James Gatter
Senior Software Engineer at Cellarity
Somerville, Massachusetts, United States
Summary
👤
Senior🎓
Top SchoolJames Gatter is a senior software engineer with eight years of experience building scalable, data-centric systems for biotech and finance, currently focused on single-cell RNA-seq infrastructure at MIT and Cellarity. He designs and operates production pipelines and APIs—automating ingestion of 100K+ publications, curating a 150M-cell ML training set, and processing millions of sequencing observations—using Python, FastAPI, Prefect, TileDB SOMA, and AWS with Terraform. Comfortable across cloud-native stacks and bioinformatics, he blends hands-on engineering (workflow re‑engineering, SQL optimization, REST APIs, React UIs) with domain knowledge in molecular biology. Notably, he has led efforts to standardize heterogeneous biological metadata via public ontologies and built agentic LLM workflows to reduce manual curation overhead. Based in Somerville, MA, he prefers purely computational roles where he can scale reproducible data platforms for scientific discovery.
7 years of coding experience
6 years of employment as a software developer
Bachelor of Science (BS), Biochemistry and Molecular Biology (Major), Computer Science (Minor), Bachelor of Science (BS), Biochemistry and Molecular Biology (Major), Computer Science (Minor) at University of Massachusetts Amherst
Github Skills (104)
infrastructure10
pipeline10
prefect9
dataflow9
python9
automation9
transcriptomics9
owl9
orchestration9
biomedical-ontologies9
bioinformatics9
data-science9
observability9
semantics8
data-engineering8
Programming languages (12)
Github contributions (5)
ShalekLab/alexandria
Dec 2019 - Mar 2021
The Alexandria project aims to facilitate single-cell data analysis for users through providing an accessible data repository along with workflows, notebooks, and scripts
Contributions:1 release, 4 commits, 1 PR in 1 year 3 months
data-analysispythondata-repositorydata-managementdata-science
jggatter/dotfiles
Jan 2023 - Feb 2025
Contributions:5 PRs, 43 pushes, 6 branches in 2 years 2 months
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