- Job Title
- Senior Bioinformatician / Developer (Analysis Pipelines)
- Post Number
- Closing Date
- 19 May 2021
- Starting Salary
- £40,785 - £49,750
- Hours per week
- Expected/Ideal Start Date
- 01 Jul 2021
- Months Duration
Main Purpose of the Job
Take a lead role in design, coding, and implementation of analysis pipelines.
The successful candidate will design, build and test production-quality bioinformatic software tools and pipelines for efficient processing of high-throughput genomic data, 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. Lead software development projects, with responsibility for delivering key tasks and 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.
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
- Take a lead role in design, coding, and implementation of analysis pipelines.
- Explore new analytical algorithms for determining biological insights from large-scale data sets, develop software and enhance data processing and analysis tools.
- Perform data analysis, such as de novo genome assembly, variant calling, annotation, differential expression analysis and taxonomic classification of metagenomic data.
- Follow prescribed practices for software version control, documentation, testing, and release engineering.
- Collaborate with groups across EI and external collaborators to develop, implement and refine computational tools and gather requirements by working with domain experts.
- 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.
- 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.
- As agreed with line manager, any other duties commensurate with the nature of the role.
Education & Qualifications
- PhD or equivalent experience in a relevant subject area (e.g. bioinformatics, computational biology, computer science).
Specialist Knowledge & Skills
- High level of skill and experience of Python, including the ability to interpret legacy code.
- Strong software development skills.
- Experience in bioinformatics workflow pipeline design and implementation.
- Broad understanding of bioinformatics tools.
- Proficient skills with UNIX tools and version control (such as git, subversion).
- Experience developing software in C/C++ or Java.
- Project management skills.
- Experience developing and applying new bioinformatics software tools and workflow/pipelines to solve problems in computational genomics.
- Experience with next generation sequencing (RNA-Seq, DNA-Seq) and large-scale data analysis.
- Demonstrated ability to effectively manage concurrent technical tasks with competing priorities and meet deadlines.
- Have experience using High Performance Computing (HPC) resources and job scheduling systems.
- Understanding of testing frameworks and best practices in software development
- Experience of working in a high throughput genomics environment with disciplined delivery of high quality usable data sets.
- Experience managing projects and co-workers.
Interpersonal & Communication Skills
- Excellent communication, teamwork and leadership skills.
- Strong organisational, time management and record keeping skills.
- Capable of working with domain specialists to gather system requirements.
- Demonstrated ability to work independently, using initiative and applying problem solving skill.
- Open to collaboration and willing to train others when required.
- Capable of writing academic papers and grants.
- Networking and influencing skills and the ability to build effective collaborative links.
- Attention to detail.
- Promotes equality and values diversity.
- Willingness to participate in occasional training of other institute members and visitors, and as part of formal training programmes hosted at the institute.
- Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work.
- Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute.
- Willingness to work outside standard working hours when required.
- Promotes equality and values diversity
- Attention to detail
Who We Are
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.
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.
Management and Leadership
- Ability to lead projects to a successful conclusion.
- Coordinate work with others on collaborative projects.
Living in Norfolk
Senior Bioinformatician / Developer (Analysis Pipelines)
Applications are invited for a Senior Bioinformatician / Developer to join the Laboratory of Dr David Swarbreck in the Digital Biology Programme at the Earlham Institute, based in Norwich, UK.
The Core Bioinformatics Group employ 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 successful candidate will be responsible for designing, implementing 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. Typically, this will involve developing flexible and robust pipelines that increase throughput and consistency, provide transparency of the process through logging and auditing, make efficient use of EI’s HPC resources and maximize interoperability. The role will work with Bioinformatics Scientists, Analysts and other specialists to implement and augment data analysis software and pipelines according to requirements and specifications and support members of the group in developing new software.
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.
• Run analysis workflows on a range of data types in conjunction with internal faculty and external collaborators/customers.
• Developing scripts and plugins for existing software.
• 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, bioinformatics or computer science and 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.
Salary on appointment will be within the range £40,785 to £49,750 per annum depending on qualifications and experience. This is a full-time post for a contract of 30 months.
As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.
The closing date for applications will be 19 May 2021.