Ben Weisburd
Computational Biologist
Boston, Massachusetts, United States
Summary
🤩
Rockstar🎓
Top SchoolBen Weisburd is a computational biologist with 16 years of experience building and productionizing genomics software and pipelines at institutions including the Broad Institute and Novartis. He leads development of key resources for rare disease research—owning STR, SMN, and RNA‑seq pipelines, launching the first STR gnomAD callset, and driving the seqr analysis platform and gnomAD browser improvements. Equally comfortable in Java and Python, he has contributed backend fixes and features to high-profile open-source projects like Hail and Picard and maintained utilities such as ConfigArgParse. Ben combines deep domain expertise in NGS analysis with practical engineering: optimizing performance, adding robust configuration and testing, and integrating new data sources (e.g., VEP/Cassandra). Based in Boston, he brings a researcher’s attention to experimental detail together with a software engineer’s focus on reproducible, production-ready tools.
16 years of coding experience
5 years of employment as a software developer
Bachelor of Science (BS), Computer Science, Bachelor of Science (BS), Computer Science at Brandeis University
English, Russian, Hebrew
Stackoverflow
1,231reputation
369kreached
16answers
12questions
Github Skills (30)
unit-testing10
lib10
back-end-development10
cassandra10
python10
configuration-management10
environment-variables10
java10
scala10
argparse10
javas10
bioinformatics10
command-line-tool10
bam9
testing9
Programming languages (20)
Github contributions (5)
bw2/ConfigArgParse
May 2015 - Oct 2021
A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:26 releases, 15 reviews, 132 commits in 6 years 6 months
Contributions summary:Ben significantly contributed to the `configargparse` library by adding new features and fixing bugs, as evidenced by the commit messages that included enhancements and fixes. These contributions involved adding constructor arguments for features like dumping configurations and setting prefixes for environment variables. The user also refactored code related to handling unknown configuration file options and addressed other core functionalities. The contributions also demonstrate an effort to improve the library by adding Python 2.6 support.
environment-variablesconfigurationdrop-inargparseoptions
hail-is/hail
Aug 2016 - Jul 2020
Cloud-native genomic dataframes and batch computing
Role in this project:Back-end Developer
Back-end DeveloperContributions:15 commits, 34 PRs, 10 pushes in 3 years 11 months
Contributions summary:Ben primarily contributed to the back-end functionality of the Hail project, focusing on data processing and exporting tasks within a genomic context. They addressed bugs related to table and keyspace handling in Cassandra, ensuring the correct error messages were displayed. Additionally, they modified the code to use "start" and "end" in place of "pos" for genomic coordinates and added functionality to create and drop Cassandra tables. Further contributions included addressing VEP integration, fixing a typo in the source code, and fixing a .json path for hailctl start with VEP GRCh38.
scalabledata-analysispythongeneticshail
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