POINT

Protein Ortholog Interaction Neighbourhood Tool is an HTML/JS tool to visualize pairs of proteins and the orthology relationships between their interactomic neighbours.

Getting Started

Due to web browser security restrictions, POINT must be deployed over a web server.

Prerequisites

POINT can be used in any modern web browser, though it has only been tested extensively in Firefox.

Java 8 is required to execute included POINT source code to generate files for specific proteins not included in the examples.

Due to web browser security restrictions, POINT must be deployed over a web server. If you do not have a web server already set up, you can set one up easily using Python. You can download and install Python, 2 or 3, at http://www.python.org.

Instructions

Utilizing POINT:

1. Open a command prompt.
2. Navigate to the directory were POINT was downloaded.
3. If using Python 3, enter: 
     python3 -m http.server
   If using Python 2, enter:
     python -m SimpleHTTPServer
4. Open a web browser and access POINT at http://localhost:8000/web/test.html
5. Open a POINT JSON file using the available dialog.

To generate new POINT JSON files:

1. Compile the Java files included in /java
2. Run core.JsonTest with four arguments: 
     species-of-interest-1 protein-of-interest-1 species-of-interest-2 protein-of-interest-2
3. The output JSON file will be placed in web/json/

Data Sources

Included with POINT are the following data files:

1. Network data from iRefIndex v15.
2. Domain, sequence, orthology, and identifier data from Ensembl v89.
3. Orthology data from Homologene and OrthoMCL downloaded c. May 2017.
4. The Molecular Interactions Controlled Ontology downloaded c. May 2017.
5. SH3 interaction data from the Bader Lab.

Users may wish to update these data sources at their own discretion. There is source code provided to utilize BioGRID network data in Networks.java, which can be toggled in Constants.java.

Built With

• Cytoscape.js
• Cytoscape Context Menus
• JSColor - Modified under the GNU Public License 3.0 from version 2.0.5, c. 2018.

Authors

• Brian Law - Primary developer
• Gary D. Bader - Supervisor

License

This project is made available under the GNU Public License 3.0.