Work history

• Work history
  • 2002-2007
  • 2007-2009
  • 2009-2022
    • Analysis pipelines
    • Genome browsers
    • Global projects
    • Containers for reproducible science
    • Full stack development experience
    • Readers note
  • 2022 onwards
  • Consultancy work
    • September 2021 - March 2022

2002-2007

• Junior Bioinformatician
• Bioinformatician
• Seniour Bioinformatician

I originally joined the Cancer Genome Project (CGP) at the Sanger Institute (now CASM) in 2002 on completion of my M.Sc in Bioinformatics. At that time I was responsible for developing an integrated Laboratory Information Management System (LIMS) to support PCR heteroduplex analysis. This involved database design, Perl-CGI web-development and integration of TECAN lab robots. This system continues to be used largely unchanged for sample tracking in the CASM laboratory. During this time I also contributed to very early versions of the COSMIC database.

During 2004 CGP moved heavily into capillary sequencing (also known as Sanger sequencing). Once the LIMS was adapted I moved on to developing a high throughput pipeline to run the autoCSA analysis software. The control software was written using JAVA, and a public desktop application, a.k.a. StandaloneCSA, was created for external use and released early 2007. This was a large project involving many developers working together on various aspects including database design, the analysis pipeline itself and a web-application used for visual inspection of the called variants by scientific staff.

2007-2009

• Clinical Programmer

In 2007 I left the CGP and joined Roche Pharmaceuticals as a Clinical Programmer. Here I gained experience of good clinical practice while building data capture and cleaning tools using Oracle Clinical.

2009-2022

• Seniour Bioinformatician
• Principal Software Developer / Bioinformatician

After 2 years at Roche I returned to the CGP in 2009. Although this may seem an unusual career choice the advent of next generation sequencing had significantly changed the challenges and work being undertaken. One of the primary differences in the data was the sheer volume being generated.

Analysis pipelines

The initial project was to create a pipeline to run the mapping of Illumina paired-end sequencing, supporting multiple species and builds.

Over 6 months I extended an existing database, developed a new web-application and file tracking system to control the scheduling and flow of data into and out of a Platform LSF compute farm. After the initial 6 months the success of the project resulted in it being extended to support the downstream analysis tools with more of the team moving in to aid in both support and development. During this phase of the project the web-interfaces were extended significantly to allow the scientific staff to manage their data and analysis.

The system proved to be a work-horse for the group for 6 years. The core jobs submission mechanism has been reworked by the group in the last few years, but the core database and much of the web-application has remained largely unchanged.

Genome browsers

As part of the analysis pipeline work I brought GBrowse into the the group as a centrally managed genome browser. GBrowse relies on server side compute and a traditional database backend to provide the images. In 2012 JBrowse matured to a state where BAM data could be directly handled in the browser. Due to this, and no further development on GBrowse, we have been actively working with the GMOD community to ensure features of GBrowse that our scientific staff consider important are replicated. We formally retired our GBrowse instance a few years ago.

During 2016 I developed a plugin for JBrowse, proportionalMultiBw (prototyped in my own time) to aid in the visualization of allele fraction in regions of very high sequencing depth. I've additionally produced a general purpose tool for automating generation of screen shots, see cgpJBrowseToolkit. The new JBrowse 2 embraces this screenshot feature making this a core component of this new version of the tool (not based on my code).

Global projects

In 2014 the CGP became involved in the ICGC PanCancer Analysis of Whole Genomes project. As part of this a significant portion of the IT team spent 6 months preparing all of the core algorithms we use in house for public use. In addition to this work I was a member of the technical working group advising on tools, mapping strategy and creating tools to aid the submission of the raw sequencing data from the sequencing sites around the world. Working closely with the IT group at OICR I implemented the 'Sanger' pipeline into the framework to be used in multiple data centers around the world. This pipeline ran successfully in 13 locations on a variety of base infrastructures including AWS, Azure, OpenStack and traditional HPC.

Following on from this project I continue to advise in the ICGC-ARGO data management group and the PPCG technical working group.

Containers for reproducible science

In 2016 I developed cgpbox as an initial prototype providing our wholegenome analysis platform in a convenient to use docker image. This was well received and we continue to build on this with the dockstore framework (see above). Variations on "cgpbox" have been used to drive the PPCG project analysis and are in use by ICGC-ARGO at GDC

Following on from this I have lead the initiative to convert all of our analysis pipelines to use containers. This has allowed us to offer our users the ability to fix algorithm versions for the life of their analysis projects.

Full stack development experience

During 2017 I prototyped a full-stack system for receipt of external sequencing data via web-interface and S3, backed by web-services hosted in our OpenStack flexible compute farm. Some of this can be viewed here. Following on from this a small team was formed to take this project further, developing the service architecture to validate the input data. Sadly the decision was taken to pause this project, however a great deal of new technology was investigated and this has proven to be valuable for subsequent projects.

Readers note

Above I have detailed projects that I have been heavily involved in. Although I may have worked exclusively on some of these it should be noted that I value the advice and expertise of those around me. The 'cancerit' team is an excellent group of people from varied backgrounds who draw on each others strengths. The team is also supported by the core informatics and infrastructure groups at the Sanger Institute.

2022 onwards

• Head of Health Informatics Platforms, Health Innovation East
  • Formerly: Head of Service, Clinical Computational Research Informatics

Eastern AHSN (Academic Health Science Network) changed its name to Health Innovation East in October 2023.

Initially focused on the delivery and development of the CYNAPSE platform to modernise and future-proof the computational infrastructure for genomics and wider ‘omics’ data across the NIHR Cambridge BioResource Centre (BRC).

A significant portion of the position being around requirements gathering and development of a sustainable service delivery team supporting a diverse 'omic research community.

2023, role expanded to cover a larger portfolio of work including the NHS Sub-National Secure Data Environment for the East of England. The team has now expanded to a total of 6 technical members covering cloud infrastructure, data management and information analysts, supporting projects across Cambridge University Health Partners (CUHP), University of Cambridge, NHS data strategy projects as well as smaller ad-hoc contracts in the research space.

Consultancy work

Short term consultancy projects are listed here.

September 2021 - March 2022

Eastern AHSN (Academic Health Science Network), project scoping exercise for CYNAPSE. The aim of CYNAPSE is to modernise and future-proof the computational infrastructure for genomics and wider ‘omics’ data across the NIHR Cambridge BioResource Centre (BRC). Insights sought on:

• data storage practices for genomic data
• workflow technologies
• cloud platforms
• division of responsibilities