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washu_ris_tools

Dockerfiles and documentation for use with the WashU RIS Compute platform

https://github.com/Brain-Development-and-Disorders-Lab/washu_ris_tools

Science Score: 52.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization brain-development-and-disorders-lab has institutional domain (sites.wustl.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.9%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Dockerfiles and documentation for use with the WashU RIS Compute platform

Basic Info
  • Host: GitHub
  • Owner: Brain-Development-and-Disorders-Lab
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 34.2 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

RIS Guides

A collection of Dockerfiles, documentation, and other scripts used on the WashU RIS Compute platform.

Dockerfiles

  • CaImAn: Docker image and scripts for using the CaImAn tool on RIS.

  • cisTarget: Docker image and scripts for using the createcisTargetdatabases tool on RIS.

  • DeepLabCut: Docker image and scripts for using DeepLabCut on RIS, making use of GPUs. Updated from rob-the-bot/washu_hpc. Includes: updated DEEPLABCUT.yaml conda environment that works alongside the Docker image; job_deeplabcut.sh script to execute from $HOME directory; and train.py for long jobs submitted outside the general-interactive job queue.

  • RStudio: Docker image and scripts for using the RStudio application on RIS.

  • SCENIC+: Docker image and scripts for using the SCENIC+ Python library with Jupyter Notebook on RIS, making use of GPUs.

Documentation

  • Transferring Data: Guidance on how to use the rclone tool to transfer large files and folders between RIS and Box.

License

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Issues and Feedback

Please contact Henry Burgess <henry.burgess@wustl.edu> for all code-related issues and feedback.

Owner

  • Name: Brain Development and Disorders Lab
  • Login: Brain-Development-and-Disorders-Lab
  • Kind: organization
  • Email: corpuscallosumresearch@wustl.edu
  • Location: United States of America

Brain Development and Disorders Lab at Washington University School of Medicine, Department of Neuroscience, St. Louis MO

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use any of these Docker images, please cite them as below."
authors:
- family-names: "Burgess"
  given-names: "Henry"
  orcid: "https://orcid.org/0000-0002-3481-952X"
title: "<Name of Docker image>"
version: 1.0.0
date-released: 2024-03-19
url: "https://github.com/Brain-Development-and-Disorders-Lab/ris_docker"

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