Benjamin Doran
Graduate Student Of Molecular Engineering
Chicago, Illinois, United States
Summary
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Senior🎓
Top SchoolBenjamin Doran is a PhD candidate in Molecular Engineering at the University of Chicago with nine years of experience at the intersection of computational biology and machine learning. He translates molecular-level insights into scalable computational workflows, combining hands-on software engineering—from improving Seurat's H5AD import—to automating cross-platform binary builds in the JuliaPackaging/Yggdrasil ecosystem. His background includes computational biology roles at MIT and teaching CS through Harvard's CS50, reflecting both deep technical skill and an ability to communicate complex ideas. Based in Chicago, he blends rigorous data-science training (Harvard Extension, cum laude) with practical automation expertise that helps move scientific software from source to reproducible, multi-platform binaries.
9 years of coding experience
2 years of employment as a software developer
Doctor of Philosophy - PhD, Molecular Engineering, Doctor of Philosophy - PhD, Molecular Engineering at Pritzker School of Molecular Engineering at the University of ChicagoBachelor of Liberal Arts and Sciences, Data Science, cum laude, Bachelor of Liberal Arts and Sciences, Data Science, cum laude at Harvard Extension School
Github Skills (16)
rna-seq10
pbuilder10
package-management10
cicd10
julia10
build-automation10
r10
matrix9
cprogramming-language9
c-language9
go8
cran8
linux7
fortran6
monorepo4
Programming languages (6)
Github contributions (5)
JuliaPackaging/Yggdrasil
Mar 2022 - May 2022
Collection of builder repositories for BinaryBuilder.jl
Role in this project:
Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:5 reviews, 10 commits, 10 PRs in 2 months
Contributions summary:Benjamin's primary contribution involves creating and updating recipes for building various bioinformatics tools within the BinaryBuilder.jl framework. Their work focuses on defining source code locations, build scripts, dependencies, and product definitions to streamline the process of creating pre-compiled binaries for multiple platforms. The user regularly integrates external software packages and manages build configurations, ensuring their successful integration into the target environment. The commit history demonstrates a commitment to automating the build process for scientific software.
repositoriesbinarybuildermonorepobuilderjulia
satijalab/seurat
Apr 2019 - Apr 2019
R toolkit for single cell genomics
Role in this project:Back-end Developer
Back-end DeveloperContributions:5 commits, 2 PRs, 5 comments in 3 days
Contributions summary:Benjamin primarily focused on modifying the `ReadH5AD` function within the R package to improve its compatibility with H5AD files. Their contributions included updating the expression matrix creation to match the size in the H5AD file, correcting argument names, and addressing issues related to columns with no expression. They also incorporated stylistic changes to adhere to the repository's coding conventions. These changes enhance the package's ability to import and process single-cell genomics data from H5AD files.
single-cell-genomicscranhuman-cell-atlasgenomicsbioinformatics
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