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Job title – Genomics Bioinformatics Software Engineer

Profession- Software Engineering

Directorate – Science

Full Time equivalent - 37.5 hours

No of Roles – 1

Contract Type – Fixed Term Contract for 2 years until 31/07/2025

Location – National, Home Working, Flexible

The role is National and may involve travel to UKHSA locations in England for some meetings and site visits

UKHSA offers hybrid working or home working for its employees The balance between home and workplace working is to be agreed with the line manager, determined primarily by business need and in line with departmental policy. This role may be principally home working with some business travel required to other UKHSA offices. Please be aware that this role can only be worked from within the UK and not overseas. Relocation expenses are not available

Working Pattern – Full Time /Hybrid Working/ Flexible Working/ Part Time/ Job Share

Grade & Salary – Grade 7. National banding - £49,592 - £58,769 Inner London - £53,396 -£62,286. Outer London - £51,494 - £60,528

The internal roles rules apply to existing Civil Servants, i.e. level transfers move on current salary or the pay range minimum, transfers on promotion move to new pay range minimum or receive 10% increase. Either case is determined by whichever is the highest.

This role is to be appointed under Civil Service Terms & Conditions. Full details on the T&C’s are found https://www.ukhsa.reed.com/.

Closing Date – 11/08/2023. 23:55pm. Unfortunately, late applications will not be considered

Interview Date – 30/08/2023 Please note, these dates are subject to change.

Introduction

The genomics team support the delivery of the UKHSA Pathogen Genomics service which comprise of a high throughput, distributed sequencing capability. The sequencing capability was developed to support the COVID pandemic response and delivery of the pathogen genomics programme.

The work of the Pathogen Genomics service is to support UKHSA’s genomics surveillance programmes, to aid detection of outbreaks and transmission of infections, to characterise and correlate genomics to virulence and antimicrobial resistance mechanisms, and generate evidence to support effective interventions, all within the wider UKHSA objective, to significantly reduce their overall public health burden.

Overview of Job

We are looking for a capable, highly motivated software developer with experience in designing / interacting with genomic software solutions (bioinformatics pipelines).

The priority is to deliver on the strategic aim of developing unified informatics solutions for assembling, analysing and reporting WGS results. This needs to be fit-for-purpose for a wide range of bacterial, viral and fungal pathogens and builds on extensive work establishing bespoke and successful routine WGS-based services for several key infectious disease agents. Solutions will need to be scalable and cope with high-throughput sequence processing yielding actionable information for public health and patient centred management. Solutions should also collect and report business intelligence information in real-time using SQL databases and dashboarding tools.

We require interfaces using modern web technologies & frameworks, so we have a broad range of software development challenges for the right person. A key activity is the establishment and deployment of robust and often novel analytical pipelines developed to a standard, which will meet necessary ISO standards and achieve UKAS accreditation.

The successful candidate will have a wide range of skills and an interest in developing applications for processing genomic data. Most of the systems to date are written in Python, however, we recognize potential advantages in migrating to C#, C++, Java and F# and require skills in these areas.

The software needs to be fully documented, modular, version-controlled and incorporated into a workflow with containerization. The software will need to be flexibly developed so it can be variably hosted on a range of computational environments including UKHSA’s high performance computer cluster, EBI and commercial cloud providers such as Amazon or Azure.

The software will need to be developed in line with the needs of users and have applications to not only support UKHSA, but partner users such as the Devolved Administrations, Animal and Plant Agency and international users.

Implement software solutions for visualization of genomic analyses linked to epidemiological and geospatial data for the better management of outbreaks.

Dissemination of software code will be through UKHSA GitLab and GitHub repositories

Provision of software engineering support and training across the Agency and beyond. The division is committed to working flexibly and collaboratively as part of a close team and will ensure the successful individual is supported to deliver challenging tasks that will enable them to progress within their career.

