Senior Bioinformatician / Developer (Genome Annotation)

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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 (Genome Annotation)
Post Number
1003512
Closing Date
25 Nov 2018
Grade
SC5
Starting Salary
£39,150 - £47,850
Hours per week
37
Expected/Ideal Start Date
04 Feb 2019
Months Duration
36

Main Purpose of the Job

Develop, implement, and document computational pipelines for the annotation of complex eukaryotic genomes. With responsibility for leading key large-scale annotation projects and delivering timely and accurate annotation of genomes from a variety of species, this will involve collaborations with biologists and computational scientists from UK and international institutions. Develop methods to support annotation across multiple genomes, aiding pan-genome analysis including evaluating the quality of gene predictions and identifying annotation errors and inconsistencies between gene sets. Expand EI’s gene annotation pipeline to incorporate new data types as well as data from the latest sequencing technologies. Preparing manuscripts for submission and presenting results at internal and external meetings.

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 is involved in the analysis of sequence data from a wide variety of sequencing platforms and works 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).

The role:

This post will focus on developing novel tools and pipelines for large scale annotation of genes and other genomic features across a diverse range of species including plants, mammals and fish.

This role will have responsibility for leading key large-scale annotation projects and continuing to develop and run EI’s annotation pipeline. A key focus will be improving and standardising gene structure annotation to support eukaryotic pan-genome analyses. The successful candidate will be involved in collaborations with biologists and computational scientists from the UK and international institutions.

Furthermore, the role will develop scalable and robust methods to identify transcript structures and analyze transcriptome complexity in eukaryotic species with large, repeat rich and polyploid genomes. The role will involve working with data from cutting edge sequencing technologies including PacBio IsoSeq and Nanopore.

As part of the Core Bioinformatics Group you will:

-     Produce high-quality, evidence-based genome annotation of protein-coding, lncRNA and pseudogenes
-     Develop methods for improving and comparing annotations across related species / accessions, supporting pan-genome analysis
-     Develop approaches for integrating data from a variety of sequencing technologies
-     Maintain and develop existing pipelines / annotation tools
-     Collaborate with UK and international partners on large-scale annotation projects

The ideal candidate:

The successful candidate will possess a PhD or equivalent experience in computational biology, bioinformatics, computer science or a similar subject. They will also have a strong background in large scale data analysis including experience of transcriptomics and genome annotation.

Candidates should possess a high level of skill and demonstrable experience of building tools and pipelines in Python, along with R and Bash scripting. Experience of the snakemake workflow management system is preferable. The ideal candidate will also be highly collaborative and have demonstrable experience of successfully managing their time to deliver analyses and input into multiple projects.

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 full time 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 interact with all EI staff and external collaborators but particularly the project leaders, domain experts and leads in relevant genomics research.

Main Activities & Responsibilities

Percentage
Design, implement and document computational pipelines for high-quality, evidence-based genome annotation of protein-coding genes, lncRNA and pseudogenes
20
Develop methods for improving and comparing annotations across related species / accessions, supporting pan-genome analysis.
20
Develop approaches for integrating data from a variety of sequencing technologies and maintain and develop existing pipelines / annotation tools
20
Generate and evaluate gene-builds and assess quality.
15
Engage in research projects and analyse, integrate and interpret project data in a variety of biological contexts.
10
Collaborate with EI faculty groups and UK and international partners on large-scale annotation and analysis.
10
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
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
Knowledge of methods for genome annotation
Essential
Knowledge of pipeline workflow programming
Essential
Broad and in-depth understanding of bioinformatics tools
Essential
Proficient skills with UNIX tools and version control (such as git, subversion)
Essential
Have a high level of skill and experience of Python and Bash scripting, including the ability to interpret legacy code
Essential
Experience developing software in C/C++ or Java
Desirable

Relevant Experience

Requirement
Importance
Experience designing and implementing computational methods, tools and algorithms for data analysis
Essential
Experience with next generation sequencing (RNA-Seq, DNA-Seq) and large-scale data analysis
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
Essential
Experience in genome annotation
Desirable
Experience of working in a high throughput genomics environment with disciplined delivery of high quality usable data sets
Desirable
Experience of the snakemake workflow management system
Desirable

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 and leadership skills
Essential
Capable of working with domain specialists to gather system requirements
Essential
Strong organizational and record keeping skills
Essential
To be able to communicate clearly with EI staff at all levels
Essential
Able to work independently
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
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
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
Essential