Sam Nicholls
Director Of Bioinformatics Software Development
Oxford, England, United Kingdom
Summary
👤
Senior🎓
Top SchoolSam Nicholls is a Director of Bioinformatics Software Development with 14 years of experience building and leading teams that turn sequencing data into actionable results, currently heading Oxford Nanopore’s Optimised Workflows for Life Sciences (OWLS) program. He combines deep hands-on engineering—contributing to staple tools like samtools and fixing memory/test-suite issues—with a track record of shipping large-scale genomics platforms such as the CLIMB-COVID system. Known for squeezing more performance and reliability out of pipelines, he moves fluidly between low-level C work, workflow engineering, and test automation. A PhD in Computational Biology and a background that ranges from burger flipping to intern roles at Google and the Sanger Institute give him a pragmatic, creative approach to problem solving. Not obvious from the job titles: he thrives on hunting subtle bugs and refactoring test frameworks to make complex bioinformatics software robust in production.
14 years of coding experience
4 years of employment as a software developer
Doctor of Philosophy (Ph.D.), Computational Biology, Doctor of Philosophy (Ph.D.), Computational Biology at Aberystwyth UniversityBSc (Joint Hons), Computer Science, Statistics, First Class with Honours, BSc (Joint Hons), Computer Science, Statistics, First Class with Honours at University of Wales, AberystwythCisco Networking Academy - CCNA Exploration, Cisco Networking Academy - CCNA Exploration at Swansea Metropolitan University
Stackoverflow
881reputation
107kreached
29answers
0questions
Github Skills (22)
memory-management10
c1110
c1710
bioinformatics10
test-automation10
bash9
script9
file-handling8
file-processing8
file-access8
fileio8
git8
django-views6
django-templates6
django-models6
Programming languages (18)
Github contributions (5)
samtools/samtools
Apr 2014 - Aug 2015
Tools (written in C using htslib) for manipulating next-generation sequencing data
Role in this project:
Backend Developer & Test Automation Engineer
Backend Developer & Test Automation EngineerContributions:24 commits, 10 PRs, 65 comments in 1 year 5 months
Contributions summary:Sam primarily contributed to improving the `samtools` codebase by fixing memory leaks and addressing issues in test cases. Their work involved correcting memory management problems within the test suite, ensuring proper resource deallocation. They also addressed errors in test scripts, enhancing the robustness of the testing framework. Furthermore, the user refactored the test suite with added support to compare output files using new test functions.
next-generationsequencing-datanext-generation-sequencinggenomicssequencing
SamStudio8/minidot
Jan 2019 - Feb 2020
Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
Contributions:10 commits, 9 pushes, 1 branch in 1 year 1 month
ggplot2bioinformaticsgenomesminimap
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