Software and Bioinformatics Engineers to deliver an MVP for a new genomic healthcare service

Tender description

Summary of the work Genomics England require software developers and bioinformatics engineers with experience in Python, genomic data analysis and digital healthcare systems to implement a new genomic testing pathway for cancer patients as part of the NHS Genomic Medicine Service. Expected Contract Length 6 months plus 1.5 months extension Latest start date Thursday 1 December 2022 Budget Range Maximum budget of £600,000 Why the Work is Being Done When a clinician submits a request via the NHS Genomic Medicine Service for a cancer patient’s genome to be sequenced, it is both the tumour and healthy (germline) genomes that are studied. This sample can only be taken 4-10 weeks after diagnosis after completion of the initial rounds of treatment. Due to these challenges, results are likely to be returned to clinicians 6 weeks after diagnosis at the earliest, missing the opportunity to inform critical treatment decisions. The Tumour Only service will facilitate the sequencing of tumour samples only, with the patient’s healthy genome either not being sequenced at all or only in due course. By introducing a service focused solely on tumour sequencing, GEL expects that the cancer pipeline turnaround time will reduce. This will result in clinicians receiving a greater number of actionable insights, thereby improving outcomes for patients. Problem to Be Solved Clinicians cannot receive the results of tumour samples without needing to wait for full sequencing of the healthy tissue Who Are the Users As an NHS clinician I want to receive the results of tumour sequencing without needing to wait for sequencing of the healthy tissue to complete so that I can make more informed and earlier decisions about cancer patients' treatment. Work Already Done GEL has conducted some technical and design discovery work for a Tumour Only pipeline in both the National Genomic Information System (NGIS) and Pipeline services. Existing Team The existing team comprises a Solution Architect, Product Manager, Service Designer and two Service Owners Current Phase Discovery Skills & Experience • Have experience working in a successful agile delivery environment enforcing best practice delivery and support processes in line with customers' coding standards • Have experience working on large and complex existing codebases, integrating new features and ensuring no regressions are introduced and that best practices are followed throughout delivery • Have experience using Python, Docker, PostgreSQL and MongoDB in a complex multi-component system • Have experience delivering on AWS public cloud with a particular focus on Fargate, Terraform, S3, CloudTrail, Lamdba and other Serverless technologies • Have experience developing monitoring and alerting tools using DataDog, OpsGenie and associated tooling • Have experience working on large-scale data processing systems, including high-performance compute and storage systems • Have experience working with genomics data and associated tools to perform quality control, short-read alignment, variant calling and results reporting • Have experience using Linux, scientific computing tools and batch processing systems Nice to Haves • Demonstrate experience with OAuth, OKTA and Active Directory • Demonstrate experience with the Atlassian toolset (with a focus on Jira) and GitLab • Demonstrate experience with the IBM Spectrum LSF platform and the Nextflow workflow manager (or similar technologies such as Cromwell, WDL) Work Location The majority of work will take place remotely via Microsoft Teams. Please note there may be a requirement on occasion to visit the GEL offices: * 13 Clerkenwell Road, London, EC1M 5PA (until end of 2022) * 1 Canada Square, London, E14 5AB (from 2023 onwards) Working Arrangments The supplier will be required to work during GEL's core hours 9.00am to 17:30 Mon - Fri with 30 minutes for lunch. No weekend or evening work is expected. All travel and subsistence expenses will require prior approval. No. of Suppliers to Evaluate 5 Proposal Criteria • Technical capability and experience • Approach to resourcing • Delivery of solutions Cultural Fit Criteria • Provide demonstrable evidence of being able to work as part of an integrated, effective, and efficient delivery team, integrating into, and improving client culture and capability • Have a robust approach to sharing knowledge within and external to the team with clear processes for transferring knowledge to permanent staff • Demonstrate the ability to communicate effectively to express freedom of thought and innovation, positively challenge and advocate positive change Payment Approach Capped time and materials Assessment Method • Case study • Presentation Evaluation Weighting Technical competence 70% Cultural fit 10% Price 20% Questions from Suppliers No questions have been answered yet.