Vacancy Details: Bioinformatician

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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 Number1003362
Job TitleBioinformatician
Closing Date26 Apr 2018
Starting Salary£31,250 - £38,100
Hours per week 37
Project Title Building a toolbox for wheat functional genomics
Expected/Ideal Start Date 21 May 2018
Months Duration 24
Main purpose of the job This group member will be working with the latest wheat genomic data and building a toolbox for functional analyses. Specifically, the candidate will be involved in developing software tools to help understand how new variation in NLR immune receptors is generated, updating variant calling pipelines to examine natural and induced variation in complex wheat genomes and integrating this information to enable functional characterization of wheat genes. The candidate will work independently and with members of the Swarbreck (EI) and Krasileva (UC Berkeley) Groups to develop computational tools and pipelines to analyse large datasets and interpret them in a variety of biological contexts. The successful candidate will play an active part in EI’s collaborative wheat genomics efforts aimed at advancing wheat research through data integration and enhancing communication between bioinformaticians, wheat scientists and breeders. The candidate will work closely with the Grassroots Genomics, WheatIS, Ensembl Plants and other collaborative wheat projects to ensure integration and uptake of tools and resources.
Department Genomics Pipelines Group
Group Details This position is within the Core Bioinformatics group working in collaboration with Ksenia Krasileva (University of California, Berkeley).

The Core Bioinformatics Group led by David Swarbreck provides high quality computational analyses of a range of sequence data types and develops software and analysis pipelines that support the Institute’s Core Strategic Programmes and National Capability in Genomics and Single Cell Analysis (NCGS). The National Capability provides access to state of the art genomics technologies for research groups throughout the UK as well as delivering sequencing and genomics services to the associated Science Faculty groups and commercial customers. The group are involved in the analysis of sequence data from a wide variety of sequencing platforms and work alongside Earlham research groups to establish new software tools and analysis methods.

The Krasileva Lab studies plant genomics and plant-pathogen interactions. We combine new technologies with fundamental biology and translational research to make an impact on agriculture and food security. The projects in the group include comparative genomic analyses to understand the evolution of plant innate immunity, developing and working with wheat TILLING populations and CRISPR technologies to engineer favourable traits, specifically disease resistance. The Lab has a long-standing interest in wheat, combining new genomic datasets and applying them to investigate disease resistance. We are also interested in evolution of plant NLR immune receptors with long-standing goal of engineering new pathogen recognition specificities. An important philosophy of the group is to conduct science in a way that bridges the gap between bioinformaticians, biologists and breeders.
Advert Text Bioinformatician

The Earlham Institute (EI, Norwich, UK) is looking for a highly motivated bioinformatician to join an exciting collaborative project between the Swarbreck (Core Bioinformatics, EI) and Krasileva (UC Berkeley) groups to integrate and translate wheat genomics data into functional applications.

We are looking for a candidate driven to make a change in providing solutions to agricultural problems through coding and implementation of new software. In particular, this role will be responsible for the design, implementation and deployment of software pipelines for the integration of the genomic and genetic data available for wheat and related species, building a toolbox for functional analyses of the wheat genome.
To be considered for this role candidates must have the following qualifications, skills and experience:

•     Experience in computational biology with background in Big Data analyses (PhD is desirable but not essential).
•     Knowledge of good practice principles for software engineering.
•     Proven track record in the use of programing languages (e.g. Perl, Python, Java, R).
•     Experience with bioinformatics tools and working with high throughput datasets.
•     Experience with genome variation analysis.
•     Experience in Graphical User Interface development is a big plus.
•     Ability to communicate clearly with EI staff at all levels.
•     Ability to work as part of an effective team, and a good team player.

We highly encourage candidates from all disciplines and backgrounds to apply.

About the Earlham Institute

The Earlham Institute (EI) is a research institute focused on exploring living systems by applying computational science and biotechnology to answer ambitious biological questions and generate enabling resources. We host one of the largest computing hardware facilities dedicated to life science research in Europe; and one of our aims is to ensure that biological science in the UK has access to a skill base in genomics and bioinformatics to deliver programmes leading to improved food security, advances in industrial biotechnology and improved human health and wellbeing.

Additional information:

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience. This post is for a contract of two years.

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 1003362.

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: Line reporting to Dr. David Swarbreck and working closely with other groups at EI and the Krasileva group at UC Berkeley.
Main Activities & ResponsibilitiesPercentage
To develop computational tools and pipelines to analyse wheat genomic data and to work with other group members to implement them for functional analyses25
To participate in evaluating genomic data generated with latest emerging sequencing technologies20
To incorporate variant calling from natural and induced diversity sets into the newest wheat genome assemblies20
To engage in research projects and analyse, integrate and interpret project data in a variety of biological contexts.10
Independently design, analyse and interpret certain research projects.10
To facilitate communication with and data integration to international public repositories 5
Write and edit reports for both internal use and publication.5
As agreed with line manager, any other duties commensurate with the nature of the post5

Education & QualificationsRequirementImportance
Educated to Masters level or possess equivalent experience in molecular or computational biologyEssential
PhD in a relevant subjectDesirable

Specialist Knowledge & SkillsRequirementImportance
Have a high level of skill and experience of Perl, Python and Bash scripting, including the ability to interpret legacy code.Essential
Have a good understanding of the Next Generation Sequencing Technologies.Essential
Have a keen eye for detail, can identify potential problems before they happen and be a good problem solver.Essential
Apply analytical skills and creativity to solve diverse and challenging problems.Essential
Familiar with good practice principles for software engineering. Essential
Good knowledge of molecular biology and computational methods for sequence analysis and interpretationDesirable

Relevant ExperienceRequirementImportance
Experience of working in a high throughput datasets.Essential
Have demonstrated experience of developing production quality software, with the ability to work and develop code as part of a team.Essential
Experience with processing and analysis of sequencing data.Essential
Experience of working with high throughput datasets.Essential
Experience with Graphical User Interface developmentDesirable
Have experience using High Performance Computing (HPC) resources and job scheduling systemsDesirable

Interpersonal & Communication SkillsRequirementImportance
Excellent communication skills, both written and oral, including the ability to present complex information with clarity Essential
Good interpersonal skills, with the ability to work as part of a teamEssential
To be able to communicate clearly with EI staff at all levels.Essential

Additional RequirementsRequirementImportance
Promotes equality and values diversityEssential
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to workEssential
Ability to maintain confidentiality and security of information where appropriate Essential
Willingness to work outside standard working hours when required Essential