software engineer Remote
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Job summary
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.
Job description
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.
Person specification
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.
Benefits
- 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%
Things you need to know
Selection process details
You will be required to complete an application form. This will be assessed and sifted in line with the essential criteria.
This vacancy is using Success Profiles, and will assess your Behaviours and Experience
Stage 1: Application & Sift
As part of the application process, you will be asked to provide a Statement of Suitability in no more than 1250 words providing examples of how you meet the essential criteria. It should also detail what you and your experience can bring to the role. We suggest using the STAR (situation, task, action, result) method to demonstrate real-life examples for the specified essential criteria. Please note, only information provided within the stated word count will be considered.
If you are successful at this stage, you will progress to interview
Stage 2: Panel Interview
All applicants that progress to interview will be assessed on behaviours/ strengths/ experience / technical / ability through Success Profiles. The interview will be hosted remotely over teams and you will be required to do a 10 minute presentation
The Behaviours tested during the interview stage will be:
- Seeing the Bigger Picture
- Managing a Quality Service
- Delivering at Pace
Reserve List:
Candidates who pass the interview criteria but are not offered a post will be kept on a reserve list for 12 months and may be contacted if similar roles become available.
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.
DBS - People working with government systems must complete Basic Personnel Security Standard (BPSS) checks which includes a disclosure and barring security check. Successful candidates must meet the security requirements before they can be appointed. The level of security needed for this role is BPSS however there may be a requirement for this role to be SC cleared and you should familiarise yourself with the criteria of security clearance.
This role is Open to all external applicants (anyone) from outside the Civil Service (including by definition internal applicants. Appointments to roles within UKHSA will be made in accordance with the Civil Service nationality rules. These can be found at https://www.gov.uk/government/publications/nationality-rules This job is broadly open to the following groups:
- UK nationals
- Nationals of Commonwealth countries who have the right to work in the UK
- Nationals of the Republic of Ireland
- Nationals from the EU, EEA or Switzerland with settled or pre-settled status or who apply for either status by the deadline of the European Union Settlement Scheme (EUSS)
- Relevant EU, EEA, Swiss or Turkish nationals working in the Civil Service
- Relevant EU, EEA, Swiss or Turkish nationals who have built up the right to work in the Civil Service
- Certain family members of the relevant EU, EEA, Swiss or Turkish nationals
We recruit by merit on the basis of fair and open competition, as outlined in the Civil Service Commission's Recruitment Principles.
The Civil Service embraces diversity and promotes equal opportunities. As such, we run a Disability Confident Scheme (DCS) for candidates with disabilities who meet the minimum selection criteria.
The Civil Service welcomes applications from people who have recently left prison or have an unspent conviction. Read more about prison leaver recruitment.
Once this job has closed, the job advert will no longer be available. You may want to save a copy for your records.
Government baseline personnel security standard
It’s important to note that there are currently exceptions to applications being considered if your conviction relates to any of the following:
- life sentences
- arson
- sexual offences
- hate and terror offences
Some departments will also consider the specific offence against the nature of the business, i.e., a conviction for fraud may rule you out for a finance role
Contact Details – [email protected]
Feedback will only be provided if you attend an interview or assessment.
Security
Nationality requirements
This job is broadly open to the following groups:
- UK nationals
- nationals of Commonwealth countries who have the right to work in the UK
- nationals of the Republic of Ireland
- nationals from the EU, EEA or Switzerland with settled or pre-settled status or who apply for either status by the deadline of the European Union Settlement Scheme (EUSS) (opens in a new window)
- relevant EU, EEA, Swiss or Turkish nationals working in the Civil Service
- relevant EU, EEA, Swiss or Turkish nationals who have built up the right to work in the Civil Service
- certain family members of the relevant EU, EEA, Swiss or Turkish nationals
Working for the Civil Service
We recruit by merit on the basis of fair and open competition, as outlined in the Civil Service Commission's recruitment principles (opens in a new window).
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