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Journal articles on the topic 'Cytoscape app'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Lotia, S., J. Montojo, Y. Dong, G. D. Bader, and A. R. Pico. "Cytoscape App Store." Bioinformatics 29, no. 10 (2013): 1350–51. http://dx.doi.org/10.1093/bioinformatics/btt138.

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2

Demchak, Barry, David Otasek, Alexander R. Pico, et al. "The Cytoscape Automation app article collection." F1000Research 7 (June 20, 2018): 800. http://dx.doi.org/10.12688/f1000research.15355.1.

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Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic functionality, it relies on community-written apps to deliver specialized functions and analyses. To date, Cytoscape’s CyREST feature has allowed researchers to write workflows that call basic Cytoscape functions, but provides no access to its high value app-based functions. With Cytoscape Automation, workflows can now call apps that have been upgraded to expose their functionality. This article collection is a resource to assist readers in quic

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Pico, Alexander R., Gary D. Bader, Barry Demchak, et al. "The Cytoscape app article collection." F1000Research 3 (July 1, 2014): 138. http://dx.doi.org/10.12688/f1000research.4642.1.

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As a network visualization and analysis platform, Cytoscape relies on apps to provide domain-specific features and functions. There are many resources available to support Cytoscape app development and distribution, including the Cytoscape App Store and an online “cookbook” for app developers. This article collection is another resource to help researchers find out more about relevant Cytoscape apps and to provide app developers with useful implementation tips. The collection will grow over time as new Cytoscape apps are developed and published.

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Morris, John H., Samad Lotia, Allan Wu, et al. "setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges." F1000Research 3 (August 5, 2015): 149. http://dx.doi.org/10.12688/f1000research.4392.2.

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setsApp (http://apps.cytoscape.org/apps/setsapp) is a relatively simple Cytoscape 3 app for users to handle groups of nodes and/or edges. It supports several important biological workflows and enables various set operations. setsApp provides basic tools to create sets of nodes or edges, import or export sets, and perform standard set operations (union, difference, intersection) on those sets. Automatic set partitioning and layout functions are also provided. The sets functionality is also exposed to users and app developers in the form of a set of commands that can be used for scripting purpos

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Gao, Jianjiong, Chao Zhang, Martijn van Iersel, et al. "BridgeDb app: unifying identifier mapping services for Cytoscape." F1000Research 3 (July 1, 2014): 148. http://dx.doi.org/10.12688/f1000research.4521.1.

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The BridgeDb app for Cytoscape allows users to map and annotate identifiers of genes, proteins and metabolites in the context of biological networks. The app greatly simplifies the identifier mapping process in Cytoscape by providing a unified interface to different mapping resources and services. The app also provides a programming interface via Cytoscape Commands that can be utilized for identifier mapping by other Cytoscape apps. In this article we provide a technical guide to the BridgeDb app for mapping identifiers in Cytoscape.

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Treister, Adam, and Alexander R. Pico. "Identifier Mapping in Cytoscape." F1000Research 7 (August 6, 2018): 725. http://dx.doi.org/10.12688/f1000research.14807.2.

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Identifier Mapping, the association of terms across disparate taxonomies and databases, is a common hurdle in bioinformatics workflows. The idmapper app for Cytoscape simplifies identifier mapping for genes and proteins in the context of common biological networks. This app provides a unified interface to different identifier resources accessible through a right-click on the table's column header. It also provides an OSGi programming interface via Cytoscape Commands and CyREST that can be utilized for identifier mapping in scripts and other Cytoscape apps, and supports integrated Swagger docum

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Huang, Li Jun, Jeffrey N. Law, and T. M. Murali. "Automating the PathLinker app for Cytoscape." F1000Research 7 (June 12, 2018): 727. http://dx.doi.org/10.12688/f1000research.14616.1.

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PathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. Since December 2015, PathLinker has been available as an app for Cytoscape. This paper describes how we automated the app to use the CyRest infrastructure and how users can incorporate PathLinker into their software pipelines.

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Morris, John H., Dhameliya Vijay, Steven Federowicz, Alexander R. Pico, and Thomas E. Ferrin. "CyAnimator: Simple Animations of Cytoscape Networks." F1000Research 4 (August 5, 2015): 482. http://dx.doi.org/10.12688/f1000research.6852.1.

