Cyberinfrastructure & Training

Modernizing and documenting bioinformatics applications on CyVerse, ACCESS, and Tapis-backed HPC.

Overview

Ongoing work integrating CyVerse user-facing applications with Tapis-backed HPC execution, and co-developing training materials that teach researchers and cyberinfrastructure professionals to run AI- and HPC-enabled viral ecology workflows.

Scientific or practical problem

Powerful HPC and cloud research-computing resources (CyVerse, ACCESS, Tapis) are underused by domain researchers because the tooling and documentation gap between “has an HPC allocation” and “can run their analysis reliably” is often large.

My role

Cyberinfrastructure-facing bioinformatics developer. I integrate CyVerse applications with Tapis-backed execution, manage data transfer and input/output mapping, document app-update procedures and computational protocols (via Protocols.io), and co-develop training modules and example datasets for the iVirus Cyberinfrastructure Training Initiative.

Dataset or data type

Example/training datasets for viral and eco-genomics workflows (not primary research data).

Methods and technologies

• CyVerse discovery environment app development
• Tapis-backed HPC job execution
• Data transfer and I/O mapping and synchronization
• Protocol and procedure documentation (Protocols.io)
• Training-module and example-dataset development

Workflow diagram

flowchart LR
  A[CyVerse app] --> B[Tapis job submission]
  B --> C[HPC execution]
  C --> D[Output synced back to CyVerse]
  D --> E[Documented protocol / training module]

Major results or outputs

Updated and documented viral/eco-genomics analysis applications on national cyberinfrastructure platforms; contributed training modules supporting NSF-funded pipelines and future grant development.

Challenges and decisions

Prioritizing documentation and reproducibility (so others can maintain and extend the apps) alongside the underlying analysis correctness — treating “usable by someone else” as a deliverable, not an afterthought.

Publications

Not applicable (infrastructure/training work); may inform future methods papers.

Code and documentation

Documentation hosted on Protocols.io and CyVerse; specific links to be added as they are finalized.

Collaborators

iVirus Cyberinfrastructure Training Initiative; OSU Microbiome Working Group; CyVerse/ACCESS/Tapis teams.

Current status

Ongoing.

Limitations or confidentiality note

None — describes infrastructure and training contributions, not confidential research results.