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Related Concept Videos

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks09:49

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Network analysis was applied to evaluate the association of various ecological microbial communities, such as soil, water and rhizosphere. Presented here is a protocol on how to use the WGCNA algorithm to analyze different co-occurrence networks that may occur in the microbial communities due to different ecological...
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We present a freely available workflow built for rapid exploration and accurate analysis of cellular bodies in specific cell compartments in fluorescence microscopy images. This user-friendly workflow is designed on the open-source software Icy and also uses ImageJ functionalities. The pipeline is affordable without knowledge in image...
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We developed automated computer vision software to detect exocytic events marked by pH-sensitive fluorescent probes. Here, we demonstrate the use of a graphical user interface and RStudio to detect fusion events, analyze and display spatiotemporal parameters of fusion, and classify events into distinct fusion...
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Related Experiment Video

Updated: Jan 20, 2026

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

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Cytoscape Automation: empowering workflow-based network analysis.

David Otasek1, John H Morris2, Jorge Bouças3

  • 1Department of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA.

Genome Biology
|September 4, 2019
PubMed
Summary
This summary is machine-generated.

Cytoscape Automation (CA) enhances the Cytoscape network analysis tool by enabling reproducible workflows through Python and R integration. This innovation expands Cytoscape

Keywords:
CytoscapeInteroperabilityMicroserviceRESTReproducibilityService-oriented architectureWorkflow

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Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images
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Related Experiment Videos

Last Updated: Jan 20, 2026

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Area of Science:

  • Network biology
  • Computational biology
  • Bioinformatics

Background:

  • Cytoscape is a widely used network biology analysis and visualization tool.
  • Its interactive nature limits its utility in creating reproducible and scalable workflows.

Purpose of the Study:

  • To introduce Cytoscape Automation (CA) for integrating Cytoscape with workflow systems like Python/R.
  • To enhance the reproducibility, scalability, and novelty of network biology analyses.

Main Methods:

  • Exposing over 270 Cytoscape core functions and 34 apps as REST-callable functions.
  • Utilizing standardized JSON interfaces with Swagger documentation.
  • Developing native Python/R interface libraries for CA.

Main Results:

  • Cytoscape Automation enables seamless integration with productive workflow systems (e.g., Python/R in Jupyter/RStudio).
  • A comprehensive set of Cytoscape functions and apps are now accessible via standardized REST APIs.
  • Independent Python/R CA interface libraries are nearing completion, facilitating workflow development.

Conclusions:

  • Cytoscape Automation overcomes the limitations of interactive tools for reproducible network biology workflows.
  • CA significantly expands the capabilities of Cytoscape for advanced computational biology research.