Scott Cain
Associate Research Professor
San Diego, California, United States
Summary
👤
Senior🎓
Top SchoolScott Cain is an associate research professor and seasoned bioinformatics project manager with 15+ years building interoperable genomic tools and databases, including long-term stewardship of GMOD and leadership roles at WormBase and the Alliance for Genome Resources. He blends hands-on development in Perl, BioPerl, JBrowse/GBrowse and modern JavaScript stacks with pragmatic project delivery using Agile practices, Docker, and relational databases like PostgreSQL. At OICR he managed national-scale efforts such as the VirusSeq COVID-19 portal and the Human Cancer Models Initiative, demonstrating the ability to coordinate distributed academic and industry teams. A core contributor to BioPerl’s database adaptors and GFF handling, he brings deep expertise in data interoperability and schema design (Chado) that quietly underpins many genome browsers. Based in San Diego, he pairs a practical engineering background (PhD Biochemical Engineering) with a strong track record of community outreach, training and cross-project collaboration.
15 years of coding experience
26 years of employment as a software developer
University of California, San DiegoBS Chemical Engineering, BS Chemical Engineering at The Ohio State University
Stackoverflow
1reputation
0reached
0answers
0questions
Github Skills (6)
bioinformatics10
bioperl10
perl10
postgresql9
database-management9
sql8
Programming languages (17)
Github contributions (5)
bioperl/bioperl-live
Jul 2010 - Jun 2014
Core BioPerl 1.x code
Role in this project:
Back-end Developer / Database Engineer
Back-end Developer / Database EngineerContributions:14 commits, 3 comments in 3 years 11 months
Contributions summary:Scott primarily contributed to bug fixes and improvements in the BioPerl codebase, focusing on database adaptors and GFF handling. They resolved issues related to table creation and SQL queries in the PostgreSQL adaptor. Additionally, the user addressed problems with file globbing, GFF3 warnings, and URI unescaping within the GFF and Fasta modules, and GenBank to GFF3 script. Their work focused on ensuring the correct handling of data and improving interoperability with different file formats.
bioperlpdb-filesbiologytoolkitbioinformatics
alliance-genome/agr_amplify_jbrowse2
Feb 2023 - Apr 2025
Contributions:75 PRs, 308 pushes, 7 branches in 2 years 1 month
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