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Related Experiment Video

Updated: Feb 7, 2026

Using an Automated Hirschberg Test App to Evaluate Ocular Alignment

Using an Automated Hirschberg Test App to Evaluate Ocular Alignment

Published on: March 24, 2020

Automating the PathLinker app for Cytoscape.

Li Jun Huang¹, Jeffrey N Law², T M Murali^1,3

¹Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA.

|July 31, 2018

Summary

This summary is machine-generated.

PathLinker reconstructs signaling pathways by finding short paths between receptors and transcription factors (TFs) in protein networks. This study details automating the PathLinker Cytoscape app for pipeline integration.

Keywords:

CyREST API Network Biology Pathway Reconstruction Shortest Paths

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Last Updated: Feb 7, 2026

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Published on: November 10, 2016

Area of Science:

Systems biology
Bioinformatics
Computational biology

Background:

Signaling pathway reconstruction is crucial for understanding cellular processes.
PathLinker is a graph-theoretic algorithm for identifying pathways.
The PathLinker Cytoscape app has been available since 2015.

Purpose of the Study:

To automate the PathLinker Cytoscape app using CyRest infrastructure.
To enable seamless integration of PathLinker into user software pipelines.
To enhance the accessibility and utility of pathway reconstruction tools.

Main Methods:

Utilized CyRest infrastructure for app automation.
Developed methods for incorporating PathLinker into computational workflows.
Leveraged graph-theoretic algorithms for pathway analysis.

Main Results:

Successfully automated the PathLinker Cytoscape app.
Established a framework for integrating PathLinker into software pipelines.
Demonstrated efficient reconstruction of signaling pathways.

Conclusions:

Automated PathLinker enhances its usability in bioinformatics research.
CyRest integration facilitates the application of pathway analysis in diverse computational pipelines.
PathLinker remains a valuable tool for dissecting complex signaling networks.