Vacancy Details: Genomics Pipeline Software Developer

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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.

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Advancing gender equality in science, engineering and technology.

Post Number1003294
Job TitleGenomics Pipeline Software Developer
Closing Date9 Aug 2017
GradeSC6
Starting Salary£30,750 - £37,750
Hours per week 37
Months Duration Indefinite
Main purpose of the job The Genomics Pipelines Software Developer will be part of the Genomics Pipeline Group at the Earlham Institute. They will be responsible for the delivery and management of the critical software infrastructure to support the group including the Laboratory Information Management System (LIMS).

The Group currently use an open-source, Java-based, in-house LIMS (MISO), that can support a range of next-generation sequencing (NGS) technology platforms. The LIMS needs to support a customer portal, automated communications, transparency of lab operations and audit trail. It must also deliver management reporting for our genomic platforms. This is delivered in a fast-paced environment of technology development and the LIMS must cope with experiments with processes to deliver high quality data for projects.

The post will report to the Project Management Team Leader and work closely with the rest of the Group. They will have a key objective to ensure the LIMS contributes to the efficient, effective and safe operations of the laboratory work. They will also be responsible for the Quality Assurance and Documentation for the LIMS, for good business continuity. Additional responsibility for maintenance and integration (via RESTful and non-RESTful APIs) of project management infrastructure (JIRA, Salesforce, Desk.com) with the LIMS system is anticipated.

The Group may at times consider other LIMS, and the post holder would form a fundamental part of the project team considering these systems. They would also take a leading role in the implementation of any new LIMS. The post-holder will be expected to contribute to the wider development of MISO across an international team of open-source developers.

They will work as part of a wider team ensuring that the output from the Group is delivered on time and to high quality with the aim of supporting Earlham’s strategic science programmes and the National Capability in Genomics and Single Cell Analysis.
Department Genomics Pipelines Group
Advert Text The Genomics Pipelines Software Developer will be part of the Genomics Pipeline Group at the Earlham Institute. They will be responsible for the delivery and management of the critical software infrastructure to support the group including the Laboratory Information Management System (LIMS).

The Group currently use an open-source, Java-based, in-house LIMS (MISO), that can support a range of next-generation sequencing (NGS) technology platforms. The LIMS needs to support a customer portal, automated communications, transparency of lab operations and audit trail. It must also deliver management reporting for our genomic platforms. This is delivered in a fast-paced environment of technology development and the LIMS must cope with experiments with processes to deliver high quality data for projects.

The post will report to the Project Management Team Leader and work closely with the rest of the Group. They will have a key objective to ensure the LIMS contributes to the efficient, effective and safe operations of the laboratory work. They will also be responsible for the Quality Assurance and Documentation for the LIMS, for good business continuity. Additional responsibility for maintenance and integration (via RESTful and non-RESTful APIs) of project management infrastructure (JIRA, Salesforce, Desk.com) with the LIMS system is anticipated.

The Group may at times consider other LIMS, and the post holder would form a fundamental part of the project team considering these systems. They would also take a leading role in the implementation of any new LIMS. The post-holder will be expected to contribute to the wider development of MISO across an international team of open-source developers.

They will work as part of a wider team ensuring that the output from the Group is delivered on time and to high quality with the aim of supporting Earlham’s strategic science programmes and the National Capability in Genomics and Single Cell Analysis.
Key relationships Internal: Genomics Pipeline Group – All members of the Genomics Project Management and Pipeline teams, including the senior RAs, other RAs, Team Leaders and Head of Genomic Pipelines. The Regulatory Genomics Group delivering genomics annotation and bioinformatics services. The teams providing the Plant and Microbe DNA Foundry. The Technology Development Team leader and team members. EI’s Science and Research Groups. EI’s communications and outreach team. EI’s Advanced Training Groups. EI’s Director(s) and business support colleagues on quality and Health and Safety Issues.
External: Collaborator and National Capability Customers. Potential employees, NBIP colleagues, Health and Safety co-ordinators, Next Generation Sequencing Suppliers, Conference attendees, BBSRC, other funders, and other key stakeholders. Other LIMS users and external community using or interested in MISO.
Main Activities & ResponsibilitiesPercentage
Plan and manage their daily work, and a programme of development work, working as part of a wider team or independently. Maintain the LIMS system ensuring continued function following the inclusion of new features, and to provide timely bug fixes. Work with the Genomics Pipelines and Regulatory Genomics Group to identify a roadmap for LIMS development to provide efficient lab management, good customer communication and management reporting. Maintain LIMS documentation for business continuity. Assist with investigation into system and user issues, trouble shooting or any area where the team needs support from the LIMS to achieve the desired result. Consider best practice on other LIMS and consider how these could be incorporated into MISO, or the LIMS in operation at EI. Integrate the LIMS with additional systems for project management by understanding and exploiting the RESTful and non-RESTful API’s available in JIRA, SalesForce and Desk.com 80
Ensure a timely release cycle for MISO, whilst the lab is using this system, to the open-source community via Github collaborative coding service: https://github.com/TGAC/miso-lims Aid the external developer and user communities by providing accurate up-to-date documentation and support. 10
Continually assess the LIMS system, considering other LIMS on the market. Contribute to the project team that considers strategic changes in IT infrastructure. Support the development and roll out of new systems, and be responsible for future upgrades, and bespoke coding required for the Group. As agreed with line manager, any other duties commensurate with the role. 10

Education & QualificationsRequirementImportance
Bachelor’s degree in Computer Science or Information Technology, or similar significant experience in software development Essential
Master’s degree with a clear focus on software development Desirable

Specialist Knowledge & SkillsRequirementImportance
Provable programming experience in Java, preferably including Spring, Java EE, JSPs/servlets.Essential
Experience in XML technologies, including XSD, XSLT, DTD.Desirable

Relevant ExperienceRequirementImportance
Involvement in successful software development projects using established development methodologies. Essential
Experience in developing computational methods and/or algorithms.Desirable

Interpersonal & Communication SkillsRequirementImportance
Demonstrated ability to work independently, using initiative and applying problem solving skillsEssential
Promotes and strives for continuous improvementEssential
Excellent time management and organisation skillsEssential
Excellent oral and written communication skillsEssential
Experience with Agile Programming practicesDesirable

Additional RequirementsRequirementImportance
Promotes equality and values diversityEssential
Ability to work flexibly when required.Essential
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to workEssential
Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the InstituteEssential
Ability to maintain confidentiality and security of information where appropriateEssential
Must be able to travel and work a non-conventional work pattern at times.Desirable