Bioinformatician (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
Bioinformatician (Analysis Pipelines)
Post Number
1003514
Closing Date
16 Sep 2018
Grade
SC6
Starting Salary
£31,250 - £38,100
Hours per week
37
Expected/Ideal Start Date
01 Nov 2018
Months Duration
36

Main Purpose of the Job

Run and test computational workflows that assure timely and accurate processing of sequencing data from EI’s numerous and varied sequencing platforms. Work alongside members of our genomics and project management teams to define and implement quality control metrics, increase automation of tasks and assess new sequencing technologies and applications. Work on multiple projects in parallel both independently and in conjunction with our internal science faculty as well as external customers and collaborators. Projects include de novo genome assembly and annotation of complex non-model organisms but will range in scale, type and complexity from variant calling analysis on model organisms to custom analysis of large multi-sample, multi-omics datasets. Contribute to the development of bioinformatics workflows and pipelines, to expand and increase capability for delivering future projects.

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 skilled Bioinformatician to join the Core Bioinformatics Group at the Earlham Institute (EI).

Background:

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 role will have responsibility for running and testing computational workflows 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 as well as with our internal science faculty, their collaborators and external customers to deliver on a wide variety of bioinformatics projects.

Projects include de novo genome assembly and annotation of complex non-model organisms but will range in scale, type and complexity from variant calling analyses on model organisms to custom analysis of large multi-omics datasets. The role will also be involved in designing, building, extending and automating pipelines, where possible, to increase capability for delivering future projects.

As part of the Core Bioinformatics Group you will:

-     Identify and test analysis tools to assist in the development of tailored workflows for large scale genome analysis.
-     Deliver high-quality genome analyses including genome assembly and annotation
-     Run sequencing QC pipelines, assess QC metrics and provide feedback to our sequencing teams.
-     Perform high-quality bespoke data analysis on a range of data types in conjunction with internal faculty and external collaborators/customers.
-     Collaborate with UK and international partners.
-     Work independently and collaboratively on multiple projects in parallel

The ideal candidate:

The successful applicant will possess at least an MSc or equivalent experience in Computer Science, Bioinformatics, Genetics or related fields and will have experience in bioinformatics in a high-performance computing environment to deliver on a range of genomics and transcriptomics analyses. Good scripting skills in Python, Bash and R as well as good interpersonal skills are also required.

Additional information:

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience. This is a fulltime post 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
Perform data analysis, such as de novo genome assembly, variant calling, annotation, differential expression analysis and taxonomic classification of metagenomic data.
40
Contribute to the development of bioinformatics workflows and pipelines, defining workflows, researching methods, identifying relevant tools, benchmarking, testing and building automated pipelines
20
Running our primary analysis QC pipeline and ensuring sequencing data is correctly extracted, processed and analysed from our sequencing platforms.
10
Participate in the design, implementation and testing of the quality control analysis systems and defining application specific quality control metrics.
10
Work alongside our project management and lab teams to ensure data is processed according to project requirements.
5
Keep up-to-date with the latest bioinformatics tools and sequencing technologies.
5
Follow prescribed practices for software version control, documentation, testing, and release engineering.
5
Present technical and analytical status in weekly meetings, contribute to publications and present to external audiences.
5
As agreed with line manager, any other duties commensurate with the nature of the post

Education & Qualifications

Requirement
Importance
MSc or higher in bioinformatics or computer science, or similar, or have equivalent relevant experience.
Essential

Specialist Knowledge & Skills

Requirement
Importance
Good scripting skills in Python, Bash and R
Essential
Extensive and broad experience in the computational analysis of NGS datasets
Essential
Experience in genome assembly and annotation
Desirable
Experience in designing and implementing bioinformatics workflows
Desirable
Have experience using High Performance Computing (HPC) resources and job scheduling systems
Desirable
Knowledge of the software and algorithms for sequence alignment, genome annotation, genome and transcriptome assembly, phylogenetic tree reconstruction and functional annotation
Desirable

Relevant Experience

Requirement
Importance
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
Preparation of manuscripts for publication and the delivery of presentations to internal and external audiences
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Have strong team working and communication skills.
Essential
Demonstrated ability to work independently, using initiative and applying problem solving skills
Essential
Ability to follow instructions/Standard Operating Procedures when required
Essential
Excellent time management and organisational skills
Essential
Open to collaboration and willing to train others when required
Essential
Be a good multi-tasker
Essential
An interest in outreach activities and communication of science to wider audiences
Essential

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
Willingness to work outside standard working hours when required
Essential
Ability to undertake occasional travel (national and international) related to collaborations and/or seminars
Essential