Specialized Applications

Rockfish supports a variety of specialized scientific and data transfer tools that extend beyond traditional batch computing workflows.

This section provides targeted guides for installing, configuring, and running advanced applications:

• AlphaFold3 — DeepMind’s protein structure prediction suite

• Aspera CLI — High-speed data transfer tool for downloading genomic data

• MATLAB Parallel Server — Scalable parallel computing for MATLAB users on the cluster

• Nextflow — Workflow manager for scalable and reproducible scientific pipelines

Whether you’re running large-scale inference, transferring datasets from external servers, building reproducible workflows, or parallelizing MATLAB jobs, these tutorials walk you through the complete process for success on ARCH systems.

Questions? Contact help@arch.jhu.edu for assistance.

• AlphaFold3
• Aspera CLI
• Matlab Parallel Server
• Nextflow