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Code to accompany the paper: ”ProteinNetworkSight efficiently transforms co-expressed protein lists into interactive networks and offers suggestions for their modifications”

Files

routes.py

This file contains the Flask routes and API endpoints for the application.

src/

This folder contains various modules and functions used by the Flask application.

src/validate.py

This file contains the cal_string_id function used in the /api/validate route to validate a name and return a matching ID.

src/graph_data.py

This file contains the make_graph_data function used in the /api/graphs route to generate nodes and links for creating a graph.

src/organism_list.py

This file contains the get_organism_list function used in the /api/organism route to retrieve a list of available organisms.

src/user_register.py

This file contains the register_user function used in the /api/user route to create a new user table.

src/names.py

This file contains the cal_string_suggestions function used in the /api/names route to provide suggestions for matching names.

Routes

  • /api/ (GET): Returns a welcome message.
  • /api/organism (GET): Returns a list of available organisms.
  • /api/names (POST): Given a list of organism names and an organism, returns a list of matching names with suggestions.
  • /api/validate (POST): Given a name and an organism, returns a matching ID.
  • /api/user (POST): Creates a new user table with provided proteins, IDs, and string names.
  • /api/graphs (POST): Given a user ID, values map, and thresholds, returns nodes and links for creating a graph.

Installation

This is not a full installation for this project some parts are left out. (like a postgres installation with the STRING DB)

This is left out due to security reasons

  1. Clone the repository.
  2. Install the required dependencies (e.g., Flask, Flask-CORS).

Execution

  1. Navigate to the project directory.
  2. Run the Flask application with python routes.py.
  3. The server will start running on http://0.0.0.0:3000.

Data

The application likely uses some data sources or databases to retrieve information about organisms, proteins, and their interactions. The specific data sources are not included in the provided code.