Vacancy Details: Scientific Computing Specialist

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Earlham Institute

Earlham Institute is a vibrant, contemporary research institute and registered charity, working in an area of rapid technological development and innovation.

Earlham Institute is strategically funded by the BBSRC to lead the development of a skill base in bioinformatics and a genomics technology platform for UK bioscience. The Institute is located on the Norwich Research Park, together with its partners: the John Innes Centre, the Institute of Food Research, The Sainsbury Laboratory, the University of East Anglia and the Norfolk and Norwich University Hospital. The research park has an excellent reputation for research in plant and microbial sciences, interdisciplinary environmental science and food, diet and health, to which Earlham Institute contributes strengths in genomics and bioinformatics. Close links exist between the NRP partners and new opportunities for collaboration in exciting new initiatives are under development. The NRP recently received £26M of government investment to facilitate innovation and further develop infrastructure to attract science and technology companies to the Park to enhance the vibrant environment and realise economic impact from research investment.

Earlham Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. This has been boosted recently by an e-Infrastructure grant to expand the data storage capacity to a multi-petabyte unit, deploying a high performance cluster and large-memory server enabling the allocation of processes requiring several terabytes of computing memory.

Earlham Institute’s state of the art DNA sequencing facility operates multiple complementary technologies for data generation that provide the foundation for analyses furthering our fundamental understanding of genomes and how they function. We aim to be at the forefront of technological advances and are developing and implementing technologies to generate and analyse new types of data. We also develop novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational bioscience. Earlham Institute has one fully owned subsidiary, Genome Enterprise Ltd (GEL) via which it offers genomic and bioinformatics services on a trading basis and works with commercial providers on a partnership basis. Earlham Institute also receives specific funding to enable knowledge exchange programmes which are supported across the institute teams.

disability confident employer

Advancing gender equality in science, engineering and technology.

Post Number1003366
Job TitleScientific Computing Specialist
Closing Date8 Jan 2018
Starting Salary£39,150 - £47,850
Hours per week 37
Expected/Ideal Start Date 22 Jan 2018
Months Duration Indefinite
Main purpose of the job This role will serve as a technical domain expert in supporting staff in the use of HPC for their research, and advising the inclusion of technical HPC information in grant proposals. The post holder will join a team of scientific computing experts based on the NRP who are playing a key role in providing scientific computing and HPC support at EI. The post holder will be responsible for:
- Supporting effective utilisation and monitoring of EI HPC platforms
- Providing HPC utilisation metrics as detailed reports to EI Senior Management
- Compiling, debugging, optimizing and profiling bioinformatics applications on EI HPC systems
- Improving parallel-scaling and load-balancing of EI research code and workflows
- Liaising with the EI’s Open Data Committee on data management best practices and policies
- Consulting and interacting with faculty and their research groups on a one-to-one basis to enable them to fully utilise the EI computational resources and other national computational resources for their scientific research
- Supporting EI research groups in evaluating novel compute and storage technologies for cutting-edge bioinformatics
- Designing, creating and presenting training tutorials, hands-on workshops, and documentation
- Representing EI on the Scientific Computing Steering Committee
Department Scientific Computing
Group Details The Scientific Computing Specialist will be situated within the Scientific Computing team of the Data Infrastructure group at EI, working closely with researchers at the Earlham Institute (EI) and NBIP Computing Infrastructure for Science (CiS) to support High-Performance Computing (HPC) at EI.
Advert Text Scientific Computing Specialist

Applications are invited for a Scientific Computing Specialist to join the Scientific Computing Group at the Earlham Institute.

About the Earlham Institute:

By partnering closely with HPC technology leaders, Earlham Institute (EI) boasts world-class compute and storage infrastructure that allows our scientists to undertake some of the most challenging data-intensive research in the fields of genomics and biosciences. High-Performance Computing technology allows our scientists to both store and analyse the huge amounts of data that are characteristic of modern genomics research.

We generate and store over 10 terabytes of new data per week, while the thousands of processing compute cores and terabytes of large-memory architecture supercomputers allow computational tasks to finish in hours or days rather than the months or years on standard desktop computing resources. These resources have enabled such projects as the completion of a new hexaploid wheat genome by EI, using new open data and new open source tools in November 2015.

About the Scientific Computing Group:

A primary objective of the Scientific Computing Group is to work very closely with EI researchers to enable them to make the most efficient and effective use of the High-Performance Computing infrastructure at EI. This includes code debugging, profiling and optimisation, support with developing job batch submission scripts, file I/O tuning and the development of ongoing user training and documentation.

The EI Scientific Computing Group carry out these activities in partnership with the core Computing Infrastructure for Science (CiS) team who administer the HPC compute and storage resources. This includes the planning and procurement of new infrastructure for the refresh or replacement of existing resources.

In association with leading technology partners, the Scientific Computing Group also undertake research and evaluation of new software tools and hardware technologies that can improve user productivity and software performance. The group also publish whitepapers, articles and present talks both internally and externally on these activities.