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CyAnimator (http://apps.cytoscape.org/apps/cyanimator) is a Cytoscape app that provides a tool for simple animations of Cytoscape networks. The tool allows you to take a series of snapshots (CyAnimator calls them frames) of Cytoscape networks. For example, the first frame might be of a network shown from a ”zoomed out” viewpoint and the second frame might focus on a specific group of nodes. Once these two frames are captured by the tool, it can animate between them by interpolating the changes in location, zoom, node color, node size, edge thickness, presence or absence of annotations, etc. Th

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Morris, John H., Dhameliya Vijay, Steven Federowicz, Alexander R. Pico, and Thomas E. Ferrin. "CyAnimator: Simple Animations of Cytoscape Networks." F1000Research 4 (December 30, 2015): 482. http://dx.doi.org/10.12688/f1000research.6852.2.

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CyAnimator (http://apps.cytoscape.org/apps/cyanimator) is a Cytoscape app that provides a tool for simple animations of Cytoscape networks. The tool allows you to take a series of snapshots (CyAnimator calls them frames) of Cytoscape networks. For example, the first frame might be of a network shown from a ”zoomed out” viewpoint and the second frame might focus on a specific group of nodes. Once these two frames are captured by the tool, it can animate between them by interpolating the changes in location, zoom, node color, node size, edge thickness, presence or absence of annotations, etc. Th

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10

Morris, John H., Allan Kuchinsky, Thomas E. Ferrin, and Alexander R. Pico. "enhancedGraphics: a Cytoscape app for enhanced node graphics." F1000Research 3 (July 1, 2014): 147. http://dx.doi.org/10.12688/f1000research.4460.1.

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enhancedGraphics (http://apps.cytoscape.org/apps/enhancedGraphics) is a Cytoscape app that implements a series of enhanced charts and graphics that may be added to Cytoscape nodes. It enables users and other app developers to create pie, line, bar, and circle plots that are driven by columns in the Cytoscape Node Table. Charts are drawn using vector graphics to allow full-resolution scaling.

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11

Fitts, Braxton, Ziran Zhang, Massoud Maher, and Barry Demchak. "dot-app: a Graphviz-Cytoscape conversion plug-in." F1000Research 5 (October 20, 2016): 2543. http://dx.doi.org/10.12688/f1000research.9751.1.

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dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (*.dot, *.gv) files, also known as DOT files due to the *.dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including GraphViz, Gephi, neato, smyrna, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis f

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Fitts, Braxton, Ziran Zhang, Massoud Maher, and Barry Demchak. "dot-app: a Graphviz-Cytoscape conversion plug-in." F1000Research 5 (July 10, 2017): 2543. http://dx.doi.org/10.12688/f1000research.9751.2.

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dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (.dot, .gv) files, also known as DOT files due to the .dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including Graphviz, Gephi, Tulip, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions av

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13

Treister, Adam, and Alexander R. Pico. "Identifier Mapping in Cytoscape: idmapper." F1000Research 7 (June 11, 2018): 725. http://dx.doi.org/10.12688/f1000research.14807.1.

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Identifier Mapping, the association of terms across disparate taxonomies and databases, is a common hurdle in bioinformatics workflows. The idmapper app for Cytoscape simplifies identifier mapping for genes and proteins in the context of common biological networks. This app provides a unified interface to different identifier resources accessible through a right-click on the table's column header. It also provides an OSGi programming interface via Cytoscape Commands and CyREST that can be utilized for identifier mapping in scripts and other Cytoscape apps, and supports integrated Swagger docum

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14

Rinnone, Fabio, Giovanni Micale, Vincenzo Bonnici, et al. "NetMatchStar: an enhanced Cytoscape network querying app." F1000Research 4 (August 5, 2015): 479. http://dx.doi.org/10.12688/f1000research.6656.1.

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We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.

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Rinnone, Fabio, Giovanni Micale, Vincenzo Bonnici, et al. "NetMatchStar: an enhanced Cytoscape network querying app." F1000Research 4 (November 3, 2015): 479. http://dx.doi.org/10.12688/f1000research.6656.2.

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We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.

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Nishida, Kozo, Keiichiro Ono, Shigehiko Kanaya, and Koichi Takahashi. "KEGGscape: a Cytoscape app for pathway data integration." F1000Research 3 (July 1, 2014): 144. http://dx.doi.org/10.12688/f1000research.4524.1.

