Thank you for visiting my GitHub profile!

I thought I would add a little guide to help you navigate my profile more easily.

I have created a contribution guide repository which maps out all the contributions I made to the organisations I have worked for throughout my career.

• Pipeline Development (Nextflow, nf-core, nf-test with a little bit of Groovy and Java)
• Containerisation (Docker, Singularity/Apptainer)
• Cloud Infrastructure Deployment (AWS EC2, AWS S3)
• CI/CD (Git, GitHub actions, GitPod)
• HPC Job Scheduling (IBM LSF, Sun Grid Engine)
• Downstream scRNAseq analysis (Python, R)
• Environment Package Management (conda, mamba)
• Experience Training New Bioinformaticians (Unix, Docker and Singularity/Apptainer, HPC architecture, scRNAseq analysis in Python and R)

• Sept 2019 - Dec 2023:

  • Cellular Genetics Informatics - I worked as a Bioinformatician with the Cellular Genetics Informatics team at the Wellcome Sanger Institute for four years whilst earning my degree. My job was to support the Cellular Genetics Faculty by developing high throughput scRNAseq analysis pipelines for their research, building containers with docker and singularity to add additional software to Sanger's IBM LSF HPC, fixing faculty built environments managed by conda and aiding faculty to navigate the infrastructure and job scheduler on the Sanger HPC.

• Jan 2024 - May 2024:

  • Eco-Flow - I worked as a Senior Research Technician - Bioinformatics at UCL as the Technical Lead on the Eco-Flow project. This project is designed to build gold standard nf-core compliant Nextflow pipelines for ecologists at varying universities throughout the UK. The aim is to alleviate the strain they experience when trying to complete high through put analysis on their universities' HPC by providing portable, containerised pipelines.

• May 2024 - Present:

  • I am currently working as a Bioinformatics Engineer at Genomics England.

If you wish to contact me please use: simondonaldmurray [at] gmail [dot] com