Download 0000880790 - University of Oxford

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Experimental Medicine Division
Job description and selection criteria
Job title
Software Engineer - OxBRC Infection Theme
Division
Medical Sciences
Department
Nuffield Department of Clinical Medicine (NDM), Experimental
Medicine Division
Location
Microbiology Research, John Radcliffe Hospital, Oxford
Grade and salary
Grade 7: £29,541 - £36,298 per annum
Hours
Full time
Contract type
Fixed-Term. Up until 31/12/2015 in the first instance. Contract
may potentially be extended thereafter
Reporting to
Vacancy reference
Additional
information
Principal Investigator, Professor Derrick Crook
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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 21,000.
Most staff are directly appointed and managed by one of the University’s 130 departments or
other units within a highly devolved operational structure - this includes 5,900 ‘academicrelated’ staff (postgraduate research, computing, senior library, and administrative staff) and
2,820 ‘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 2009/10 was £879.8m. Oxford is one of Europe's most innovative and
entrepreneurial universities: income from external research contracts exceeds £367m p.a.,
and more than 60 spin-off companies have been created.
For more information please visit www.ox.ac.uk
Medical Sciences
The Medical Sciences Division is an internationally recognized 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 Clinical Medicine (NDM)
The Nuffield Department of Clinical Medicine (NDM) 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. The
Department also has a substantial research programme which requires high quality
administrative management. For this purpose, the Department is split into six groupings, with
the Experimental Medicine unit forming one of these groups.
NDM has significant financial turnover and complexity, resulting from its diverse research
portfolio, its geographical spread and its close links with NHS funding and strategic teams
involved in the development and delivery of increasingly integrated clinical research
platforms.
For more information please visit: http://www.ndm.ox.ac.uk/home
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Experimental Medicine
Experimental Medicine is part of the Nuffield Department of Clinical Medicine. We have staff
based at the John Radcliffe Hospital, Churchill Hospital, Peter Medawar and Weatherall
Institute of Molecular Medicine sites.
Research within Experimental Medicine spans fundamental basic science to translational
and experimental medicine approaches including clinical trials. We seek to understand the
pathophysiology of disease and apply this knowledge to develop enhanced diagnostics and
treatments for human disease.
Experimental Medicine's thematic research includes immunology, dermatology, stroke
medicine, geratology, behavioural science, infectious diseases, gastroenterology, palliative
care and respiratory medicine. The research is undertaken within different groups and
research units and includes clinical trials.
For more information please visit: www.expmedndm.ox.ac.uk/home
Job description
Overview of the role
The post is in software engineering working jointly with the Oxford Biomedical Research
Clinical Informatics theme led by Professor Jim Davies, Computer Science. You will join an
established vigorous multi-disciplinary team as part of Modernising Medical Microbiology
(MMM) and associated projects of approximately 50 researchers working across the UK,
~40 are situated in Oxford, predominantly at the John Radcliffe Hospital. The team includes
bioinformaticians,
statistical
geneticists,
software
engineers
(5
posts),
epidemiologists/biostatisticians, microbiologists, molecular biologists, clinicians, nurses and
infection control professionals. The group is taking a lead in pathogen research focussed on
investigating micro-evolution and population genetics using whole genome sequencing, and
translating findings into clinical medicine with the ultimate goal of improving patient
outcomes in the field of infectious diseases. MMM undertakes large scale epidemiological
studies and sampling of pathogens and has developed and is improving high-throughput
methods for processing and analysing complete sequences of thousands of an expanding
set of pathogens, currently including TB, Staphylococcus aureus, Clostridium difficile,
Escherichia coli, Norovirus and Hepatitis C virus.
This multi-disciplinary approach is revolutionizing microbiology and infectious diseases
research. Specifically, this post creates the opportunity to contribute both to a radically
changing research field and to improving delivery of microbiology and infectious diseases
services for patients. Substantial grant funding in the region of £10m supports the objectives
of the group. A major component is a UK-CRC consortium programme funded from 2009
until the end of 2013 and entitled: “Modernising Medical Microbiology: establishing how
revolutionary new technologies can be optimally integrated into microbiology
research and service”. A follow-on MMM linked programme funded by the Health
Innovation Challenge Fund (HICF) entitled: “Implementation of microbial whole-genome
sequencing for individual patient care, local outbreak recognition and national
surveillance” will commence in 2013 and end in 2016. These major programmes are
embedded within the NIHR Oxford Biomedical Research Centre (OxBRC), Infection Theme,
funded until the end of 2017. The overall aim of these programmes is to translate the newest
sequencing technologies, analytical algorithms and sophisticated web-based databases for
characterising and tracking pathogens into clinical practice. The core objective is to
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undertake research that improves pathogen diagnostics, infection treatment and detection,
and national surveillance of infectious disease. This work is being done in close collaboration
with the Health Protection Agency (soon to become Public Health England).
One part of the MMM project’s ‘Track infection and prevent’ concept is to implement a
unified software and database framework for infection control nurses and clinicians to
access hospital records, epidemiological data and genomic data through a single, secure
web interface. The system will provide richer information with which to make decisions about
individual patient treatment and infection control procedures in the hospital or region.
As in any research group involved in medical informatics and genomics, the rapid evolution
of sequencing technologies, bioinformatics, statistics and computing technologies means
that the scope of the project is likely to evolve over time. We believe that whole genome
sequencing will provide new information that can aid the identification, treatment and
tracking of infectious diseases at a scale that was not possible. Whole genome sequencing
technologies are currently at the stage where routine sequencing of pathogens is
commercially viable. The next step in facilitating the deployment of these technologies in
health-care centres around the country is developing the software required to deploy these
technologies to revolutionise infection control in the 21st century.
The sensitive and complex nature of the data presents technical challenges in the areas of
network security, web security, database / data warehousing and data visualisation. We are
seeking to add to a team of software engineers who will work together with scientists,
mathematicians, bioinformaticians and experts in software engineering (Professor Jim
Davies). They will complement and extend existing expertise in our group and help
implement a proof-of-principle system that demonstrates how bringing together hospital
records from disparate systems and augmenting these records with whole-genome
sequences of pathogens can deliver tangible health benefits in the day-to-day treatment of
patients.
Relationships
You will report to the Principal Investigator, Professor Derrick Crook and where necessary to
Professor Jim Davies. The delegated key working relationships will be with the Modernising
Medical Microbiology IT Leads. Liaison with potential end users of the service to be
developed, including infection control nurses and other members of the UK CRC MMM and
HICF research team, will be an important part of the work.
Professional development
You should pursue a programme of continuous professional development in accordance with
any relevant professional registration or statutory requirements, whilst maintaining
appropriate awareness of service provider requirements.
This position will be based at the John Radcliffe Hospital, Oxford.
Responsibilities/duties
Project

