Keywords
Cytoscape, Automation, App, Network Biology, Network Analysis, Network Visualization
This article is included in the Cytoscape gateway.
Cytoscape, Automation, App, Network Biology, Network Analysis, Network Visualization
Cytoscape is an open source software platform for interactive analysis, integration and visualization of networks and network data1. At heart, Cytoscape provides basic network analysis functionality (e.g., network import/export, network data analysis, visualization and layout) in a menu-driven desktop format. Most importantly, it also enables and encourages users to add extensions (called apps) that deliver custom features important for specific workflows (e.g., ClueGO2 for enrichment analysis relative to various ontologies). To date, Cytoscape users can choose among over 330 apps written by over 550 authors.
In 2014, the CyREST app3 was created to allow external programs to exercise core Cytoscape functionality as part of custom workflows. By authoring such workflows in common languages (such as R and Python), users can combine the best features of Cytoscape with those available in language-specific libraries, thus creating new value much more quickly and cheaply than writing conventional Cytoscape apps. Furthermore, such workflows can more easily integrate external applications (e.g., GenePattern and iGraph) and multiple large datasets. Finally, external workflows enable reproducibility not available using Cytoscape’s standard mouse/keyboard/display interaction mode.
In 2018, Cytoscape Automation was created to enable external workflows to also call functionality in apps. For an app to be callable, it must be upgraded to support automation via either a Commands or Functions interface. As of March, 2018, app authors upgraded and released 22 apps.
This collection of Cytoscape app articles at F1000Research is intended to serve as a resource to researchers (as workflow authors) and app developers to understand the features and interfaces exposed by automation-enabled apps. They are written by the app authors themselves according to a template that calls for explaining newly available functions, how they can be called, and with real world examples. We intend that readers be able to quickly and economically incorporate Cytoscape app functionality as reproducible workflows that scale independently to large data sets and production runs.
No data are associated with this article.
This work was supported with funding from the National Resource for Network Biology (NRNB) under award number P41 GM103504 and the National Institute of General Medical Sciences (NIGMS) under award number R01 GM070743, both assigned to TI.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Views | Downloads | |
---|---|---|
F1000Research | - | - |
PubMed Central
Data from PMC are received and updated monthly.
|
- | - |
This article is an Editorial and has not been subject to external peer review.
Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. Consider the following examples, but note that this is not an exhaustive list:
Sign up for content alerts and receive a weekly or monthly email with all newly published articles
Already registered? Sign in
The email address should be the one you originally registered with F1000.
You registered with F1000 via Google, so we cannot reset your password.
To sign in, please click here.
If you still need help with your Google account password, please click here.
You registered with F1000 via Facebook, so we cannot reset your password.
To sign in, please click here.
If you still need help with your Facebook account password, please click here.
If your email address is registered with us, we will email you instructions to reset your password.
If you think you should have received this email but it has not arrived, please check your spam filters and/or contact for further assistance.
Comments on this article Comments (0)