Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences

Nuffield Department of Clinical Medicine

Job description and selection criteria

Job title

Data Scientist

Division

Medical Sciences Division

Department

Nuffield Department of Orthopaedics, Rheumatology and

Musculoskeletal Sciences
Nuffield Department of Clinical Medicine

Location

Botnar Research Centre, Windmill Road, Oxford

SGC, Old Road Campus Research Building, Oxford

Grade and salary

Grade 7: 30,434 - 37,394 per annum

Hours

Full time

Contract type

Fixed-Term for 2 years

Reporting to

Brian Marsden (PI Research Informatics, NDORMS/KIR/SGC)

and Udo Oppermann (NDORMS)

Vacancy reference

118131

Additional
information

This post will be split 60% to work on projects at the Botnar

Research Centre and 40% to work on a project at the SGC
This will be a joint appointment and the post-holder will be
employed 60% by NDORMS and 40% by NDM.

Introduction
The University
The University of Oxford is a complex and stimulating organisation, which enjoys an
international reputation as a world-class centre of excellence in research and teaching.
It employs over 10,000 staff and has a student population of over 22,000.
Most staff are directly appointed and managed by one of the Universitys 130 departments or
other units within a highly devolved operational structure this includes over 6,500
academic-related staff (postgraduate research, computing, senior library, and administrative
staff) and over 2,700 support staff (including clerical, library, technical, and manual staff).
There are also over 1,600 academic staff (professors, readers, lecturers), whose
appointments are in the main overseen by a combination of broader divisional and local
faculty board/departmental structures. Academics are generally all also employed by one of
the 38 constituent colleges of the University as well as by the central University itself.
Our annual income in 2012/13 was 1,086.9m. Oxford is one of Europe's most innovative
and entrepreneurial universities: income from external research contracts exceeds 436.8m
p.a., and more than 80 spin-off companies have been created.
For more information please visit www.ox.ac.uk/staff/about_the_university

Medical Sciences Division

The Medical Sciences Division is an internationally recognised centre of excellence for
biomedical and clinical research and teaching. We are the largest academic division in the
University of Oxford.
World-leading programmes, housed in state-of-the-art facilities, cover the full range of
scientific endeavour from the molecule to the population. With our NHS partners we also
foster the highest possible standards in patient care.
For more information please visit: www.medsci.ox.ac.uk

Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal

Sciences
The Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences
(NDORMS) is part of the Medical Sciences Division and is one of the largest academic and
clinical departments of orthopaedics, rheumatology and musculoskeletal sciences in Europe.
The department is based at the Nuffield Orthopaedic Centre (NOC), which is the largest
musculoskeletal clinical centre in the UK. We currently employ approximately 320 staff, have
a grants portfolio worth 80 million, and an annual turnover in excess of 26 million.
The Botnar Research Centre, on the NOC site, provides a unique setting in which basic
science researchers from cell biology, genetics and engineering backgrounds can interact
with each other as well as with practising clinicians, and have access to patients.
The Institute provides facilities for approximately 200 research staff.
For more information please visit: www.ndorms.ox.ac.uk
The Kennedy Institute of Rheumatology is world famous for its development of anti-TNF
therapy for the treatment of the chronic debilitating disease, rheumatoid arthritis, which has
improved the lives of millions of patients. The Institute carries out research in the fields of
immunology, autoimmunity, inflammation, matrix biology and tissue destruction, with a long
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term objective of translating this research into clinical application. The major diseases of
interest are rheumatoid arthritis and the equally debilitating disease of osteoarthritis.
The Institute provides facilities for approximately 180 research staff.
For more information please visit: www.ndorms.ox.ac.uk

