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.
It should be noted that 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
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Getting started with paraSBOLv - This provides a basic introduction to the
paraSBOLVlibrary and the core data types of functions available. It is recommended that this is used together with the examples gallery. -
Creating parametric SVG glyph files - If you are looking to create new parametric glyphs to use with this library then this provides an overview of the core elements that need to be added. If you are creating a new glyph that you think others in the synthetic biology might find useful, please consider also submitting to the SBOL Visual standard.
To inspire you to make your own tools, we created some simple plotting tools using paraSBOLv as a convenient foundation.
genbank2sbolv - visualises the coding regions within a GenBank file.
sbolv-cli - streamlined CLI version of paraSBOLv for rapid generation of designs from the command line.
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", Synthetic Biology, 2021 doi:10.1093/synbio/ysab022