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
• X11 display (or xvfb-run on headless Linux) — tests use java.awt.Desktop which requires a display

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 open-cyweb
make install

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

Code Formatting

This project uses Spotless for code formatting and import organization.

Format your code manually:

# Format all Java files and organize imports
mvn spotless:apply

Check code formatting:

# Verify code is properly formatted (fails if not)
mvn spotless:check

Note: The build process automatically runs spotless:check during the verify phase. If your code is not properly formatted, the build will fail. Run mvn spotless:apply to fix formatting issues before committing.

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