Structural Genomics Consortium

The SGC is a not-for-profit, public-private partnership that conducts pre-competitive research
to facilitate the discovery of new medicines.
Based at the University of Oxford and
University of Toronto the SGC's work contributes to new hypotheses in understanding and
treating human disease, and the subsequent identification of new targets for drug discovery.
The SGCs primary objectives within Oxford are to produce and characterise the 3dimensional structures of soluble proteins and of integral membrane proteins, to generate
selective chemical probes for epigenetic proteins and kinases, and to release these into the
public domain without restriction on use.
As part of its mission the SGC generates medically relevant reagents and knowledge related
to human proteins and proteins from human parasites, which it shares through over 250
collaborations with researchers worldwide. Since 2004 the SGC has solved over 1400
protein structures, generated over 20 inhibitors of epigenetic proteins, and regularly
contributed articles to leading publications including Nature and Science.
The SGC is part of the Nuffield Department of Clinical Medicine (NDM), which is one of the
largest departments of the University of Oxford and is part of the Medical Sciences Division,
with responsibility for a significant part of the teaching of clinical students within the Medical
School.
For more information please visit:
http://www.ndm.ox.ac.uk/home
http://www.sgc.ox.ac.uk

Athena Swan
The University of Oxford is a member of the Athena SWAN Charter and holds an institutional
Bronze Athena SWAN award in recognition of its support of good employment practices for
women in Science, Engineering and Technology (SET), and of its efforts to introduce
organisational and cultural practices that promote gender equality in SET and create a better
working environment for both men and women. In April 2014, NDORMS was successful in
achieving an Athena SWAN Bronze award. This recognises the ongoing work of developing
the Department as a supportive, caring and flexible environment for the people who are
driving forward significant musculoskeletal research.
The Athena SWAN Awards specifically recognise success in developing employment
practices to further and support the careers of women in science, technology, engineering,
maths and medicine (STEMM) departments in academia. Within NDORMS, we feel that we
have an established culture of equality but are using the process to spur ongoing
improvement that benefits everyone involved in the Department.

Job description
Overview of the role
Three large-scale research projects with Bayer HealthCare, Arthritis Research UK (ARUK),
and European Community Innovative Medicines Initiative (IMI) have been initiated and
coordinated at the Botnar Research Centre (NDORMS) and the SGC. We are looking for a
skilled Data Scientist that will participate across the projects to ensure that the diverse types
of data that is generated is captured, managed and made available by building and
maintaining the research informatics infrastructure.
The successful candidate will be responsible for the management and development of the
LIMS platform in the context of major projects described below. The generation of a custom
database schema to capture all aspects of the project work will be necessary and will involve
close interactions with project scientists to understand the data being generated and to
perform training to ensure the platform is used to its fullest extent. In particular, the proactive
coordination of data capture and dissemination between partners will be a key responsibility.
Reporting to the PI, Research Informatics at SGC/NDORMS/Kennedy Institute and Prof.
Oppermann, you will work with other Informaticians and data scientists who use this platform
within Oxford. You will be based jointly at the Botnar Research Institute and at the SGC on
the Old Road Campus. There will be opportunities to develop enhancements, often webbased, that enable the projects scientists to operate more efficiently by employing new,
emerging, technologies for data capture, experimental design and dissemination of
bioinformatics, cheminformatics and high-content information.
Primarily using Python, web-based technologies and the Lab Information Management
platform (currenly Molsoft / Scarab) this is a unique opportunity for a skilled data scientist or
informatician who wishes to develop scientifically-relevant informatics solutions and software
that will have significant impact on our understanding of the biology of proteins and drug
targets related to human health. Where possible, components of the platforms that will be
created will be made available as open source code. It is also anticipated that much of the
software and novel methods results generated by this position will be published in peerreview journals.
You will possess a degree (preferably postgraduate such as a PhD) in a biochemistry or
molecular biology-related field with significant experience in informatics. The ability to code
rapidly and possessing a hunger for learning and understanding unfamiliar and complex new
science rapidly is essential. You will be comfortable working closely with scientists, clinicians
and software developers in diverse geographical locations who possess a wide range of
skillsets and knowledge. A strong knowledge of RDMBS systems such as Oracle and
MySQL are essential as well as proven experience of coding in Perl/Python, web
technologies and producing intuitive, functional graphical user interfaces.
Enquires about this role should be directed to Dr Brian Marsden or Professor Udo
Oppermann.

