The Bioinformatics and Whole Genome Sequencing (WGS) Software Development unit is part of Data Analytical Sciences within UKHSA's National Infection Service Division. The unit is globally pre-eminent in the design, construction, validation, and deployment of bioinformatics pipelines for the automated analysis of Whole Genome Sequence (WGS) data for human bacterial and viral pathogens. Our High-Performance Compute (HPC) cluster runs fully reproducible in-house pipelines for more than 20 bacterial and viral pathogens including SARSCOV2. We also provide support to The National TB unit and the 7 TB control boards by running a TB pipeline in collaboration with Oxford University. The Unit consists of 3 groups, respectively headed by Leads for In-House pipelines, for pipeline development, and for TB sequence service delivery. Contributions from members of each group are not constrained by group membership and are encouraged to be intra-group.
The postholder will contribute across the broad scope of the unit's NGS Service activities, from maintenance and support of existing pipelines to extension of their deployment to further computational architectures (distributed, cloud, local, remote, external).
Main Duties of the Job
The postholder will contribute across the broad scope of the unit's NGS Service activities, from maintenance and support of existing pipelines to extension of their deployment to further computational architectures (distributed, cloud, local, remote, external).
- Be responsible for day-to-day running and maintenance of the software and computer systems delivering existing UKHSA Whole Genome Sequencing (WGS) pipelines.
- Be accountable in providing Team Leads with progress of work which in turn will feed in to reporting to the Unit Head and Assurance Board
- Be able to work autonomously and flag concerns accordingly that might impact the smooth running of the business
- Contribute to expanding deployment of existing WGS pipelines to additional computational platforms (on-prem and cloud)
- Support the identification and sharing of best bioinformatics practice.
- Keep your knowledge and technical skills current ensuring the best value for money is achieved
- Be able to report on deliverables to Team Leads and the wider organisation
- Accept responsibility for refactoring existing WGS software components
- Develop tested, validated, and versioned software components for WGS analyses, incorporate into and validate new WGS pipeline versions
- Influence decision makers to strive to improve quality and performance
- Build strong working relationships both internally and with external stakeholders
- Be able to support and guide Junior grades on complex or contentious matters
- Satisfy support requests logged through helpdesk
- Analyse data from projects to which you are assigned, accepting responsibility for generating reports within agreed timelines.
- Lead on the preparation of reports posters and publications arising from data. The processing of bacterial or viral whole genome sequencing data from Public Health relevant pathogens through our pipelines. Posters to be presented at Scientific conferences, publications are submitted to academic journals and reports for UKHSA internal stakeholders or project based collaborators.
- Represent UKHSA at internal, National, and international meetings.
- Work consistent with the Bioinformatics Unit quality management system, ISO and other accreditation standards; participate in quality audits to support the unit's accredited service.
- Comply with safety and quality protocols and procedures at all times
Communication and key working relationships
The post holder will develop working relationships and communicate regularly with a wide range of individuals, clinical and non-clinical, internal and external too. This will require a high level of communication and influencing skills, disseminating complex technical information and an ability to communicate complex programmatic and IT issues to non-specialist groups in 'layman' terms. This will include.
Internal
- Substantial interactions with members of the Bioinformatics Team and the Central Sequencing Lab (CSL)
- Regular interactions with Laboratory scientists, embedded bioinformaticians and epidemiologists.
- Substantial interactions within DAS and with central IT (ICT) colleagues.
External
- Interaction with external scientific computing experts to deliver appropriate technologies through external cloud-based resource and utilising UKHSA computing infrastructure.
- Interactions with collaborating centres (Oxford University, EBI) to deliver software process for analysing WGS data. In addition, a high level of drafting skills is crucial in this role along with the ability to assimilate data.
Essential Criteria
- Degree in Bioinformatics or a related life science.
- Postgraduate training in Bioinformatics
- Familiar with Linux/unix; proficient on the CLI
- Knowledge of Next Generation Sequencing technologies and associated bioinformatic analytical approaches.
- Experience of applying diverse bioinformatics tools, preferably to the analysis of microbial DNA
- Experience of developing, modifying, debugging code used for data analysis, preferably python
- Highly motivated, enthusiastic, and hard working
- Interested in the advancements of medical microbiology and genomics
- Problem solving skills and ability to respond to sudden unexpected demands
- Must be able to use initiative to identify and implement tested solutions with a view to process and service improvement
- Must have ability to anticipate and resolve problems before they arise
- Ability to analyse complex facts and situations, develop a range of options, make recommendations
- An understanding of and commitment to equality of opportunity and good working relationships.
Desirable Criteria:
- PhD in a relevant subject
- Experience of VCS systems (e.g. git) for software versioning and documentation
- Knowledge of software containerization (e.g. Docker, Singularity)
- Knowledge of PostgreSQL or similar RDBMS
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