Cytoscape Product Roadmap

Introduction

Cytoscape was initially released in 2002, and has undergone numerous development sprints. The most recent major sprint ended in 2014 with the release of Cytoscape v3, which refactored major internal data models and greatly improved support for third party plugin applications (via the App Store, semantic versioning disciplines, published APIs, and code management via OSGi).

Since v3, we have focused on addressing outstanding bugs and upgrading a number of user-facing features, including visual styles (VizMapper), fast node filtering, network capacity, and overall speed and UI consistency. The Cytoscape app developer community has upgraded a number of v2 plugins into v3 apps, and has contributed a steady stream of new apps (apps.cytoscape.org).

As of late 2023, our efforts have been rewarded, as Cytoscape has become more popular than ever – 20,000 downloads per month worldwide.

This page explains our roadmap for future deliveries and activities. Feel free to contribute to this discussion our community and user documentation pages.

Cytoscape is going down a number of roads simultaneously:

• Cytoscape Desktop
• Cytoscape Expansion to the Cloud
• Cytoscape Community Outreach

This page describes the Cytoscape Desktop roadmap and inroads into the wider Cloud Ecosystem.

Vision: Cytoscape Automation

Cytoscape has traditionally relied on the Cytoscape Apps mechanism for defining and delivering novel calculations and workflows, and the Cytoscape App Store has proven successful at collecting and disseminating them. We are developing Cytoscape Automation features to enable the Cytoscape community to economically create novel workflows using state of the art tools such as Python/Jupyter, R/RStudio and GenomeSpace while leveraging their feature rich libraries and web presence.

Cytoscape Automation will enable users to create workflows executed entirely within Cytoscape or by external tools, and whose results are reproducible. This will enable Cytoscape to scale to large collections of datasets and to larger more complex workflows than is practical via keyboard and mouse.

Cytoscape Automation will exist in two skins – the Commands interface and the Functions interface. Both will accomplish similar results, but will be focused on different usage styles. Commands will reprise user-initiated interactions (e.g., open session, import data, export image), whereas the Functions interface will enable programmers to manipulate and operate on networks as internal Cytoscape data. Commands and Functions will both available via a REST interface.

Under the Cytoscape Automation vision, all new and many existing apps will be upgraded to respond to REST calls. Additionally, most Cytoscape core functions will be exposed via REST calls. In the ideal, all Cytoscape functionality will become controlable from outside workflow systems.

For more information on Cytoscape Automation, consult the Cytoscape Automation wiki.

Vision: Cytoscape Core and Core Apps

Before v3.3, we viewed Cytoscape as consisting of the Cytoscape Core as augmented by the Cytoscape Apps. As of v3.3, we have created a middle ground: the Cytoscape Core Apps. The Core is the code that organizes, displays, reads, and writes networks but is agnostic as to network meaning or use – the Core does not contain biology-related functionality. Cytoscape Core Apps are installable modules that perform non-Core functions but are still integral to most Cytoscape usage (e.g., network biology).

Fig. 1: Cytoscape Desktop

To date, a Cytoscape release has consisted of the Core + Core Apps (Fig. 1). Beginning in v3.3, the Core Apps are available individually in the App Store, though they are all installed with the Core when Cytoscape is installed. However, unlike previous Cytoscape versions, Core Apps are upgradable without releasing all of Cytoscape. (For example, bugs can be fixed or features can be added to the Network Merge at any time.) This enables the Cytoscape team to upgrade specific features much more quickly than in the past.

A close cousin to Core Apps is the App Store concept of Collections, which are bundles of apps that apply to a particular workflow. Installing a Collection causes the installation of all apps in the Collection. From time to time, we will add new Collections or add to existing Collections.

As Cytoscape use cases evolve, we expect to add Core Apps to the Cytoscape release, thereby packaging advanced functionality useful in common workflows. The criteria for promoting an app to a Core App is ultimately decided by the Cytoscape Core developers, but includes:

• Availability in the App Store and intensive evaluation of requirements, proper targeting and other feedback over a period of at least six months
• Assessment and agreement by Cytoscape Core developers
• Realistically maintainable by multiple developers
• Minimal (or no) biological domain-specific semantics

Additional criteria include:

• How much other apps or workflows depend on it
• Value in driving user behavior to achieve higher productivity
• Incremental size contributed to Cytoscape installer
• Specific maintenance plan (including maintainability by core developers)
• Open source and in Cytoscape github repository
• Expected size of interested user community
• Appeal as compared to existing alternatives
• Evaluation of usability and stability
• Existence of high quality documentation and tutorials

Vision: Key Workflows

A top priority for Cytoscape development is to enable efficient execution of new and existing key workflows, including:

• Cytoscape Main (core network analysis)
• Functional enrichment analysis
• Network analysis of proteomics data
• Pathway analysis of gene expression data

Functionality that implements the Core Apps feature is used to enable the user to customize Cytoscape quickly and easily to implement various workflows. Using a Collection (i.e., an app that represents multiple apps), the user can install all apps needed to execute the Functional Enrichment workflow.

Vision: Themes and Features