• 
  Contribute to the development and implementation of a strategy, jointly with partners, for creating software processes for WGS processing, analysis, reporting and storage within UKHSA.
• To design and deploy processes to collect and report business intelligence information in real-time using SQL databases and dashboarding tools.
• To support delivery of routine WGS-based services including managing issues and tickets raised by customers.
• To coordinate the UKHSA contribution to development of new software and design with appropriate architecture for more efficient and scalable ways of automated processing, analysis, interpretation and visualisation of sequence and epidemiological data.
• To work with bioinformatics colleagues to migrate, as appropriate, current analytical pipelines to the new architecture for software solutions.
• To ensure best practice for software development, testing and implementation is followed in the WGS Development and Implementation Service and across UKHSA.
• To ensure compliance with quality procedures and achieve appropriately recognised software accreditation
• To support software improvements required to enhance current UKHSA service delivery.

OTHER

• The role is National and may involve travel to UKHSA locations in England for some meetings and site visits.
• The above is only an outline of the tasks, responsibilities and outcomes required of the role. You will carry out any other duties as may reasonably be required by your line manager.
• The job description and person specification may be reviewed on an ongoing basis in accordance with the changing needs of the division and UKHSA.
• It should be noted that the work of the division is of a confidential nature and must not be communicated to other persons except where required for authorised purposes.

PROFESSIONAL DEVELOPMENT

• Identify, discuss and action own professional performance and training / development needs with your line manager through appraisal / individual development plan. Attending internal / external training events
• To participate in all mandatory training as required, i.e., fire safety, information governance and all other mandatory training.

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 to UKHSA. This will include.

Internal:

• Members of Pathogen Genomics Teams
• Laboratory staff across the UKHSA
• ICT & Technology teams
• Members of Laboratory Quality Manager Teams
• Staff within Laboratory Informatics Team

External:

• LIMS vendors
• NHS Trust ICT & Technology teams
• External stakeholders including customers and diverse external institutions
• National and international regulatory authorities

We pride ourselves as being an employer of choice, where Everyone Matters promoting equality opportunity to actively encourage applications from everyone, including groups currently underrepresented in our workforce.

UKHSA ethos is to be an inclusive organisation for all our staff and stakeholders. To create, nurture and sustain an inclusive culture, where differences drive innovative solutions to meet the needs of our workforce and wider communities. We do this through celebrating and protecting differences by removing barriers and promoting equity and equality of opportunity for all.

Essential Criteria:

• Higher degree (i.e., MSc or above) in Computer Science or related discipline
• Extensive experience of designing, developing and delivering large and complex software solutions
• Experience of distributed computer resources e.g., Docker, Singularity
• Demonstrable skills in developing user interfaces for complex software systems
• Proven ability to write high quality software documentation and implementation of quality standards for coding among a team.
• Expert knowledge/experience of Unix, PostgreSQL or similar RDBMS. Knowledge of Cassandra or similar NoSQL Database architectures and Proven expert skills in at least one object-oriented programming language, preferably Java or C++
• Knowledge of deploying code on distributed computational resources – HPC, public / private cloud
• Proven skills in developing and modifying code used for data analysis
• An understanding of and commitment to equality of opportunity and good working relationships, both in terms of day-to-day working practices, but also in relation to management systems

Desirable Criteria

• Excellent academic background in a relevant discipline preferred
• Experience of software used for pipeline development, e.g., NextFlow, Snakemake, Ansible
• Experience using data processing and visualization packages such as pandas, matplotlib and Plotly
• Experience of achieving software accreditation
• Experience in industry or academia of delivering multi-disciplinary projects within deadlines
• Experience of bioinformatics and an understanding of Next Generation Sequencing analytical techniques and advancements of medical microbiology and genomics.
• Experience in writing parallel code using libraries such as MPI
• Skills in project management of software delivery, in a collaborative environment using best practices concerning testing, documentation and version control using Git
• An understanding of the main concepts of public health microbiology.

• Learning and development tailored to your role
• An environment with flexible working options
• A culture encouraging inclusion and diversity
• A Civil Service pension with an average employer contribution of 27%

Job contact :

Name :
sophie rigney
Email :
sophie.rigney@reed.com

Recruitment team

Email :
hradmin@phe.gov.uk