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A HDDM docker image

This is dockerHDDM github repo hddm:1.0.1: Python 3.9, HDDM 1.0.1. This version is a more versatile version compatible for both amd64 and arm64.

In the OfficialTutorial folder, you can look for official jupyter notebooks from HDDM that have been tested and verified to work.

The dockerHDDM_Quick_View.ipynb and dockerHDDM_Workflow.ipynb are new notebooks using new functions from dockerHDDM (more details see dockerHDDM paper).

Report issues

If you have any problem in using this docker image, please report an issue at the github repo

How to cite us

If you used this docker image in your research, please cite Wiecki et al 2013 and our preprint:

Pan, W., Geng, H., Zhang, L., Fengler, A., Frank, M., ZHANG, R., & Chuan-Peng, H. (2024). dockerHDDM: A user-friendly environment for Bayesian Hierarchical Drift-Diffusion Modeling. Advances in Methods and Practices in Psychological Science. preprint: https://doi.org/10.31234/osf.io/6uzga

How to use this docker image

First, make sure you have successfully installed and started docker. you can find very user-friendly instructions on the official Docker website.

Second, pull the docker image from docker hub:

docker pull hcp4715/hddm:1.0.1

Third, run the docker image with the following command:

docker run -it --rm\
-v $(pwd):/home/jovyan/work \
-p 8888:8888 hcp4715/hddm:1.0.1 jupyter notebook
  • -v $(pwd):/home/jovyan/work allows you to mount the current working directory to the docker container.
  • you can change the $(pwd) to any directory (e.g., "D:/hddm" in Windows) you want to mount to the docker container.
  • Note, for Windows users, $(pwd) only work in Powershell other than cmd.exe.

Finally, open your browser and go to the following URL （After running the code above, bash will has output like this）:

....
....
To access the notebook, open this file in a browser:
        file:///home/jovyan/.local/share/jupyter/runtime/nbserver-6-open.html
Or copy and paste one of these URLs:
    http://174196acc395:8888/?token=75f1a7a8ffcbb55f0c2802433a9a5d57ac00868e05089c09
 or http://127.0.0.1:8888/?token=75f1a7a8ffcbb55f0c2802433a9a5d57ac00868e05089c09
  • Copy the full url (http://127.0.0.1:8888/?token=.......) to a browser (firefox or chrome) and it will show a web page, this is the interface of jupyter notebook! Note, in Windows system, it might be localhost instead of 127.0.0.1 in the url.
  • The jupyter notebooks (e.g., dockerHDDM_Workflow.ipynb) mentioned above also exists in the Jupyter interface.

External Resources

Youtube Video Tutorial

dockerHDDM installation and usage guide | cognitive modeling | RT modeling | tutorial

Bilibili Video Tutorial

dockerHDDM安装和使用介绍视频

How this docker image was built

We also provide a Dockerfile at root path to build the customized docker image.

We built this docker image under Ubuntu 22.04. This Dockerfile is modified by Dr. Rui Yuan @ Stanford, based on the Dockerfile of jupyter/scipy-notebook. We installed additional packages for HDDM. See Dockerfile for the details

Code for building the docker image (don't forget the . in the end):

docker build -t [username]/hddm:[tag] -f Dockerfile .
  • [username] is your username on Docker Hub.
  • [tag] is docker images tag, e.g., latest or 1.0.1.

Acknowledgement

Thank @madslupe for his previous HDDM image, which laid the base for the current version.

Thank Dr Rui Yuan for his help in creating the Dockerfile.

We would like to express our gratitude to the HDDM package for providing the dataset cavanagh_theta_nn.csv as an example in our study. Please note that this dataset is not owned by us and is used for illustrative purposes only. For reference, the dataset can be found at HDDM GitHub repository.