About the Scientific Computing Specialist role:

This Scientific Computing Specialist role will undertake the core objectives of the Scientific Computing group, enabling EI's researchers in fulfilling their analytical requirements through active support of our HPC environments including: our commodity linux cluster; our SGI UV large-memory supercomputing machines; our DRAGEN and Xeon Phi co-processor architectures; our scale-out Isilon, NAS, and object store storage layers.

The postholder will help administer, maintain, and develop the effective local, remote, and cloud solutions necessary to meet EI's scientific needs, as well as advising staff on meeting their data management responsibilities and practices.

Finally, this role will need to be involved with compiling, debugging, optimising and profiling bioinformatics applications on EI HPC systems, evaluating novel compute and storage technologies for cutting-edge bioinformatics, and designing, creating and presenting training tutorials, hands-on workshops, and documentation.

Additional information:

Salary on appointment will be within the range £39,150 to £47,850 per annum depending on qualifications and experience. This if a fulltime, permanent contract.

For further information and details of how to apply, please visit our web site or contact the Human Resources team on 01603 450462 or quoting reference 1003366.

As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.
Key relationships Internal: All members of the Research Faculty, including EI’s Institute Strategic Programme (ISP); the EI National Capability in e-Infrastructure team; the National Capability Genomics Platform Group who deliver genomics annotation and bioinformatics services to EI sequencing customers; the National Capability Single Cell Genomics group;the DNA Foundry; EI’s Communications and Outreach teams; EI’s Advanced Training Groups; EI’s Director(s) and business support colleagues.

External: Collaborators and National Capability Customers who are accessing EI’s HPC; NBIP colleagues; CiS; HPC and associated hardware vendors and suppliers; conference attendees and visitors; BBSRC and other funders; and other key stakeholders such as crop breeders.
Main Activities & ResponsibilitiesPercentage
Work with the NBIP CiS Team, support EI staff and faculty in making effective and efficient use of EI HPC resources including our range of SGI UV large-memory machines. This includes user support, compiling and optimising users’ research code and workflows, and data management of enterprise storage tiers.55
Continuously develop and communicate HPC documentation and best practices to EI staff via face-to-face meetings, online help, and reporting processes. Run regular training sessions on how to use the HPC platforms effectively. Work with the Data Infrastructure group leader to manage EI’s Data Management Policy.15
Work with CiS staff and EI developers to investigate and evaluate hardware and software technology and process to improve the performance of existing bioinformatics workloads, as well as security testing of externalised web services.10
Sit on the NBI Computing Steering Committee, representing EI users. Work with EI and the NBI Scientific Steering Committee to monitor and provide advice on EI’s Scientific Computing Policies. To manage EI’s Data Management Policy, and deal with routine problems.10
Liaise with and support external users on access to and charges for in the use of the EI HPC facilities as part of the e-infrastructure National Capability.5
Provide support with HPC connectivity for the installation and deployment of new laboratory instruments and associated robotics/bioinformatics. This will require the direct interaction with NBIP CiS to discuss aspects of connectivity and security.5
Any other duties commensurate with the role.

Education & QualificationsRequirementImportance
Degree Level Qualification in computational science or equivalent.Essential
MSc or PhD in a relevant discipline, e.g. computer science, computational science, bioinformatics.Desirable

Specialist Knowledge & SkillsRequirementImportance
Proficiency in the UNIX shell and one or more programming and scripting languages (such as C++, C, Python).Essential
Demonstrable experience in the use of software and systems for data management, preferably in the bioinformatics domain.Essential
Demonstrable experience in the physical hardware management of HPC clusters and storage systems.Desirable
Demonstrable experience in developing bioinformatics software or supporting bioinformatics researchers.Desirable

Relevant ExperienceRequirementImportance
Good knowledge of the concepts and key elements of high-performance computing (HPC).Essential
Experience with the installation of scientific software on UNIX-based systems.Essential
Demonstrable experience in the identification and resolution of software bugs and hardware issues.Essential
Experience benchmarking HPC systems and scientific software, including performance analysis and profiling tools.Desirable
Experience in the configuration of workflow management systems (e.g. Galaxy).Desirable
Experience with HPC compiler optimization techniquesDesirable
Experience in bioinformatics related to high-throughput DNA sequencing.Desirable

Interpersonal & Communication SkillsRequirementImportance
Excellent communication skills and ability to listen to others.Essential
Ability to communicate clearly with EI staff at all levels.Essential
Ability to represent EI to a high standard externally with a range of different stakeholders within academia, industry and the broader scientific community.Essential
Open minded, positive, and enthusiastic, champion EI’s reputation and the wider team.Essential
Clear and concise presentation skills.Essential
Track record in providing a computational support environment to users.Desirable
Excellent negotiation skills.Desirable

Additional RequirementsRequirementImportance
Respectful attitude and a motivation to promote diversity and equality in data science.Essential
Diligent approach to working, with an eye for detail and methodical troubleshooting.Essential
Promotes equality and values diversityEssential