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Table of Contents

This repository contains the main guides and quick references for setting up modeling environments and working on HPC.

  • python_environment_setup.md — Primary install and environment guide (Miniconda, conda envs, packages, NEURON, BMTK, mpi4py, CoreNEURON, verification and troubleshooting).

  • hellbender_hpc_guide.md — Hellbender HPC quick-start: OnDemand and SSH workflows, Slurm tips, and helper scripts (start_hellbender.sh, start_hellbender.ps1).

  • expanse_hpc_guide.md — Expanse HPC quick-start: SSH access, VS Code setup, Slurm job submission, and environment modules.

  • lab_server_guide.md — Lab server quick-start: SSH access, VS Code setup, and environment modules.

  • globus_guide.md — Globus data transfer guide: Account setup, managed endpoints, personal endpoints, and collections for lab and Hellbender.