CellNEST-Interactive

CellNEST-Interactive is an interacive exploration tool for CellNEST output.

Zoom and pan exploration

Ligand-Receptor pair filtering

Vertex (spot or cell) color changing

Communication color changing

Increase range of reliable signals

Python package dependencies:

django
numpy
scipy
matplotlib
pandas
altair
django-cors-headers

Required preprocessed metadata and output files from the CellNEST model

We need the following five files:

1. cellbarcode*.csv file generated by CellNEST in the data preprocessing step.
2. coordinates_*.csv file generated by CellNEST in the data preprocessing step.
3. *_self_loop_record.gz file generated by CellNEST in the data preprocessing step.
4. Optional *_annotation.csv file, if available.
5. CellNEST_*_top20percent.csv file generated by CellNEST in the data postprocessing step.

Keep these five files under the same directory and use that directory path (e.g., server/data/files/ ) while running the interactive version as explained below.

Instructions to run CellNEST-Interactive:

Navigate into the pulled cellnest_interactive directory. Please run the following command with two arguments:

1. Desired port to run the frontend, e.g., 8080
2. Path to the directory having CellNEST output and required metadata files, e.g., barcode, coordinates, etc.

A sample command is provided below:

bash cellnest_interactive 8080 server/data/files/

However, if you are interested to run the frontend and backend separately, you can follow the instructions below.

Frontend:

1. If VSCode is installed, adding the "Live Server" extension from Ritwick Dey makes spinning up a server easy. Access the server hosted at http://127.0.0.1:5500/HTML%20file/CellNEST-vis.html
2. Otherwise
   • Run python -m http.server 8080 from the root directory
   • Open http://localhost:8080/ and navigate to "HTML file" then "CellNEST-vis.html"
   • Server should be hosted at http://localhost:8080/HTML%20file/CellNEST-vis.html

Backend:

• Navigate into the server directory (cd server)

• Install pipenv

• Run pipenv shell then pipenv install

  • The required packages that are installed:

  django
  numpy
  scipy
  matplotlib
  pandas
  altair
  django-cors-headers
  

• Run cd ..

• Run python ./server/manage.py setdata server/data/files/

• Run python ./server/manage.py runserver