How can we best use Cytoscape for proteomics data analysis?

[marclegeay]

Abstract

Cytoscape is an open-source software to visualize and analyze biological networks. Developers can add new features to Cytoscape by developing their own Java-based apps by utilizing the Cytoscape API. An example for such an app, developed in our group, is the stringApp. It can be used to retrieve and analyze STRING networks in Cytoscape in order to analyze long lists of genes or proteins resulting from high-throughput experiments such as proteomics (Doncheva et. al. 2019). The stringApp has been downloaded more than 50 000 times since its first release in 2015. Recently, we also released the OmicsVizualizer app, which further aids the stringApp in omics data visualization with a special focus on analyzing phosphoproteomics data.
During the hackathon, we would like to discuss usability of Cytoscape and corresponding apps for the proteomics community and brainstorm for new features of the existing apps or new apps that could be developed during the meeting. If you do not know how to develop a Cytoscape app, we could train you on this point.
The Cytoscape community also maintains a REST API that enables Cytoscape and most of its apps to be used from R and python in a more automated way. We would like to also discuss how this API could be used for the automation of proteomics analysis workflows.
The developed apps could be released in the Cytoscape App store and published in the F1000 Cytoscape channel.

Work plan

• Introduction to Cytoscape and major apps with potential use in proteomics
• Short tutorial on Cytoscape automation
• Short tutorial on how to develop a Cytoscape app
• Brainstorming about what features and apps are missing and if they could be implemented
• Brainstorming about how to use Cytoscape in R or python workflows to improve proteomics data analysis

Technical details

Programming languages are R or python for the pipeline scripting, Java for the app development. Knowledge of Cytoscape can be beneficial, but is not required or expected.

Contact information

Nadezhda T. Doncheva
Novo Nordisk Foundation Center for Protein Research
Center for non-coding RNA in Technology and Health
University of Copenhagen
Denmark
nadezhda.doncheva@cpr.ku.dk

Marc Legeay
Novo Nordisk Foundation Center for Protein Research
University of Copenhagen
Denmark
marc.legeay@cpr.ku.dk

[scaramonche]

In this project, we suggested two different directions in which one can use Cytoscape for proteomics data analysis:

1. working on a (new) app for Cytoscape or
2. automation of analysis

We would like to encourage participants to comment here if they are rather interested in 1) or 2) or both.

[marclegeay]

The gitHub repository for this project: https://github.com/scaramonche/EuBIC2020_Cytoscape