Bayer Healthcare Project

The University of Oxford and Bayer HealthCare have entered into a strategic collaboration to
identify and validate novel drug targets for endometriosis and uterine fibroids. Bayer
HealthCare is the world leader in the field of hormonal contraception and a pioneer in
women's healthcare focusing on innovations in contraception and gynaecological therapies.
This strategic research alliance in the area of gynaecological therapies is for an initial period
of two years, but is open for extension to up to five years. The multi-target collaboration will
focus on endometriosis and uterine fibroids with the goal of discovering and developing
4

innovative treatment options for these diseases, which affect millions of women worldwide
and are still poorly understood. Research projects will be jointly performed at the Bayer
HealthCare RD Centre in Berlin, Germany, and at several University of Oxford centres and
institutes participating in the alliance.
Target discovery and pre-clinical validation will be performed by the Target Discovery
Institute under the lead of Professor Stefan Knapp together with the Botnar - Kennedy
Tissue platform located at the Botnar Research Centre (Professor Udo Oppermann). Clinical
expertise will be provided by the Oxford Endometriosis CaRe Centre, a collaboration
between the Oxford University Hospitals NHS Trust and the Nuffield Department of
Obstetrics and Gynaecology, which is one of the leading centres in the world for clinical care
and research in endometriosis.

Arthritis Research UK Project

A multi-centre, public-private partnership, spearheaded by NDORMS has recently been
funded by Arthritis Research UK (ARUK) to systematically study proteins involved in
epigenetics in the context of bone and inflammation biology. A wide range of experimental
techniques will be used to dissect the function and effect of these proteins in disease. This
will result in a diverse and heterogeneous set of data being generated by scientists from
many different backgrounds. This data must be efficiently collated, stored and made
available to all members of the project across many sites.
ULTRA-DD Project
Finally, this position is also jointly funded by ULTRA-DD, a European-wide consortium
funded by the Innovative Medicines Initiative (IMI), which comprises academics throughout
the University of Oxford (including SGC, NDORMS/Kennedy Institute), ETH (Switzerland),
Karolinska Institutet (Sweden) and the University of Toronto (Canada), in close cooperation
with the pharmaceutical biomedical industry (Bayer, DiscoveRx, Jansen, Novartis and
Pfizer). The role of ULTRA-DD (Unrestricted Leveraging of Targets for Research
Advancement and Drug Discovery) is to define and validate new protein targets by
generating and testing high quality chemical probes and antibodies in models of human
inflammatory disease based on clinical samples, to facilitate drug discovery and to promote
greater understanding of disease pathology.

Responsibilities/duties
1. Responsibility for the design, coding, implementation and maintenance of novel
informatics software solutions relating to the bio- and cheminformatics requirements
of NDORMS and in particular the ARUK, Bayer Healthcare and ULTRA-DD projects.
2. To coordinate data capture and dissemination from and between ULTRA-DD
partners.
3. To work with other Data Scientists and Informaticians within the University of Oxford
to assist in the implementation of the LIMS platform.
4. To build relationships with scientists and other software developers to assess the
utility of current software, areas for change and the direction of future developments.
5. To maintain and further develop informatics tools which enable further efficiency in
key projects.
6. Responsibility for the maintenance, backup and disaster recovery of the NDORMS
informatics and LIMS databases.
7. Responsibility for the training of NDORMS and ARUK scientists in the use of existing
and novel informatics platforms.
8. Participation in and support of the public engagement and widening access activities
of NDM and the University. This is anticipated to be not more than 2 days per year.
5

9. To carry out any other relevant duties as may reasonably be associated with the post
and which may be required from time to time.
All employees will have to ensure that their work in the laboratory is conducted safely at all
times and, in particular, that work is undertaken following the appropriate health and safety
policies and procedures for the particular area, without compromise to their own safety or
that of others who may be affected.
The job description is not intended to be rigid or inflexible and may include other duties and
responsibilities as may be determined. The post-holder is expected to work flexibly and
respond positively to changing needs.