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In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape (http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a var

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Saha, Pritam, Özgun Babur, Chris Sander, and Augustin Luna. "Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App." F1000Research 11 (April 25, 2022): 458. http://dx.doi.org/10.12688/f1000research.109027.1.

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Introduction: CausalPath compares experimentally measured changes in molecular profiles against curated biological pathways and infers causality between changes in measured features from profiling experiments (e.g., RNA-seq or proteomics from total or phospho-protein levels). Methods: We developed the CausalPath Cytoscape App, an app (i.e., plugin) for visualizing results from the CausalPath method within the Cytoscape Java-based desktop network analysis and visualization platform. Use Cases: Users are given instruction that represents use cases in multiple cancer research areas through the vi

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Saha, Pritam, Özgun Babur, Chris Sander, and Augustin Luna. "Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App." F1000Research 11 (November 14, 2022): 458. http://dx.doi.org/10.12688/f1000research.109027.2.

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Introduction: CausalPath compares experimentally measured changes in molecular profiles against curated biological pathways and infers causality between changes in measured features from profiling experiments (e.g., RNA-seq or proteomics from total or phospho-protein levels). Methods: We developed the CausalPath Cytoscape App, an app (i.e., plugin) for visualizing results from the CausalPath method within the Cytoscape Java-based desktop network analysis and visualization platform. Use Cases: Users are given instruction that represents use cases in multiple cancer research areas through the vi

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Spohr, Philipp, Kasper Dinkla, Gunnar W. Klau, and Mohammed El-Kebir. "eXamine: Visualizing annotated networks in Cytoscape." F1000Research 7 (April 30, 2018): 519. http://dx.doi.org/10.12688/f1000research.14612.1.

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eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,200 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis wor

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Spohr, Philipp, Kasper Dinkla, Gunnar W. Klau, and Mohammed El-Kebir. "eXamine: Visualizing annotated networks in Cytoscape." F1000Research 7 (July 5, 2018): 519. http://dx.doi.org/10.12688/f1000research.14612.2.

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eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,700 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis wor

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Shaik, Faizaan, Srikanth Bezawada, and Neena Goveas. "CySpanningTree: Minimal Spanning Tree computation in Cytoscape." F1000Research 4 (August 5, 2015): 476. http://dx.doi.org/10.12688/f1000research.6797.1.

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Simulating graph models for real world networks is made easy using software tools like Cytoscape. In this paper, we present the open-source CySpanningTree app for Cytoscape that creates a minimal/maximal spanning tree network for a given Cytoscape network. CySpanningTree provides two historical ways for calculating a spanning tree: Prim’s and Kruskal’s algorithms. Minimal spanning tree discovery in a given graph is a fundamental problem with diverse applications like spanning tree network optimization protocol, cost effective design of various kinds of networks, approximation algorithm for som

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Faust, Karoline, and Jeroen Raes. "CoNet app: inference of biological association networks using Cytoscape." F1000Research 5 (June 27, 2016): 1519. http://dx.doi.org/10.12688/f1000research.9050.1.

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Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequenc

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Faust, Karoline, and Jeroen Raes. "CoNet app: inference of biological association networks using Cytoscape." F1000Research 5 (October 14, 2016): 1519. http://dx.doi.org/10.12688/f1000research.9050.2.

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Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequenc

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Legeay, Marc, Nadezhda T. Doncheva, John H. Morris, and Lars Juhl Jensen. "Visualize omics data on networks with Omics Visualizer, a Cytoscape App." F1000Research 9 (February 28, 2020): 157. http://dx.doi.org/10.12688/f1000research.22280.1.

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Cytoscape is an open-source software used to analyze and visualize biological networks. In addition to being able to import networks from a variety of sources, Cytoscape allows users to import tabular node data and visualize it onto networks. Unfortunately, such data tables can only contain one row of data per node, whereas omics data often have multiple rows for the same gene or protein, representing different post-translational modification sites, peptides, splice isoforms, or conditions. Here, we present a new app, Omics Visualizer, that allows users to import data tables with several rows

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Legeay, Marc, Nadezhda T. Doncheva, John H. Morris, and Lars Juhl Jensen. "Visualize omics data on networks with Omics Visualizer, a Cytoscape App." F1000Research 9 (June 30, 2020): 157. http://dx.doi.org/10.12688/f1000research.22280.2.

