Network Visualiser SynBio

A tool focused on visualising common data within Synthetic Biology projects via a network-centric view.

• Tailor the representation based on your requirements.
• Share data with a multi-disciplined team.

Get Started

Dependencies

NV-SB requires Python 3.x. and Python package dependencies are listed in requirements.txt.

Install

1. Download or clone repository. git clone https://github.com/intbio-ncl/net_vis_syn_bio
2. Navigate to your install directory
3. Install dependencies with python -m pip install -r requirements.txt

Example usage

1. To visualise genetic designs:

   • Valid Files:
     • SBOL (Recommended)
     • GBK.
   • To execute: python run.py <filename>
   • To View: Open browser and enter: http://127.0.0.1:5000/design/

2. To visualise build protocols:

   • Valid Files:
     • Autoprotocol (Recommended)
     • OT2 Script.
   • To execute: python run.py <filename> -t protocol
   • To View: Open browser and enter: http://127.0.0.1:5000/protocol/

Loading the application

To see an exhaustive list of inputs: python run.py -h

Using the application

• Once the application is loaded, all commands are located on the left of the screen.
• A help button is located below the title, which provides information on a given command.
• An advanced input button is located next to the help button, allowing for more control over layouts.
• Below are views - selecting specific information within a large dataset to provide a predefined perspective.
• Below are the layouts - Provide nodes with spatial coordinates. Note: Node positions can be manually changed by dragging individual nodes or groups of nodes with CTRL + click.
• Data can be exported as a static image (PNG, JPG or SVG) or as standard graph formats such as GML, GEXF, graphml.
• All remaining options are purely visual manipulations focused on highlighting attributes.