Play a key role in the design, implementation and deployment of a robust, data
linkage from heterogeneous sources. This will also involve maintaining secure
systems. Participation in developing a secure web-based system to deliver
information from heterogeneous sources to infection control health-care
professionals in collaboration with the team from the UK CRC MMM consortium is
required.
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
Work collaboratively with other members of the software development team and
users community to produce informative and intuitive depictions of complex data
sets.
Communication, Education and Training





Participate in and contribute directly to scientific discussions, both within the
laboratory and consortium and externally.
Ensure that team members are kept up to date with progress and difficulties in the
project.
Maintain confidentiality regarding research data when interacting with noncollaborating researchers.
Contribute as appropriate to the publication of research findings.
Participate in the education and training of other staff as necessary and appropriate.
General responsibilities




Be accountable for your professional conduct within the project.
Undertake such other duties as may be required from time to time that are
commensurate with the grade and responsibilities of this post. This may include
contributions to teaching activities.
To comply with all Oxford University policies and procedures.
Note: this job summary is not exhaustive, but aims to provide an overview of the key
responsibilities and a broad statement of purpose.
Selection criteria
Essential
 An undergraduate qualification in computer science, software engineering, or a related
discipline.
 Previous experience of applications development using modern web and database
technologies.
 Ability to work effectively as part of a multi-disciplinary team of developers,
researchers, and clinicians.
 Ability to work independently when required, taking responsibility for key tasks and
adapting quickly to changing goals and situations.
Desirable








Sound understanding of software engineering principles and techniques.
Excellent programming skills in Java, C#, or Python.
Good knowledge of Drupal or other content management/ portal technologies.
Development experience with web services or messaging architectures.
Keen interest in health informatics and new technology.
Expertise and experience in user interface design.
Previous experience in the implementation of mission-critical software systems.
Previous experience with visualisation of complex data sets.
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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, relating to your
skills and experience. When prompted, please provide details of three referees and indicate
whether we can contact them at this stage. You will also be required to upload a CV and
supporting statement. The supporting statement should describe what you have been doing
over at least the last 10 years. This may have been employment, education, or you may
have taken time away from these activities in order to raise a family, care for a dependant,
travel, or for any other reason. 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.
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 and this letter must be attached to any application they submit.
http://www.admin.ox.ac.uk/personnel/end/red/redproc/prioritycandidate
Should you experience any difficulties using the online application system, please email
[email protected]
Further help and support is available from http://users.ox.ac.uk/~chri1411/corehelp.htm
To return to the online application at any stage, please click on the following link
www.recruit.ox.ac.uk
Please note that you will be notified of the progress of your application by automatic e-mails
from our e-recruitment system. Please check your spam/junk mail regularly to ensure that
you receive all e-mails.
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