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

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 Monday 9 January 2023 Budget Range Maximum budget of £200,000 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 1. Could you please confirm the team members you’re looking for? (and expected quantities) We expect no more than 5 individuals will be required to fulfil this requirement, but are open to suggestion as to how our required skillsets are delivered between individual roles. 2. Your original opportunity was for £600k – we can see that has now reduced to £200k. How has the scope / ambition changed to reflect this? The overall project has the same scope, but for this procurement we are only focusing on an initial phase (a tumour-only pathway, but not the following germline-late pathway) 3. Could the Authority please confirm why this opportunity has been reissued? We have changed the scope of this procurement, see response above. 4. Could you please let us know if there is a current incumbent and who it is? There is no current incumbent 5. Please clarify the budget for this project and a preferred range We have a maximum budget of £200k for this project. It is anticipated that the majority of this budget will be used. 6. Was the recent discovery work on the Tumour Only Pipeline conducted by GEL’s internal team, or by an external agency? If external, who delivered the work? An internal team at GEL 7. Please can you give an indication of timeframes for the tender evaluation, case study presentations and contract award date? Following down-selection we will issue tender documents with the expectation of a response and presentations towards the end of November and contract award early December. However these timelines will depend somewhat on internal priorities. 8. Please can you also clarify whether you seek a solution that incorporates any level of automation or machine learning into the solution? Machine learning will not be required, automation of infrastructure deployment (with terraform) will be required. 9. Is there an expectation that the delivery team would engage with clinicians directly? No. The delivery team would engage with GEL team members (and potentially other partners working with GEL) 10. How would the delivery team work with GEL and the GMS? The team will be embedded in existing GEL development teams. 11. Would the delivery team be working with patient data, or synthetic data during the project? The team will be working with sample data, which is sometimes derived from patient data and de-identified (as generating sufficiently realistic synthetic data is non-trivial) 12. What discovery work has been done to date on the Tumour Only pipeline? We have worked with all relevant teams at GEL to understand requirements for the TO pipeline, and have a draft roadmap for delivery. 13. Would the discovery work that has been completed to date be shared with the delivery team? Yes 14. What would GEL’s ideal joint working approach be with the existing team? The team will be embedded in existing GEL development teams. 15. Who would be the alpha and beta phase testers? Will we have access to clinicians for this? The scope of this procurement will not include clinical testing 16. Please clarify the desired workflow between GMS and GEL for this Tumour Only Pipeline? The team will be embedded in existing GEL development teams. 17. Is there an expectation about the number / type of staff to be provided by the delivery partner? We expect no more than 5 individuals will be required to fulfil this requirement, but are open to suggestion as to how our required skillsets are delivered between individual roles. 18. What output is expected within the 6 months + 1.5 months time frame? Code and documentation 19. What specific bioinformatics experience is required for the project? Experience with short-read alignment and variant calling, ideally with somatic samples 20. Is the expectation for the actual implementation to be completed within this 200k budget? The expectation is that the initial phase of implementation will be completed within this budget 21. What are the SC clearance requirements for this engagement? No SC is required for this engagement 22. Is the contract length fixed at 6 months or can it be shorter? 6 months is indicative but we anticipate the majority of the work will be conducted within the first 3 months of 2023. 23. Is this a request for resource augmentation? We expect no more than 5 individuals will be required to fulfil this requirement, but are open to suggestion as to how our required skillsets are delivered between individual roles. 24. How many software engineers and bioinformatics engineers are required to join the team We expect no more than 5 individuals will be required to fulfil this requirement, but are open to suggestion as to how our required skillsets are delivered between individual roles. 25. Please can you clarify the data sources that would be made available to the successful providers? The team will be provided with access to the necessary data required to complete the task. 26. Who is the identified product owner / SRO within GEL for the tumour only pipeline? The SRO within GEL for the tumour only pipeline is the Chief Digital Officer and the work will be coordinated by the BioPipelines Service Owner and NGIS Solutions architect 27. What level of detail will be provided to the delivery partner about the bioinformatics sequencing requirement? The delivery team will not need to implement new bioinformatics workflows, but will need to integrate existing workflows into new infrastructure. They will be provided with support from the GEL teams they are embedded within. 28. Is the supplier responsible for specific deliverables associated with this work? The team will be responsible for deliverables alongside the GEL teams they will be embedded in. The precise details of those deliverables is not yet defined, but will include code, documentation, designs etc.