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Getting Started with Talapas

We can run these notebooks on Talapas using OpenOnDemand. Point your browser to https://talapas-ln2.uoregon.edu, and login using your talapas credentials.

  1. First checkout this package. In the top bar select clusters Talapas Shell Access, and type

git clone https://github.com/jsearcy1/racsml.git

and close the window.

  1. Launch a Jupyter Session. In the top Naviagation Bar click on Interactive Apps, and select Jupyter Notebook (Python3/Tensorflow). You should end with a form looking like:

alt text

Add the account you would like to run with, and click launch. Wait until your job starts, and connect. Navigate to racsml/notebooks and open Introduction.ipynb.

Getting Started with Docker

  1. Make sure you have Docker installed https://www.docker.com/get-started
  2. Clone repository in a terminal git clone https://github.com/jsearcy1/racsml.git
  3. switch to the created directory cd racsml
  4. Build the docker image docker build $PWD -t racsml
  5. At this point you should be able to see a docker image named racsml
docker images

REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
racsml              latest              885ada57256a        27 minutes ago      1.79GB
python              3.7                 4c0fd7901be8        46 hours ago        929MB
  1. Run the image
docker run -it -p 8888:8888 racsml
    
    To access the notebook, open this file in a browser:
        file:///root/.local/share/jupyter/runtime/nbserver-7-open.html
    Or copy and paste one of these URLs:
        http://(2e818c6cf771 or 127.0.0.1):8888/?token=d8ceec90df55c0a6cd2ab41669c3e8af5698f74f7904e2f4
  1. Point your browser to http://127.0.0.1:8888/ and you'll be asked to login with the token listed in the output of the run command just after the ?token= in the case above it's d8ceec90df55c0a6cd2ab41669c3e8af5698f74f7904e2f4

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Workshop for Biomedical Image Analysis with Convolutonial Neural Networks

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