Selection criteria
Essential
1. Possess a degree (preferably postgraduate) in molecular biology, biochemistry,
structural biology, cheminformatics, high-content screening, bioinformatics or related
area where programming and bioinformatics or the aggregation of diverse data types
was a key component or an equivalent combination of training and experience
2. Strong ability to rapidly program in two or more of the following languages: Python,
JavaScript, Ruby, Perl
3. An understanding of good graphical user interface design and functionality
4. A working knowledge of version control systems such as subversion and git
5. Experience in maintaining and developing for RDBMS platforms including Oracle and
MySQL
6. A working knowledge of coding under Linux and Windows and OS/X
7. Demonstrable ability to rapidly learn and apply new scientific and appropriate
development concepts
8. Excellent organisational skills with the ability to manage multiple projects with a
range of stakeholders
9. Excellent verbal and written communication skills

Desirable
1. Experience in coding for mobile platforms such as Android and iOS and / or using
and coding for the KNIME workflow platform
2. Experience in the use of R for statistical analyses and / or in systems administration
of Linux-based systems and in particular with NIS, NFS and Samba implementation
Please note that the appointment of the successful candidate will be subject to standard
compulsory pre-employment screening, such as right to work checks. Please click here to
read the candidate notes on the Universitys pre-employment screening procedures.

Working at the University of Oxford

For further information about working at Oxford, please see:
http://www.ox.ac.uk/about_the_university/jobs/professionalandmanagement/

How to apply
If you consider that you meet the selection criteria, click on the Apply Now button on the
Job Details page and follow the on-screen instructions to register as a user. You will then
be required to complete a number of screens with your application details. When prompted,
please provide details of three referees (one of which must be your current or most recent
employer/supervisor) and indicate whether we can contact them at this stage. You will also
be required to upload a CV and a supporting statement which explains how you meet the
selection criteria for the post.

Supporting Statement
The supporting statement should describe your skills and experience relevant to the post.
These may have been gained through employment, education/training, voluntary/community
work or you may have taken time away from these activities in order to raise a family, care
for a dependant, or travel for example. Your application will be judged solely on the basis of
how you demonstrate that that you meet the selection criteria outlined above and we are
happy to consider evidence of transferable skills or experience which you may have gained
outside the context of paid employment or education. We will short list for interview those
whose applications best demonstrate that the applicant meets the selection criteria,
so it is important that you use your supporting statement to explain clearly, point by
point, how you match them. Please note that a copy of a CV will not be accepted as
substitute for a supporting statement and that inclusion of the statement is a mandatory step
in the online application process.

References
Please give the details of people who have agreed to provide a reference for you. If you
have previously been employed, your referees should be people who have managed you for
a considerable period, and at least one of them should be your formal line manager in your
most recent job. Otherwise they may be people who have supervised you in a recent
college, school, or voluntary experience. It is helpful if you can tell us briefly how each
referee knows you (e.g. line manager, college tutor). Your referees should not be related
to you.
Your referees will be asked to comment on your suitability for the post and to provide details
of the dates of your employment and of any disciplinary processes which are still considered
live. We will assume that we may approach them at any stage unless you tell us otherwise.
If you wish us to ask for your permission before approaching a particular referee, or to
contact them only under certain circumstances (for example, if you are called to interview)
you must state this explicitly alongside the details of the relevant referee(s).
If you currently work, or have previously worked, for the University of Oxford, we will also
take up a reference from the head or administrator of the previous employing department.
This will be in addition to taking references from the referees you have provided.

Please save all uploaded documents to show your name and the document type.
All applications must be received by midday on the closing date stated in the online
advertisement.
Information for priority candidates
A priority candidate is a University employee who is seeking redeployment owing to the fact
that he or she has been advised that they are at risk of redundancy, or on grounds of illhealth/disability. Priority candidates are issued with a redeployment letter by their employing
departments.
If you are a priority candidate, please ensure that you:
- attach your redeployment letter to your application
- explain in your covering letter how you meet the selection criteria for the post.
Once your priority application has been submitted please email
personnel@ndorms.ox.ac.uk, disclosing your name and the vacancy reference.

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