Education & Skills

• Education \& Skills
  • Education
    • M.Sc. Bioinformatics
    • B.Sc. (Hons) Biomedical Sciences, 2:1
  • Skills
    • Soft skills
    • Scripting and programming languages
    • Cloud, virtualisation and related tools
    • Web-development
    • Databases
    • Version control
    • Genome browsers
    • Other development skills

Education

M.Sc. Bioinformatics

• University of Manchester
• 2001-2002
• Project
  • Finding the immunogenic needle in the immunological haystack: a comparative study of context dependent text mining.
  • Edward Jenner Institute for Vaccine Research
  • Supervisor Dr Darren Flower

B.Sc. (Hons) Biomedical Sciences, 2:1

• University of Durham
• 1998-2001
• Project
  • The Chromosome 19 Limb-Girdle Muscular Dystrophy Gene (LGMD2I). Candidate Gene Analysis.
  • University of Durham, Department of Biosciences
  • Supervisor Dr Rumaisa Bashir

Skills

Soft skills

• Active Bystander - September 2020
  • Wellcome Sanger Institute
• Management in Action - 2018-2019
  • Talking Ape
• Unconscious Bias in Recruitment and Selection - October 2017
  • Challenge Consultancy
• AGILE: Agile Testing Strategies - July 2013
  • Learning Tree - course 1815

Scripting and programming languages

• python (3)
  • General scripting, packages
  • Database access
  • Web-services
  • Cython, pyCuda (self taught)
• perl
  • 18 years experience
  • Object Oriented design
  • CGI, DBI
• bash
  • proficient

Cloud, virtualisation and related tools

• AWS
  • Polly for training video voice-overs.
  • S3 object storage - concepts, cost minimisation and API integration.
  • SimpleDb - Mutable structure simple database service for low data volume (1MB max per row)
  • General use of virtual instances and volumes.
  • AWS Cloud Practitioner Essentials
• OpenStack
  • Tools for host management and deployment, applicable to other environments but used mainly here:
    • Packer - image building
    • Terraform - infrastructure deployment
• Containerisation tools
  • Docker
    • Use of build stages for smaller deployments
    • Experience of docker-swarm
  • Singularity
    • Mainly usage and ensuring docker containers are compatible.
    • More portable to develop via Dockerfile and convert.
  • Specialised registries - workflow + container
    • Dockstore

Web-development

• nginx
• HTML, CSS - intermediate
• JavaScript - proficient
• React - slightly stale

Databases

• Oracle - main experience including query optimisation.
• SQLite, PostgreSQL, MySQL

Version control

• git/GitHub/GitLab
  • GitFlow/HubFLow methodology preferred
• SVN
• CVS

Genome browsers

• JBrowse
  • Configuration and usage
  • Plugin development
• GBrowse
  • Configuration and usage
• IGV
  • Configuration and usage

Other development skills

This section details languages I have some experience but would not consider myself to be proficient.

• Workflow languages
  • Common Workflow Language
  • Nexflow
• NodeJS
  • Microservice development
• C/C++
  • Compilation, Makefile correction
  • Online courses, Debugging
• R
  • Debugging, investigating and cleaning up code for pipelines/external use.
  • Library installation
• Message Queues
  • RabbitMQ (JAVA)
• JAVA
  • Used intermittently over 15 years, stale
• Ellexus optimization tools
  • I/O profiling - See collaboration whitepaper and Letter