https://github.com/logan169/egnize
EGN web server for Network analysis and visualisation
https://github.com/logan169/egnize
angularjs egn flask flask-server full-stack interactive-visualizations network-analysis perl python-2 sigmajs visualization
Last synced: about 2 months ago
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EGN web server for Network analysis and visualisation
- Host: GitHub
- URL: https://github.com/logan169/egnize
- Owner: logan169
- License: gpl-3.0
- Created: 2017-05-12T16:54:58.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2017-05-12T20:21:38.000Z (about 9 years ago)
- Last Synced: 2025-01-11T20:39:17.215Z (over 1 year ago)
- Topics: angularjs, egn, flask, flask-server, full-stack, interactive-visualizations, network-analysis, perl, python-2, sigmajs, visualization
- Homepage:
- Size: 4.08 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# EGNize
## EGN web server for Network analysis and visualisation
EGNize is a fullstack web application (Python2/AngularJS) based on an encapsulated modified version of
[EGN](https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-146) (Perl). It allows users to create networks (based on gene and genome similarities) and visualize them through an
interactive visualization tool (SigmaJS).
As analyzing data could take some times (depending on dataset size), a mail server was implemented to keep user
informed of analysis status and send output files directly to user mail when done.
Output files produced by EGNize could then either be visualized directly using EGNize's interactive visualization tool or any
other network analysis software (Cytoscape or Gephi).
The visualisation tools are highly customizable to anyone that would like for example to associate keyboard/mouse inputs in order to display any kind of metrics over a color gradient.
#### Actual available interaction are :
- Mouse wheel => zoom in and zoom out
- Click and hold => slide throught the network
- Right click on a node => display gene/genomics similarities with neighbours nodes represented with a color gradient
- Left click on a node => display only nodes sharing similarities with it
- Double click anywhere => reset to default display where nodes are colored according to the biological group they belong
For more information about EGNize, please read appDescription.pdf and EGN User Guide.pdf.
If you have any questions send a mail to
#### Dependencies
- Python 2
- Flask
- Flask mail
- Blast (should be executable through terminal)
### Initialization
#### To launch the server (Back-end)
After installing dependencies, and editing mail account information in config.py, type the following commands from 'egn_server' folder:
$ chmod +x launch_srvr.py
$ ./launch_srvr.py
#### How to use it (Front-end)
Once the server is up, type URL displayed in the terminal (after executing the last command) in your browser's URL bar.
Per default, it should be but may change depending on your flask configuration.
##### Create a network
Once connected, click on 'new analysis' in the top right corner and fill up inputs form and upload your .faa input file.
Please refer to EGN documentation for input value.
- Don't forget to enter your mail address to get back your zip archive (containing all outputs files) when the analysis is done.
- Be aware that starting several runs (with different parameters) on the same input file will return a zip archive that also contains all previous outputs analysis from same input file.
##### Visualize a network
After receiving the zip archive, reconnect to EGNize page, click on the "load a network" button and upload a json or gexf file.
After clicking on ok, modal window should close and visualization tool should display your network.
Report to the 'Actual available interaction' section above for possible interactions.
#### Example pictures
