Porting and using PanGIA for Cytoscape 3: challenges and solutions

Area of Science:

• Bioinformatics
• Computational Biology
• Systems Biology

Background:

• Cytoscape functionality relies heavily on third-party add-ons (plugins in Cytoscape 2, apps in Cytoscape 3).
• Transitioning from Cytoscape 2 to Cytoscape 3 necessitated significant porting efforts due to changes in underlying assumptions.

Purpose of the Study:

• To detail the challenges and solutions encountered while porting the PanGIA plugin to a Cytoscape 3 app.
• To highlight improvements in data analysis reproducibility achieved during the porting process.

Main Methods:

• The PanGIA plugin was converted to a Cytoscape 3 app, addressing challenges in data model transformation, concurrency, and randomization.
• New graphical user interface (GUI) features for controlling randomization were developed.

Main Results:

• The PanGIA Cytoscape 3 app successfully integrates genetic and physical interaction data analysis.
• The addition of GUI controls for randomization enhances the reproducibility of scientific analyses for users.

Conclusions:

• Porting Cytoscape 2 plugins to Cytoscape 3 apps involves surmounting technical hurdles, particularly concerning data models and concurrency.
• The PanGIA porting process yielded a more robust and user-friendly tool for analyzing and visualizing interaction data, emphasizing reproducible research.