Research Software Engineer in Bioinformatics

In this project you will take the lead on the UCL Computer Science Bioinformatics Group’s portion of the IntegraTED project. There are three principle objectives in this portion of the project. In the first objective we wish to increase the reliability and performance of the existing ML workflows that underpin the PSIPRED workbench. One target here is to integrate novel bioinformatics foundation models to accelerate methods already available via the PSIPRED Workbench. The Second major objective is to work extensively on a new web interface for the IntegraTED resource. Here you will work closely with the CATH team on our planned unified web and data portal. The third major objective is to work on the TED data generation pipeline. The successful applicant for this project will work on all of these theme areas with the possibility of working on novel ML applications in this space and will importantly take the lead on developing and maintaining the PSIPRED Workbench.

The ideal applicant will be a developer with a strong interested in building Scientific Software and prior experience of software development within academia. You should have the ability and enthusiasm to acquire new skills across the ML-Ops and Bioinformatics fields. We expect good software development skills in a least one language regularly used in scientific computing (i.e. Julia, Python, etc) and you should have an interest in good practice in software development (e.g. source control, testing, etc). We focus mainly on Python but adaptability across languages is a bonus. Eventually, you will be expected to lead the development of large long standing software engineering project, so an interest in developing skill in application design is a must.

In return, you’ll have the opportunity to make a significant impact within Student Lifecycle portfolio, working alongside talented colleagues. We offer a collaborative environment where your ideas are valued, your growth is supported, and your work directly contributes to the university’s bold strategic goals. Our people really are our greatest asset and we invest in them so that they can fulfil their potential. Equity, diversity and inclusion is important to us. We are committed to creating an environment where everyone is encouraged to give their best in a place where their unique experiences, perspectives and skills are seen as valuable assets.

As well as the exciting opportunities this role presents, we also offer some great benefits some of which are below:

• 41 Days holiday (27 days annual leave 8 bank holiday and 6 closure days)

• Additional 5 days’ annual leave purchase scheme

• Flexible working options

• Defined benefit career average revalued earnings pension scheme (CARE)

• Cycle to work scheme and season ticket loan

• Immigration loan

The UCL Bioinformatics Group is well-known for developing a widely-used suite of web-based tools based on a number of cutting edge protein structure prediction methods. Our web services have been online since 1998 and the methods available allow users to predict a variety of protein structural features, including secondary structure and natively disordered regions, protein domain boundaries and 3D models of tertiary structure. Recently we have been developing new services to assist users in prediction gene function structural domain segmentation - which we believe are vital and unique tool for biologists. Our flagship service, The PSIPRED Workbench, currently unites all our services e.g. predictive methods, online tutorials and common look and feel. Through prior BBSRC BBR grants, we have successfully integrated our suite of tools into a single web portal. In our upcoming BBSRC grant we wish to extend this integration philosophy across multiple resources.

The BBSRC funded IntegraTED project is aimed at developing a new Bioinformatics web resource hosted at UCL. Over the past 30 years the UCL Bioinformatics Group (dept of Computer Science) and the CATH Project (dept of Structural & Molecular Biology) have developed world leading web resources in structural bioinformatics. In this project we are looking to bring together three of our most important resources to develop a single, highly integrated and streamlined web platform. The aim is to provide protein structure and function researchers access to an unrivalled online research platform. The three resources involved are; the PSIPRED workbench, an online suite of machine learning based tools for analysing protein structure, The CATH-Gene3D structural classification of protein domains and The Encyclopaedia of Domains (TED) our new resource cataloguing all detectable structural domains in AlphaFoldDB., These include people from Black, Asian and ethnic minority backgrounds; disabled people; and for our Grade 9 and 10 roles, women. Our department is working towards an Athena SWAN award. We are committed to advancing gender equality within our department.

You can read more about our commitment to Equality, Diversity and Inclusion here : https://www.ucl.ac.uk/equality-diversity-inclusion/

Work at UCL pages: https://www.ucl.ac.uk/work-at-ucl