NIH-funded scientific platforms · UConn Health
From a biological question to a reproducible run.
HPC dispatch and service integration for reproducible biological simulations.
AI-generated editorial artwork; not a project screenshot or research result.
01 / Context
The problem worth solving.
Researchers needed a dependable way to submit, coordinate, and reproduce heterogeneous biological simulations without manually managing solver environments or HPC job lifecycles.
02 / My contribution
Where I made a difference.
I built a SLURM-based dispatch service that translated web-submitted biological studies into schedulable HPC workloads. I connected setup, metadata, lifecycle status, and result retrieval, packaged solver environments with Docker and Singularity, and published a reusable dispatch client through PyPI.
03 / System design
Connecting the pieces.
- 01Study submission & metadata
- 02Dispatch service & SLURM
- 03Containerized simulation engines
- 04Lifecycle status & results
04 / Engineering tradeoffs
The decisions behind the system.
One execution path, many simulators
Heterogeneous engines bring different dependencies and execution requirements. Container packaging improves portability while dispatch boundaries separate scheduling from the scientific solver.
Long-running work needs visible state
An HTTP response is not the end of a simulation. NATS-based signaling, lifecycle tracking, and recovery paths help coordinate distributed work beyond the initial request.
Independent services, connected results
Separating simulation engines, metadata, result processing, and visualization isolates failures and allows components to evolve independently. Backend APIs connect those boundaries for researchers.
05 / Outcome & evidence
Work you can evaluate.
The infrastructure enabled reproducible execution across VCell, BioSimulations, and BioSimulators and contributed to two peer-reviewed Nucleic Acids Research publications.
- VCell: virtualcell/vcell ↗
- DOI: RunBioSimulations ↗
- DOI: BioSimulators ↗
- Platform: biosimulations.org ↗
The public repositories and co-authored papers below document the scientific ecosystem. The diagram summarizes execution concepts rather than reproducing a historical deployment.