pySBOL2 is a pure Python implementation of the SBOL 2.3.0 standard Synthetic Biology Open Language (SBOL) - an open standard for the representation of in silico biological designs. It draws from libSBOL and pySBOL.
This native Python library is intended to eventually supplant the original pySBOL based on C++ wrappers.
For developers, please see CONTRIBUTING.md.
Use pip to install pySBOL2:
pip install sbol2If you get a permission error, try using the --user flag:
pip install --user sbol2By default, pySBOL2 executes its validation and conversion with the online validator/converter. These can also be done offline using the Java JAR file packaged with the library.
Java requirements are: openjdk8 or later
Java location defaults to /usr/bin/java, and can be adjusted by setting the JAVA_LOCATION config option:
Config.setOption(ConfigOptions.JAVA_LOCATION, '/my/java/path')
This short example creates a Document, adds a ComponentDefinition to the Document, and then writes the resulting Document to an SBOL file. Other examples are in the examples directory.
import sbol2
doc = sbol2.Document()
cd = sbol2.ComponentDefinition('cd1')
doc.add(cd)
doc.write('my-sbol.xml')
The unit tests are not included when installing via pip. The unit tests are included in the source distribution. To access and run the unit tests without checking out from git, download the source distribution, unpack it, and run the unit tests.
pip download --no-binary sbol2 sbol2
tar zxf sbol2-VERSION.tar.gz
cd sbol2-VERSION
python3 -m unittest discover testFull documentation for pySBOL2 is available here.
Development of this library has been supported by the DARPA Synergistic Discovery and Design (SD2) program and Raytheon BBN Technologies.
