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Begin by starting the App as described in the section Creating an Application. Select the DICOM Viewer application.
Step 1: Connect to the application
Enter the USERNAME and VNC_PW you have been provided
Press the Login button
Wait for the app to respond
Step 2: Use OHIF functionality
Click the Firefox icon and browse to localhost:3000
At this point you will be prompted for your Google user ID.
Click Next.
Google may prompt you to choose the account you wish to proceed with. If prompted, use the account with which you logged in to the App Store
Click Next.
Enter your password. The browser will ask if you want to save the password. It doesn’t matter if you do or not
Respond to the 2 step authentication. If you haven't used it before, you may be prompted to set up the 2 step authentication.
You should now see the basic OHIF screen with a large selection of projects.
Step 3: Browse to The example Data Set
Select helx-dev
Select the northamerica- northeast1 region
Select the DicomTestData dataset
Select the TestData Dicom Store
You should now see our test datasets. Chose your test data set and have fun!
On this page you will find guides for testing the CloudTop Docker, the CloudTop OHIF Docker, and the CloudTop ImageJ/Napari Docker.
Begin by starting the App as described in the section Creating an Application. Select the CloudTop Viewer application.
Step 1: Run the CloudTop Docker.
USER_NAME and VNC_PW can be whatever you want: those are the authentication info you will need to log in for Step 2. Change the tag to whichever tag you want to test.
Step 2: Connect to the running docker
Browse to localhost:8080
Enter the USERNAME and VNC_PW you specified when starting the Dockerfile
Press the Login button
Wait for Guacamole to respond
Step 3: Make sure the home directory is OK
Start a terminal emulator from the applications menu. In the resultant shell, type
You should see /home/USER_NAME where USER_NAME is the user name specified in Step 1
Note the presence of the Firefox browser icon
At this point the basic CloudTop functionality is working.
Step 1: Run the CloudTop OHIF docker:
where OUR_CLIENT_ID is found in the file.
google_health.env file in the renci_data_stage directory of our keybase account. USER_NAME and VNC_PW can be whatever you want: those are the authentication info you will need to log in for Step 2. Change the tag to whichever tag you want to test.
Step 2: Connect to the running docker
Browse to localhost:8080
Enter the USERNAME and VNC_PW you specified when starting the Dockerfile
Press the Login button
Wait for Guacamole to respond
Step 3: Make sure the home directory is OK
Start a terminal emulator from the applications menu. In the resultant shell, type:
You should see /home/USER_NAME where USER_NAME is the user name specified in Step 1
Note the presence of the Firefox browser icon
At this point the basic CloudTop functionality is working.
Step 4: Test the OHIF functionality
Exit the terminal emulator by typing “exit”
Click the Firefox icon and browse to localhost:3000
At this point you will be prompted for your Google user ID.
Click Next.
Google may prompt you to choose the account you wish to proceed with. If prompted, pick your G Suite account.
Click Next.
Enter your password. The browser will ask if you want to save the password. It doesn’t matter if you do or not
Respond to the 2 step authentication. If you haven't used it before, you may be prompted to set up the 2 step authentication.
You should now see the basic OHIF screen with a large selection of projects.
Step 5: Browse to Your Data Set
Select helx-dev
Select the northamerica- northeast1 region
Select the DicomTestData dataset
Select the TestData Dicom Store
You should now see our test datasets. Chose your test data set and have fun!
Step 1: Start the Docker
Start the docker with the following command:
where USER_NAME and VNC_PW can be whatever you want: those are the authentication info you will need to log in for Step 2. Change the tag to whichever tag you want to test.
Step 2: Connect to the running docker
Browse to localhost:8080
Enter the USERNAME VNC_PWyou specified when starting the Dockerfile
Press the Login button
Wait for Guacamole to respond
Step 3: Make sure the home directory is OK
Start a terminal emulator from the applications menu. In the resultant shell, type:
• You should see /home/USER_NAME where USER_NAME is the user name specified in Step 1
• Note the presence of the ImageJ, Napari and Firefox browser icon. If any are missing the test fails.
