A lightweight Python library designed to simplify the rendering of highly-customisable SBOL Visual glyphs and diagrams. To do this, paraSBOLv uses the Parametric Scalable Vector Graphic (pSVG) format to enable the encoding of the shape geometry and allowed parametric variations for each glyph. The best way to learn how to use paraSBOLv is to dive into our gallery of examples which cover most of the capabilities present. In addition, all functions and classes are extensively documented in code to allow usage to be easily inferred.
We are regularly asked about the relationship of parasbolv and another genetic design visualisation tool we have developed called dnaplotlib. The major difference between the two packages is that parasbolv is designed to be lightweight, include minimal additional functionality, and be tailored to tool developers to provide them with low level access to the rendering of SBOL Visual glyphs and interactions. In contrast, dnaplotlib is designed to provide a much fuller and wider range of functionalities to both developers and biologists.
As a note, dnaplotlib version 2.0, which is currently under development, will completely replace its legacy rendering pipeline with paraSBOLv. This will not only simplify maintenance, but also allow access to new glyphs ratified by the SBOL community as they become available.
paraSBOLv does not require any other dependancies when installed. However, internally it does make use of the svgpath2mpl package to handle the generation of matplotlib compatible paths from an SVG path string. Do check this package out if you'd like to know more about using SVG with matplotlib.
The easiest way to start playing with parasbolv is to clone this repository and place the parasbolv directory into you PYTHONPATH environment variable. Once done, it should be possible to then:
import parasbolv as psv
Automatically generated documentation can be accessed at: https://biocomputelab.github.io/paraSBOLv/index.html
To inspire you to make your own, we created some simple plotting tools using paraSBOLv as a convenient foundation.
plot_gff - converts .gff files to SBOLv designs.
genbank2sbolv - converts .gb files to SBOLv designs.
sbolv-cli - streamlined CLI version of paraSBOLv for rapid generation of designs
If you use this tool to create diagrams or as a basis for new software please cite the following paper. Without citations that demonstrate use it becomes difficult to support this tool.
Clark C.J., Scott-Brown J. & Gorochowski T.E. "paraSBOLv: a foundation for standard-compliant genetic design visualisation tools" (in prep.)