Genomics Bioinformatics Software Engineer at UK Health Security Agency in London - Canary Wharf

Job summary

This is an analysis role within Genomics Public Health Analysis (GPHA), delivering cutting-edge analysis to support public health decision-making, with a focus on metagenomics, horizon scanning, emerging infections and developmental genomics.

The team works at pace to meet changing public health needs, including developing analysis and reporting for the Metagenomics Surveillance, Collaboration and Analysis Programme (mSCAPE), horizon scanning for emerging threats, developing analysis methods for pathogens, supporting national outbreaks and collaborating with epidemiology, modelling and academic partners.

We are seeking a highly motivated software developer with experience of genomic software solutions and bioinformatics pipelines. The priority is increasing the use of metagenomic data across UKHSA through the mSCAPE pilot, developing scalable solutions capable of processing high volumes of bacterial, viral and fungal sequence data.

Systems are primarily written in Python, with opportunities to use other languages. Software should be modular, documented and version-controlled, with workflow management or containerisation where appropriate, and deployable across different computational environments.

The role involves working closely with UKHSA, NHS and academic partners, with code shared through GitLab and GitHub.

Working for your organisation

We pride ourselves as being an employer of choice, where Everyone Matters promoting equality of 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.

Please visit our careers site for more information https://gov.uk/ukhsa/careers

Job description

• Contribute to the development and implementation of a strategy, jointly with partners, for creating software processes for metagenomic data processing, analysis, reporting and storage within mSCAPE
• To support delivery of routine metagenomic-based analysis including managing issues raised by stakeholders
• 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 data
• To work with bioinformatics colleagues to develop and deploy, as appropriate, analytical pipelines
• To ensure best practice for software development, testing and implementation is followed in mSCAPE
• To ensure compliance with quality procedures and achieve appropriately recognised software accreditation or compliance where relevant
• To support software improvements required to enhance current UKHSA service delivery

Please note this list is not exhaustive.

Person specification

Essential role criteria:

• Higher degree (i.e., MSc or above) in Computer Science, Bioinformatics, or related discipline or equivalent experience working in a Bioinformatics team.
• Extensive experience leading the design, development and delivery of large and complex software solutions within secure, governed or regulated environments handling sensitive research, clinical or public health data
• Demonstrable skills in developing APIs, web services and data-centric applications
• Proven ability to write high-quality software documentation and implementation of quality standards for coding among a team including code review, unit testing and CI/CD principles.
• Expert knowledge/experience of Unix, PostgreSQL or similar RDBMS. Proven expert skills in at least one object-oriented programming language, preferably Python
• Knowledge of deploying code on distributed computational resources – HPC, public / private cloud or TRE infrastructures and experience with containerisation technologies such as Docker and container orchestration platforms such as Kubernetes.
• 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 role criteria:

• Proven experience acting as technical lead or principal engineer, influencing architecture, engineering standards and technical strategy across multi-disciplinary projects.
• 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.
• 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.

Benefits

Alongside your salary of £60,494, UK Health Security Agency contributes

£17,525 towards you being a member of the Civil Service Defined Benefit Pension scheme.

Find out what benefits a Civil Service Pension provides (opens in a new window).

• 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 employer contribution of 28.97%

Things you need to know

Artificial intelligence

Artificial intelligence can be a useful tool to support your application, however, all examples and statements provided must be truthful, factually accurate and taken directly from your own experience. Where plagiarism has been identified (presenting the ideas and experiences of others, or generated by artificial intelligence, as your own) applications may be withdrawn and internal candidates may be subject to disciplinary action. Please see our candidate guidance (opens in a new window) for more information on appropriate and inappropriate use.

Selection process details

This vacancy is using Success Profiles and will assess your Experience, Behaviours, and Technical skills.

