Open in Cytoscape Web

Open in Cytoscape Web is a Cytoscape App that opens a selected network in Cytoscape Web

NOTE: This service is experimental. The interface is subject to change.

Publication

Coming soon...

Requirements to use

• Cytoscape 3.10 or above
• Internet connection to allow App to connect to remote services

Installation via from Cytoscape

TODO

Requirements to build (for developers)

• Java 17 with jdk
• Maven 3.9 or above

To build documentation

• Make
• Python 3+
• Sphinx (install via pip install sphinx)
• Sphinx rtd theme (install via pip install sphinx_rtd_theme)

Building manually

Commands below assume Git command line tools have been installed

# Can also just download repo and unzip it
git clone https://github.com/idekerlab/open-cyweb

cd webbymcsearch
mvn clean test install

The above command will create a jar file under target/ named open-cyweb<VERSION>.jar that can be installed into Cytoscape

Open Cytoscape and follow instructions and click on Install from File... button to load the jar created above.

Building documentation

Documentation is stored under docs/ directory and uses Sphinx & Python to generate documentation that is auto uploaded from master branch to Read the docs TODO

# The clone and directory change can be
# omitted if done above
git clone https://github.com/idekerlab/open-cyweb

cd open-cyweb
make docs

Once make docs is run the documentation should automatically be displayed in default browser, but if not open docs/_build/html/index.html in a web browser

COPYRIGHT AND LICENSE

Click here

Acknowledgements

• TODO denote funding sources