VISPER - Visualization System for Interactions between Proteins and Drugs for Exploratory Research

Our platform provides an immersive experience for exploring and analyzing a segment of the dataset from Gonçalves et al.. With a primary focus on identifying associated proteins and drugs for individual or groups of proteins, VISPER offers comprehensive tools for in-depth research.

This repository contains the code for the Visualization System for Interactions between Proteins and Drugs for Exploratory Research(VISPER). To use VISPER locally on your PC, we recommend using the Docker version of VISPER. For detailed instructions, see the Docker installation instructions.

If you would like to access the code, please contact the authors at [email protected].

Video Tutorials

Exploration of significant associations between drug responses and protein measurements

Finding information about specific drug-protein associations and pathways of interest

Interactive Graphs

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Docker

1. Install Docker Desktop
2. Optional: Restart your pc after the installation
3. Download the docker-compose.yml from the docker folder of this repository. Important: Do not use the wrong docker-compose file!
4. Open the terminal in the folder where you placed the docker-compose.yml and run the following command:

docker-compose up

(Optional: First run docker-compose pull) This process can take some time (approximately 40 minutes). 5. Call http://localhost:7474/browser/ and execute the following Neo4j cipher (user: neo4j, password: workwork).

CREATE INDEX IF NOT EXISTS FOR (d:Drug) ON (d.name);
CREATE INDEX IF NOT EXISTS FOR (p:Protein) ON (p.name);
CREATE INDEX IF NOT EXISTS FOR (c:Cell_Line) ON (c.name);
CREATE INDEX IF NOT EXISTS FOR (d:Drug) ON (d.uid);
CREATE INDEX IF NOT EXISTS FOR (p:Protein) ON (p.uid);
CREATE INDEX IF NOT EXISTS FOR (c:Cell_Line) ON (c.uid);
CREATE INDEX IF NOT EXISTS FOR (d:Drug) ON (d.drug_id);
CREATE INDEX IF NOT EXISTS FOR (d:Drug) ON (d.CHEMBL);
CREATE INDEX IF NOT EXISTS FOR (c:Cell_Line) ON (c.COSMIC_ID);
CREATE INDEX IF NOT EXISTS FOR (p:Protein) ON (p.swiss);
CALL gds.graph.project("graph", "Protein", {PPI: {orientation: "UNDIRECTED"}});

6. The website should be running on http://localhost:3000/

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Licensed content

• DrugBank under Creative Common's Attribution-NonCommercial 4.0 International License. Link to download
• BioGRID under MIT License. Link to download
• Cell Line node picture: Image of a biology cancer cell, obtained from Iconduck and licensed under CC BY 3.0. Link to image
• Spider picture: Modified image of bug spider 2, sourced from Iconduck and licensed under CC0. Link to image