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.
NV-SB requires Python 3.x. and Python package dependencies are listed in requirements.txt.
- Download or clone repository.
git clone https://github.com/intbio-ncl/net_vis_syn_bio - Navigate to your install directory
- Install dependencies with
python -m pip install -r requirements.txt
-
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/
- Valid Files:
-
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/
- Valid Files:
To see an exhaustive list of inputs: python run.py -h
- 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.