Computational biologist transitioning to software engineering, developing research tools and modern development practices
PhD scientist with expertise in molecular microbiology and genomics, building software solutions for biological research challenges. Currently expanding into modern software engineering practices and DevOps culture.
Active projects:
- Developing a Python tool for bacterial genome analysis (SCCmec extraction)
- Created automation scripts for bioinformatics workflows, including AlphaFold3 submission utilities
- Maintaining and updating legacy Snakemake pipelines to current versions
Technical skills:
- Languages: Python, Bash
- Workflow management: Snakemake, learning Nextflow
- Containerisation: Experienced with Singularity, currently learning Docker
- DevOps Practices: Studying CI/CD, Cloud Computing, Infrastructure as Code through IBM Coursera course
- Planned implementations: GitLab CI/CD and Docker containerisation for current projects
Research computing experience:
- HPC and SLURM job management
- Data pipeline development and maintenance
- Scientific software installation and configuration
I enjoy knitting and crocheting. If I don't have a pair of socks as a work in progress, then there is something wrong with me. Love sock knitting! I have two dogs who I enjoy walking. I also volunteer for the RNLI as inshore lifeboat crew and I am currently Tier 1 crew.