At this point the basic CloudTop functionality is working. Next we will want to verify that ImageJ and Napari are working
Step 4: Make sure the ImageJ application launcher works correct
Exit the terminal application and click the ImageJ icon. There is no ImageJ test data included in the docker.
Exit ImageJ and make sure the Napari application launcher works correctly.
The docker does not contain any test data. The docker test is now complete.
Exit Napari and stop the docker.
Begin by starting the App as described in the section Creating an Application. Select the Nextflow API application.
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.
Step-1:
Launch a Nextflow API by clicking on the "New Application" button on the app manager page on HelX.
Step-2:
This brings us to the Nextflow API home page, where we can view the launched workflows and create new workflows.
Step-3:
Below is a demo of how to launch a systemsgenetics/kinc workflow. Click on "Create Workflow" button and fill in the form to give it a "Name" and specify the Pipeline (in this case systemsgenetics/kinc-nf).
Step-4:
Uploading the necessary files, a GEM file in the format "*.emx.txt" and a nextflow.config file(can upload all files at once). Click on "Upload" button.
Step-5:
Now we are all set to launch the workflow. Go ahead and click on "Launch" button. This should show all the logs of the processes/jobs running in the background on the Kubernetes cluster.
Begin by starting the App as described in the section Creating an Application. Select the Jupyter Datascience application.
Jupyter/datascience includes popular packages for data analysis from the Python, Julia and R communities and also packages are included from its ancestor images jupyter/sci-py notebook, jupyter/r-notebook and jupyter/minimal-notebook.
Some of the packages it includes are,
dask, pandas, numexpr, matplotlib, scipy, seaborn, scikit-learn, scikit-image, sympy, cython, patsy, statsmodel, cloudpickle, dill, numba, bokeh, sqlalchemy, hdf5, vincent, beautifulsoup, protobuf, xlrd, bottleneck, and pytables packages
ipywidgets and ipympl for interactive visualizations and plots in Python notebooks.
Facets for visualizing machine learning datasets.
The Julia compiler and base environment.
IJulia to support Julia code in Jupyter notebooks.
HDF5, Gadfly, and RDatasets packages.
Begin by starting the App as described in the section Starting An Existing App. Select the Jupyter-DataScience application.
Step-1:
Launch a jupyter-datascience notebook from HeLx by clicking on “Launch Application” button.
Step-2:
This brings us to the jupyter-lab panel where we can select the environment that we want to work on (Python, Julia, R).
Step-3:
Start working on it. Below code shows loading iris dataset (features, labels) from sklearn package to train/test our machine learning model.
1. Get a REDCap account for a project URL and API key
if you don’t have an account contact Adam Lee to get one
if you have an existing account use the credentials associated with it
2. Go to https://reccap.cloudapps.unc.edu/accounts/login
3. Click “New Application” and choose Blackbalsam Clinical
4. Click on “black balsam” folder and then click on RedCapAPIRDemo.ipynb
5. In the notebook, on cell 2 substitute REDCap URL and API key with your credentials
6. Run first three cells in the notebook
7. To export records, use show_forms, show_fields, or show_all_records cells
Go to https://reccap.cloudapps.unc.edu/accounts/login and login.
Click on “New Application”, choose Blackbalsam Clinical then click "Create Application".
3. Click on the "blackbalsam" directory and then launch the RestartrApiDemo.ipynb notebook.
4. In cells 3 to 6 substitute your api-key here "<put-api-key>".
5. Run the first two cells in the notebook.
The first cell imports the required dependencies.
The second cell is where data can be formatted to insert into mongodb.
6. Run the third cell to persist data into mongodb.
This cell will call the observation api and insert data into mongodb.
Upon a successful call it will return an id, for example {"id": "\"5f355dd39e55e62921768dec\""}.
7. To query the data use, query by "_id", query by sub-field, or just use query methods provided in the RestartrApiDemo.ipynb notebook.
Coming soon.
Begin by starting the App as described in the section Creating an Application. Select the ImageJ-Napari application.
Coming soon.
