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. 2015 Dec 1;31(23):3868-9.
doi: 10.1093/bioinformatics/btv460. Epub 2015 Aug 12.

cyNeo4j: connecting Neo4j and Cytoscape

Georg Summer  1 , Thomas Kelder  2 , Keiichiro Ono  3 , Marijana Radonjic  2 , Stephane Heymans  4 , Barry Demchak  3
Affiliations

cyNeo4j: connecting Neo4j and Cytoscape

Georg Summer et al. Bioinformatics. .

Abstract

We developed cyNeo4j, a Cytoscape App to link Cytoscape and Neo4j databases to utilize the performance and storage capacities Neo4j offers. We implemented a Neo4j NetworkAnalyzer, ForceAtlas2 layout and Cypher component to demonstrate the possibilities a distributed setup of Cytoscape and Neo4j have.

Availability and implementation: The app is available from the Cytoscape App Store at http://apps.cytoscape.org/apps/cyneo4j, the Neo4j plugins at www.github.com/gsummer/cyneo4j-parent and the community and commercial editions of Neo4j can be found at http://www.neo4j.com.

Contact: georg.summer@gmail.com.

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Figures

Fig. 1.
Fig. 1.
Network Analyzer Benchmark: The NetworkAnalyzer plugin implemented in Neo4j and called from cyNeo4j reduces the computation time by a factor of 4 compared to the implementation in Cytoscape. Multiple threads allow for a further decline in computation time needed. We extracted a subset of STRING with 4436 nodes and 93 286 edges
See this image and copyright information in PMC

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