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Cytoscape is an open-source software used to analyze and visualize biological networks. In addition to being able to import networks from a variety of sources, Cytoscape allows users to import tabular node data and visualize it onto networks. Unfortunately, such data tables can only contain one row of data per node, whereas omics data often have multiple rows for the same gene or protein, representing different post-translational modification sites, peptides, splice isoforms, or conditions. Here, we present a new app, Omics Visualizer, that allows users to import data tables with several rows

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Wang, Lili, Daniel S. Himmelstein, Adam Santaniello, Mousavi Parvin, and Sergio E. Baranzini. "iCTNet2: integrating heterogeneous biological interactions to understand complex traits." F1000Research 4 (August 5, 2015): 485. http://dx.doi.org/10.12688/f1000research.6836.1.

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iCTNet (integrated Complex Traits Networks) version 2 is a Cytoscape app and database that allows researchers to build heterogeneous networks by integrating a variety of biological interactions, thus offering a systems-level view of human complex traits. iCTNet2 is built from a variety of large-scale biological datasets, collected from public repositories to facilitate the building, visualization and analysis of heterogeneous biological networks in a comprehensive fashion via the Cytoscape platform. iCTNet2 is freely available at the Cytoscape app store.

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Wang, Lili, Daniel S. Himmelstein, Adam Santaniello, Mousavi Parvin, and Sergio E. Baranzini. "iCTNet2: integrating heterogeneous biological interactions to understand complex traits." F1000Research 4 (September 28, 2015): 485. http://dx.doi.org/10.12688/f1000research.6836.2.

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iCTNet (integrated Complex Traits Networks) version 2 is a Cytoscape app and database that allows researchers to build heterogeneous networks by integrating a variety of biological interactions, thus offering a systems-level view of human complex traits. iCTNet2 is built from a variety of large-scale biological datasets, collected from public repositories to facilitate the building, visualization and analysis of heterogeneous biological networks in a comprehensive fashion via the Cytoscape platform. iCTNet2 is freely available at the Cytoscape app store.

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Morris, John H., Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, and Thomas E. Ferrin. "setsApp: Set operations for Cytoscape Nodes and Edges." F1000Research 3 (July 1, 2014): 149. http://dx.doi.org/10.12688/f1000research.4392.1.

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setsApp (http://apps.cytoscape.org/apps/setsapp) is a relatively simple Cytoscape 3 app for users to handle groups of nodes and/or edges. It supports several important biological workflows and enables various set operations. setsApp provides basic tools to create sets of nodes or edges, import or export sets, and perform standard set operations (union, difference, intersection) on those sets. The sets functionality is also exposed to users and app developers in the form of a set of commands that can be used for scripting purposes or integrated in other Cytoscape apps.

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Montojo, Jason, Khalid Zuberi, Harold Rodriguez, Gary D. Bader, and Quaid Morris. "GeneMANIA: Fast gene network construction and function prediction for Cytoscape." F1000Research 3 (July 1, 2014): 153. http://dx.doi.org/10.12688/f1000research.4572.1.

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The GeneMANIA Cytoscape app enables users to construct a composite gene-gene functional interaction network from a gene list. The resulting network includes the genes most related to the original list, and functional annotations from Gene Ontology. The edges are annotated with details about the publication or data source the interactions were derived from. The app leverages GeneMANIA’s database of 1800+ networks, containing over 500 million interactions spanning 8 organisms: A. thaliana, C. elegans, D. melanogaster, D. rerio, H. sapiens, M. musculus, R. norvegicus, and S. cerevisiae. Users may

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Micale, Giovanni, Andrea Continella, Alfredo Ferro, Rosalba Giugno, and Alfredo Pulvirenti. "GASOLINE: a Cytoscape app for multiple local alignment of PPI networks." F1000Research 3 (July 1, 2014): 140. http://dx.doi.org/10.12688/f1000research.4537.1.

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Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithms. To the authors knowledge, it is the first Cytoscape app for computing and visualizing local alignments, without requiring any post-processing operations. GO terms can be easily attached to the aligned proteins for further functional analysis of alignm

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Kucera, Mike, Ruth Isserlin, Arkady Arkhangorodsky, and Gary D. Bader. "AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations." F1000Research 5 (July 15, 2016): 1717. http://dx.doi.org/10.12688/f1000research.9090.1.

