provides template-based prediction of protein structure from sequence. Work on Phyre will continue to develop complementary resources to the deep learning methods such as AlphaFold. Phyre is widely used by the community with over 50,000 unique users in 2022 and more than 7,000 citations to the 2015 paper.

The project will involve enhancing the underpinning algorithms and the dynamic web interfaces for both resources. The project will be supervised by Professor Michael Sternberg and Dr Alessia David at Imperial in collaboration with Professor Richard Houlston FRS at the Institute of Cancer Research (Sutton, London).

The appointee will be a member of the team working in the Centre for Integrative and System Biology and Bioinformatics. The Centre also run a popular master’s course in Bioinformatics and Theoretical System Biology attended by about 20 students every year. You will have the opportunity to help in supervising master’s and undergraduate projects in bioinformatics related to your research.

Duties and responsibilities

You will develop, benchmark and support the protein modelling resources Missense3D and Phyre working on both the algorithmic back end and the dynamic web site front end. In addition, you will help in disseminating and supporting the use of these resources. The post requires professional level experience in coding in a high-level language and, as the major language for software development is Python, we require experience in coding in this language. We also require a broad knowledge of bioinformatics, including about protein structure.

Essential requirements

• You must have an undergraduate degree in a biological, physical, numerical or computational discipline and ideally in addition a PhD degree in one of these disciplines or an equivalent qualification or experience.


• You must have a broad knowledge of Bioinformatics, including about protein structure, obtained via software development and/or a postgraduate degree in Bioinformatics or a very closely related discipline.


• You must have extensive experience of coding to a professional level in a high-level language such as Python or C and in particular experience of coding in Python


• You must have experience of the Linux operating system.


• In addition, it is desirable that you have (i) previously developed a bioinformatics resource, (ii) have had experience of working on computational studies on protein 3D structure, (iii) have developed algorithms using machine learning and (iv) experience of coding in the development of a dynamic web site using technologies such as HTML, Django, Flask, CSS.

Further information

As this is a readvertisement, we will not be considering previous applicants except if their skill set has changed substantially.

For informal enquiries please contact Professor Michael Sternberg via m.sternberg@imperial.ac.uk

Documents

• Job Description.pdf