Stage 1: Application & Sift

Success Profiles - GOV.UK

You will be required to complete an application form. You will be assessed on the listed 8 essential criteria, and this will be in the form of a:

• Application form (‘Employer/ Activity history’ section on the application)
• 750 word supporting statement

This should outline how you consider your skills, experience and knowledge provide evidence of your suitability for the role, with reference to the essential criteria.

You will receive a joint score for your application form and statement. (Please note you will not be able to upload your CV. You must complete the application form in as much detail as possible. Please do not email us your CV).

Healthjobs UK has a word limit of 1500, but your supporting statement must be no more than 750 words. Please do not exceed 750 words.

Longlisting: In the event of a large number of applications we will longlist into 3 piles of:

• Meets all essential criteria
• Meets some essential criteria
• Meets no essential criteria

If used, the pile ‘Meets all essential criteria’ will proceed to shortlisting.

Shortlisting: In the event of a large number of applications we will conduct an initial sift, on the lead criteria of:

• Demonstrable skills in developing APIs, web services and data-centric applications
• Proven ability to write high-quality software documentation and implementation of quality standards for coding among a team including code review, unit testing and CI/CD principles.
• Expert knowledge/experience of Unix, PostgreSQL or similar RDBMS. Proven expert skills in at least one object-oriented programming language, preferably Python

Desirable criteria may be used in the event of a large number of applications/large amount of successful candidates.

If you are successful at this stage, you will progress to interview & assessment.

Feedback will not be provided at this stage.

Stage 2: Interview

Success Profiles - GOV.UK

You will be invited to a remote interview. Behaviours and Technical skills will be tested at interview. The Behaviours tested during the interview stage will be:

• Managing a Quality Service (Lead behaviour)
• Changing and Improving
• Seeing the Bigger Picture
• Communicating and influencing

Technical skills will be assessed through a presentation. There will be a 10-minute presentation on the topic of Enhancing a Genomics API to Support Advanced Analysis Queries.

Interview dates to be confirmed.

Once this job has closed, the job advert will no longer be available. You may want to save a copy for your records.

Additional Information

Location

This role is being offered as hybrid working based at our core HQ Canary Wharf. We offer great flexible working opportunities at UKHSA and operate using a hybrid working model where business needs allow. This provides us with greater flexibility about how and where we work, to get the best from our workforce. As a hybrid worker, you will be expected to spend a minimum of 60% of your contractual working hours (approximately 3 days a week pro rata, (averaged over a month) working at our office. Our core HQ offices are modern and newly refurbished with excellent city centre transport links and benefit from co-location with other government departments such as the Department for Health and Social Care (DHSC).

Security Clearance Level Requirement

Successful candidates must pass a basic disclosure and barring security check before they can be appointed.

Successful candidates must meet the security requirements before they can be appointed. The level of security needed is Baseline Personnel Security Standard.

Eligibility Criteria

Open to all external applicants (anyone) from outside the Civil Service (including internal applicants).

Salary Information

If you are successful at interview and are moving from another government department, NHS, or Local Authority, the relevant starting salary principles for level transfers or promotions will apply. Otherwise, roles are offered at the pay scale minimum for the grade, but in exceptional circumstances there may be flexibility if you are able to demonstrate you are already in receipt of an existing, higher salary. Pay increases are through the relevant annual pay award for the role and terms.

Reserve List

If more than the required number of suitable candidates pass the interview criteria, you may be kept on a reserve list for 12 months subject to your agreement. You may be contacted, in merit-order, if similar roles with closely matching essential criteria become available and the department choose to appoint from a reserve list.

The panel will assess if candidates meet the requirement of the role first, using a specific benchmark system. If you are interviewed for the post and do not meet the required threshold for the specified grade, your application may be assessed against a similar, lower grade role and you may be offered the post should one be available.

Incident Response Activity

From time to time, the role holder may be required to support UKHSA’s incident response activity by contributing their appropriate expertise within an Incident Cell; during such periods, supported by the line manager, this work will take priority over normal day-to-day responsibilities, commensurate with their grade, skills and experience.

Qualifications and Registrations

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