Senior Bioinformatician / Developer (Analysis Pipelines)

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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.

Post Details

Job Title
Senior Bioinformatician / Developer (Analysis Pipelines)
Post Number
1003513
Closing Date
16 Sep 2018
Grade
SC5
Starting Salary
£39,150 - £47,850
Hours per week
37
Expected/Ideal Start Date
01 Nov 2018
Months Duration
36

Main Purpose of the Job

Design, build and test production-quality bioinformatic software tools and pipelines for efficient processing of high-throughput genomic data. The postholder will engage in exploring and implementing best-practices for sequencing QC, sequence assembly, gene annotation, variant detection, regulatory genomics and comparative genomics. Work with biologists, bioinformatics scientists, analysts and other specialists to implement and augment data analysis software and pipelines according to requirements and specifications. Generate comprehensive documentation, provide user-training and conduct bioinformatics analyses with the developed solutions. Maintain and extend existing bioinformatics pipelines. Take responsibility for delivering key tasks and specific interactions with internal and external groups. Work on a wide variety of bioinformatics projects in conjunction with our internal science faculty as well as external customers and collaborators.

Department

Digital Biology

Group Details

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.

Advert Text

Applications are invited for a Senior Bioinformatician/Developer to join the Core Bioinformatics Group at the Earlham Institute (EI).

Background:

The Earlham Institute is a research institute focused on exploring living systems by applying computational science and biotechnology to answer ambitious biological questions and generate enabling resources.

The Core Bioinformatics Group employs cutting edge technologies and computational approaches to deliver high-quality data analysis and develop software and analysis pipelines that support the Institute’s Core Research Programmes and UK Research community via the National Capability in Genomics and Single Cell Analysis (NCGS).

The role:

The successful candidate will be responsible for designing, implementing, testing and maintaining production-quality, high-throughput computational pipelines that assure timely and accurate processing of sequencing data from EI’s numerous and varied sequencing platforms. The post-holder will work alongside members of our Genomics Pipelines and Project Management teams to develop and implement application-specific quality metrics, increase automation of tasks and assess new sequencing applications.

The role will also involve working on a wide variety of bioinformatics projects in conjunction with our internal science faculty as well as external customers and collaborators. Projects will range in scale, type and complexity, from variant calling analyses on single model organisms, to large scale de novo genome assembly and annotation of complex eukaryotic species. The role will involve developing novel methods and algorithms plus extending and maintaining existing pipelines and automating workflows.

As part of the Core Bioinformatics Group you will:

-     Build scalable, tested and validated informatics pipelines automating analysis of sequence data for a diverse range of applications.
-     Design and develop specialised sequencing QC pipelines for different sequencing platforms and applications, run analysis and assess QC metrics in conjunction with our sequencing teams
-     Perform high-quality bespoke data analysis on a range of data types in conjunction with internal faculty and external collaborators/customers.
-     Define guidelines and generate documentation to support analysis workflows
-     Collaborate with UK and international partners.
-     Work independently and collaboratively on multiple projects in parallel

The ideal candidate:

The successful candidate will possess a PhD or equivalent experience in computational biology, computer science or bioinformatics. They will have a high level of skill of Python and additional knowledge in Java or C++, demonstrable experience of developing production-quality software (preferably working as part of a team responsible for pipeline delivery) and familiarity of developing applications to run in a high-performance computing environment. Extensive and broad experience in the computational analysis of NGS datasets as well as good project management and interpersonal skills are required.

Additional information:

Salary on appointment will be within the range £39,150 to £47,850 per annum depending on qualifications and experience. This is a fulltime contract for a period of 3 years.

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

Reporting to David Swarbreck (Head of Core Bioinformatics) and interacting on a daily basis with members of the core bioinformatics group. Will liaise with the EI Genomics Pipelines and project management teams regarding sequencing. Will interact with all EI staff but particularly the project leaders, domain experts and leads in scientific computing.

Main Activities & Responsibilities

Percentage
Develop bioinformatics workflows and pipelines, defining workflows, researching methods, identifying relevant tools, benchmarking, testing and building automated pipelines.
40
Explore new analytical algorithms for determining biological insights from large-scale data sets, develop software and enhance data processing and analysis tools
20
Perform data analysis, such as de novo genome assembly, variant calling, annotation, differential expression analysis and taxonomic classification of metagenomic data.
20
Follow prescribed practices for software version control, documentation, testing, and release engineering.
5
Collaborate with groups across EI and external collaborators to develop, implement and refine computational tools and gather requirements by working with domain experts.
5
Communicate the work of EI in oral (both in internal seminars and external conferences) and written presentations and to publish novel findings and technology/tool development in scientific journals.
5
To network widely with academic and industrial groups on the NRP, throughout the UK and internationally, including with the Wellcome Trust Sanger Institute and the European Bioinformatics Institute.
5
As agreed with line manager, any other duties commensurate with the nature of the post

Education & Qualifications

Requirement
Importance
PhD or equivalent experience in a relevant subject area (e.g. bioinformatics, computational biology, computer science)
Essential

Specialist Knowledge & Skills

Requirement
Importance
Have a high level of skill and experience of Python and Bash scripting, including the ability to interpret legacy code
Essential
Experience in bioinformatics workflow pipeline design and implementation
Essential
Knowledge of the software and algorithms for sequence alignment, genome annotation, genome and transcriptome assembly, phylogenetic tree reconstruction and functional annotation
Essential
Proficient skills with UNIX tools and version control (such as git, subversion)
Essential
Experience developing software in C/C++ or Java
Desirable
Demonstrable experience in Software Engineering
Desirable

Relevant Experience

Requirement
Importance
Experience developing and applying new bioinformatics software tools and workflow/pipelines to solve problems in computational genomics
Essential
Experience with next generation sequencing (RNA-Seq, DNA-Seq) and large-scale data analysis
Essential
Experience of working in a high throughput genomics environment with disciplined delivery of high quality usable data sets
Essential
Demonstrated ability to effectively manage concurrent technical tasks with competing priorities and meet deadlines
Essential
Have experience using High Performance Computing (HPC) resources and job scheduling systems
Essential
Understanding of testing frameworks and best practices in software development
Essential

Management and Leadership

Requirement
Importance
Ability to lead projects to a successful conclusion
Essential
Coordinate work with others on collaborative projects
Essential

Interpersonal & Communication Skills

Requirement
Importance
Excellent communication, teamwork and leadership skills
Essential
Strong organizational, time management and record keeping skills
Essential
Capable of working with domain specialists to gather system requirements
Essential
Demonstrated ability to work independently, using initiative and applying problem solving skills
Essential
Open to collaboration and willing to train others when required
Essential
Capable of writing academic papers and grants
Essential
Networking and influencing skills and the ability to build effective collaborative links
Desirable

Additional Requirements

Requirement
Importance
Attention to detail
Essential
Promotes equality and values diversity
Essential
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
Essential
Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute
Essential
Must be able to travel and work a non-conventional work pattern on occasion
Essential
Willingness to participate in occasional training of other institute members and visitors, and as part of formal training programmes hosted at the institute
Essential