LONDON’S GLOBAL UNIVERSITY

Job Description
Research Fellow in Bioinformatics Grade: 7

Department: Computer Science Location: Darwin Building,

Bloomsbury Campus, London

in unix server administration, application deployment,

Reports to continuous integration and excellent source control
Professor of Bioinformatics practices.

Another key aspect of the role will be to help promote

Context PSIPRED in the scientific community, to develop online
The PSIPRED Protein Structure Analysis Workbench, training materials and to support users i.e. answering e-
an ELIXIR-UK Node Service has been in operation since mail queries and responding to any raised problems.
1998. The web-based tools available through PSIPRED
are based on the cutting-edge bioinformatics methods In addition to the primary task of maintaining and further
developed within the Jones lab, and allow users to developing PSIPRED, the post holder will also be
predict a variety of protein structural features, including encouraged to get involved with various research
secondary structure and natively disordered regions, projects within the lab and to publish refereed articles. A
protein domain boundaries and 3D models of tertiary focus in this phase of the server development will be to
structure. More recently we have been developing new integrate recent developments in deep learning into
services to assist users in prediction gene function and bioinformatics applications, and so experience in
protein-protein interactions - all of which we believe are applying modern machine learning methodology to
vital developments to make PSIPRED a vital and unique biological problems would be advantageous.
tool for biologists. PSIPRED employs a number of
features to help users become familiar with the software This post is funded by a recently awarded BBSRC BBR
e.g. online tutorials and common look and feel. Through grant, for up to 5 years in the first instance. The project
work done in previous BBSRC BBR grant funded is joint with Dr Daniel Buchan at Goldsmiths College,
projects, we have successfully integrated our suite of who has played a key role in developing the PSIPRED
tools, resulting in the only single site worldwide which, resource to date.
after learning one simple user interface, provides all of
the following prediction services to biologists:
comparative modelling, fold recognition, ab initio (new
fold) prediction, transmembrane protein structure Main purpose of the job
prediction, disorder prediction, domain boundary  Software development and testing
prediction, binding hotspot prediction, ligand binding site  Building of databases and web servers
prediction, and several novel approaches to gene
function prediction. The successful applicant for this post  Design and benchmarking of new methods
will be expected to take a leading role in continuing to  Background literature reviews and preparation of
maintain and promote the PSIPRED server. papers, posters, presentations, relevant training
materials
The current services employ a range of modern web-
 Mathematical/statistical modelling of data and
development technologies, such as Django, Django-rest-
framework, python-celery, Grid Engine, Javascript and js analysis and other tasks as detailed in Duties and
web frameworks. We would expect these frameworks to Responsibilities (below).
continue to be used, though newer technologies can be
deployed during the project if appropriate. A key aspect
of the role is being able to professionally support the
general operation of the service which required expertise
  As duties and responsibilities change, the job
Duties and responsibilities
description will be reviewed and amended in
 To be involved in a range of software development
consultation with the postholder.
and empirical activities. Software development
 The postholder will carry out any other duties that
should be carried out according to best practice in
are within the scope, spirit and purpose of the job
the field.
as requested by the line manager or Head of
 To take a lead role in the development and
Department.
maintenance of the group’s Web services and
 The postholder will actively follow UCL policies
software resources as a whole.
including Equal Opportunities and Equality policies.
 To help promote the service to the user community
 The postholder will maintain an awareness of and
and provide user support and training.
observe Fire and Health & Safety Regulations.
 To contribute to the design of a range of
experiments in relation to the project goals.
 To set up and run empirical activities (to include
data collection, experiments, program building etc)
in consultation with the Principal Investigator,
ensuring that experiments are appropriately
supervised and supported.
 To record, analyse and write up the results of
experiments in a timely fashion, and to ensure that
results, methods and generated data are properly
archived.
 To lead in the planning and documentation of the
project.
 To prepare and present findings of research activity
to colleagues for review purposes.
 To represent the project at workshops and
conferences.
 To contribute to the drafting and submitting of
papers to appropriate peer reviewed journals and
conferences.
 To prepare progress reports on research for funding
bodies and the advisory board as required.
 To contribute to the preparation and drafting of
research bids and proposals.
 To develop and maintain suitable relevant web
pages.
 To contribute to the overall activities of the research
team and department as required.
 To supervise project students if requested.
 To periodically record your skills training and
continuing professional development activities on
UCL’s web-based system.
 Responsible for ensuring that equipment is safe
and maintained in working order and that work
complies with departmental security policy.
Person Specification
Criteria Essential or Assessment method
Desirable (Application/Interview)
Qualifications, experience and knowledge

A PhD in Bioinformatics, Computational Biology or Computer Science. Essential Application

PhDs in other areas (e.g. Engineering, Mathematics, Physics,
Biochemistry) will be considered if the primary subject of the thesis was
bioinformatics or there is evidence of success in postdoctoral
bioinformatics research. Candidates without a PhD may be considered in
exceptional cases, only if there is an extensive proven track record of
relevant work.

Knowledge of research techniques and methodologies relating to protein Essential Both

sequences and/or structures.

Experience of working in a research environment. Essential Application

Experience of developing and testing algorithms for bioinformatics Essential Both

applications.
Experience of developing and operating bioinformatics web servers Essential Both

Experience of applying AI/deep learning algorithms in bioinformatics. Desirable Both

Experience of using currently deployed software technologies (e.g, Django, Desirable Both
python-celery, Grid Engine)

Experience of web-based data visualisation (i.e. d3.js) Desirable Interview

Skills and abilities

Good Linux software development skills with an good working knowledge Essential Both
of best practice in the scientific computing field (e.g. in proper
documentation, testing and version control).

Expertise in several programming languages with a high proficiency in Essential Both

Python essential.

General scientific research skills (theoretical and empirical, planning and Essential Both
documentary)
Ability to analyse and write up data Essential Both

Effective written and verbal communication skills Essential Both

Personal attributes

Ability to work to deadlines whilst maintaining accuracy and an eye for Essential Interview
detail

Excellent organisational ability Essential Interview

Ability to work effectively in a team Essential Interview

Criteria Essential or Assessment method
Desirable (Application/Interview)