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 <mailto:help@arch.jhu.edu>`__ for assistance.

.. toctree::
   :maxdepth: 1

   Tutorial_alphafold3
   Tutorial_aspera_cli
   Tutorial_Matlab_ParallelServer
   Tutorial_Nextflow