Alden Deran
Programmer at UC Santa Cruz Genomics Institute
California, United States
Summary
🤩
Rockstar🎓
Top SchoolAlden Deran is a programmer with 11 years of experience specializing in backend systems, workflow engines, and bioinformatics pipelines at the UC Santa Cruz Genomics Institute. He combines a physics undergraduate background and ongoing PhD work in computational biology to tackle complex genome-scale problems, notably contributing to the Cactus genome aligner and the Toil workflow engine. His contributions include refactoring pipelines for immutable storage, integrating Toil Job.Service for service management, improving batch system integrations, and adding Prometheus/Grafana monitoring—demonstrating strong DevOps and containerization skills. Based in California, he focuses on making large-scale genomic workflows more reliable and reproducible in production environments. A detail that sets him apart is his ability to bridge deep scientific domain knowledge with practical engineering fixes that unblock whole pipelines (e.g., enabling Cactus runs via fileStore refactors).
11 years of coding experience
University of California Santa Cruz
Github Skills (21)
docker10
python10
cloud-infrastructure10
grafana10
batchfile10
dockers10
infrastructure10
prometheus10
aws10
bioinformatics10
batch10
batch-processing10
mesos9
workflow-engine9
pipeline9
Programming languages (3)
Github contributions (5)
ComparativeGenomicsToolkit/cactus
Sep 2015 - Jan 2018
Official home of genome aligner based upon notion of Cactus graphs
Role in this project:
Back-end Developer
Back-end DeveloperContributions:227 commits, 1 PR, 202 pushes in 2 years 3 months
Contributions summary:Alden primarily contributed to the development and improvement of the Cactus genome aligner pipeline. Their work involved refactoring the blast pipeline to leverage immutable fileStore, which enabled the whole pipeline to run. They also integrated the use of Toil Job.Service for managing ktservers and made significant modifications to the preprocessor. Moreover, they addressed issues related to Docker containerization.
genomenotioncactusalignergenomics
DataBiosphere/toil
Aug 2015 - Oct 2017
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
Role in this project:DevOps Engineer & Backend Developer
DevOps Engineer & Backend DeveloperContributions:41 commits, 12 PRs, 89 pushes in 2 years 2 months
Contributions summary:Alden primarily focused on improving the `toil` workflow engine by addressing batch system integrations. Contributions include fixing the Parasol batch system, enhancing test coverage, and preventing the return of killed jobs. The user also implemented the Prometheus/Grafana monitoring system, demonstrating expertise in containerization and infrastructure setup. Furthermore, the user modified the AWSJobStore, which points to work being done in the backend.
pythoncommon-workflow-languagemesosawsslurm
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