Christopher Tomkins-tinch
Consultant And Independent Contractor at Software and Hardware Design Consulting
Greater Burlington Area United States
Summary
🤩
Rockstar🎓
Top School
Top expert inComputational Genomics and Bioinformatics Workflow Development
Christopher Tomkins-tinch is a versatile consultant and software engineer with 14 years of experience building end-to-end systems that span embedded hardware, firmware, data pipelines, and web and macOS/iOS applications. He combines a PhD in Organismic and Evolutionary Biology with hands-on engineering at institutions like the Broad Institute, enabling him to translate complex scientific problems into robust production software and instrumentation. An active open-source contributor, he’s improved workflow tooling in Snakemake and enhanced the popular xbar/xbar-plugins ecosystem for macOS, showing fluency from shell scripting to backend integrations and cloud storage providers. Comfortable from PCB layout to data visualization, he’s known for tackling automation in laboratory instruments and bioinformatics packaging (Bioconda), bringing both experimental rigor and practical deployment experience.
14 years of coding experience
11 years of employment as a software developer
BS Bioinformatics minor in Imaging Science, BS Bioinformatics minor in Imaging Science at Rochester Institute of TechnologyDoctor of Philosophy - PhD Organismic and Evolutionary Biology, Doctor of Philosophy - PhD Organismic and Evolutionary Biology at Harvard University
English
Stackoverflow
1,083reputation
23kreached
6answers
1question
Github Skills (40)
tooling10
file-management10
boto10
package-management10
python10
scripting10
bitbar10
conda10
bash10
plugin10
xmobar10
automation10
aws-s310
bioinformatics10
workflow-management10
Programming languages (19)
Github contributions (5)
snakemake/snakemake
Sep 2015 - Sep 2017
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:
Back-end Developer
Back-end DeveloperContributions:104 commits in 2 years
Contributions summary:Christopher's commits primarily focused on the development and modification of the Snakemake workflow management system. They implemented and refactored features related to remote file handling, including the addition of remote providers for various storage solutions (S3, GS, SFTP, FTP, and HTTP) and the associated functionality for downloading, uploading, and managing remote files within Snakemake workflows. They also made changes to the job execution and scheduling components. Moreover, the user addressed several bug fixes and improvements in response to feedback.
management-systemworkflow-management-systemgeneral-informationreproducibilitysnakemake
bioconda/bioconda-recipes
Oct 2015 - Oct 2022
Conda recipes for the bioconda channel.
Role in this project:Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:4 reviews, 598 commits, 511 PRs in 7 years 1 month
Contributions summary:Christopher primarily contributes to the development and maintenance of recipes for the bioconda channel, focusing on automating the build and packaging of bioinformatics tools. Their work includes creating build scripts (build.sh) and wrapper scripts (e.g., .py, .sh) to facilitate the installation and execution of various software packages within the conda environment. Key contributions involve integrating new tools like ghostx, k-slam, and xatlas, as well as updating existing packages like meraculous and krakenhll. The user also demonstrates expertise in adapting build processes for specific platforms (e.g., OSX) and managing dependencies.
recipescondabiocondabioinformaticspackage-management
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