This is the main REVIGO web server that implements the web interface and visualizations.
The Web server can be run as a command line utility on All Operating systems that .net framework supports. The Web server Service is currently only supported on Linux (as systemd service) and Windows (as native service) systems. Please enable 'IsSystemService' constant in csproj file to run the Web server as a service.
A set of precompiled databases: Gene Ontology and Species annotations, or build your own databases with RevigoGenerateDatabases command line utility.
Following JavaScript libraries: JQuery, JQuery-UI (with Accordion, Button, Tabs, Dialog, Datepicker, Selectmenu and Tooltip widgets), D3, X3Dom, LCSwitch and Cytoscape.
For the web statistics functionality you also need the MySqlConnector library (The 'IsWebStatistics' constant needs to be enabled in csproj file).
Optional: Install and compile with Visual Studio Code or Visual Studio for Windows.
To compile from command line:
- It is best to compile on a target OS that you are going to use, altrough, it is possible to use compiled console version with dotnet command on all systems.
- Install .NET core 8.0 from Microsoft (Install .NET for Windows, Install .NET for Linux)
- mkdir Revigo
- cd Revigo
- git clone https://github.com/rajko-horvat/RevigoCore
- git clone https://github.com/rajko-horvat/RevigoWeb
- cd RevigoWeb
- Configure 'IsSystemService' and 'IsWebStatistics' constants in RevigoWeb.csproj file
- Configure 'appsettings.json' file (rename from 'appsettings.example.json', 'appsettings.linux-example.json' or 'appsettings.Development.example.json'), specifically 'AppSettings' and 'AppPaths' section.
- Download and copy all JavaSript libraries mentioned above to 'wwwroot/js/' directory
- Copy compiled databases to 'wwwroot/Databases/' directory
- dotnet build -c Release
- For console version: run generated binary file (under RevigoWeb/bin/Release/net8.0/).
- For system service copy contents of entire directory 'RevigoWeb/bin/Release/net8.0/' to a target location. For example: 'C:\Revigo' or '/var/www/Revigo'. The Linux systemd service example is given in revigo.linux-example.service file.
- Important: the web server doesn't need any write permission on files, so they should not be modifiable by 'NetworkService' or 'www-data' user or group.
Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret.
REVIGO is a successful project to summarize long, unintelligible lists of Gene Ontology terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures.
For any further information about REVIGO project please see published paper and Frequently Asked Questions page