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Networks often contain regions of tightly connected nodes, or clusters, that highlight their shared relationships. An effective way to create a visual summary of a network is to identify clusters and annotate them with an enclosing shape and a summarizing label. Cytoscape provides the ability to annotate a network with shapes and labels, however these annotations must be created manually one at a time, which can be a laborious process. AutoAnnotate is a Cytoscape 3 App that automates the process of identifying clusters and visually annotating them. It greatly reduces the time and effort requir

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Wu, Lin, Min Li, Jianxin Wang, and Fang-Xiang Wu. "CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis." Bioinformatics 34, no. 8 (2017): 1428–30. http://dx.doi.org/10.1093/bioinformatics/btx764.

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Nersisyan, Lilit, Graham Johnson, Megan Riel-Mehan, Alexander R. Pico, and Arsen Arakelyan. "PSFC: a Pathway Signal Flow Calculator App for Cytoscape." F1000Research 4 (August 5, 2015): 480. http://dx.doi.org/10.12688/f1000research.6706.1.

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Cell signaling pathways are sequences of biochemical reactions that propagate an input signal, such as a hormone binding to a cell-surface receptor, into the cell to trigger a reactive process. Assessment of pathway activities is crucial for determining which pathways play roles in disease versus normal conditions. To date various pathway flow/perturbation assessment tools are available, however they are constrained to specific algorithms and specific data types. There are no accepted standards for evaluation of pathway activities or simulation of flow propagation events in pathways, and the r

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Nersisyan, Lilit, Graham Johnson, Megan Riel-Mehan, Alexander R. Pico, and Arsen Arakelyan. "PSFC: a Pathway Signal Flow Calculator App for Cytoscape." F1000Research 4 (April 3, 2017): 480. http://dx.doi.org/10.12688/f1000research.6706.2.

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Cell signaling pathways are sequences of biochemical reactions that propagate an input signal, such as a hormone binding to a cell-surface receptor, into the cell to trigger a reactive process. Assessment of pathway activities is crucial for determining which pathways play roles in disease versus normal conditions. To date various pathway flow/perturbation assessment tools are available, however they are constrained to specific algorithms and specific data types. There are no accepted standards for evaluation of pathway activities or simulation of flow propagation events in pathways, and the r

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Wang, Lili, Takuya Matsushita, Lohith Madireddy, Parvin Mousavi, and Sergio E. Baranzini. "PINBPA: Cytoscape app for network analysis of GWAS data." Bioinformatics 31, no. 2 (2014): 262–64. http://dx.doi.org/10.1093/bioinformatics/btu644.

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Díaz–Montaña, Juan J., Norberto Díaz–Díaz, Carlos D. Barranco, and Ignacio Ponzoni. "Development and use of a Cytoscape app for GRNCOP2." Computer Methods and Programs in Biomedicine 177 (August 2019): 211–18. http://dx.doi.org/10.1016/j.cmpb.2019.05.030.

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Marazzi, Lauren, Andrew Gainer-Dewar, and Paola Vera-Licona. "OCSANA+: optimal control and simulation of signaling networks from network analysis." Bioinformatics 36, no. 19 (2020): 4960–62. http://dx.doi.org/10.1093/bioinformatics/btaa625.

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Abstract Summary OCSANA+ is a Cytoscape app for identifying nodes to drive the system toward a desired long-term behavior, prioritizing combinations of interventions in large-scale complex networks, and estimating the effects of node perturbations in signaling networks, all based on the analysis of the network’s structure. OCSANA+ includes an update to optimal combinations of interventions from network analysis software tool with cutting-edge and rigorously tested algorithms, together with recently developed structure-based control algorithms for non-linear systems and an algorithm for estimat

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Ono, Keiichiro, Tanja Muetze, Georgi Kolishovski, Paul Shannon, and Barry Demchak. "CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API." F1000Research 4 (August 5, 2015): 478. http://dx.doi.org/10.12688/f1000research.6767.1.

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As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks.In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improv

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Ceccarelli, Francesco, Denes Turei, Attila Gabor, and Julio Saez-Rodriguez. "Bringing data from curated pathway resources to Cytoscape with OmniPath." Bioinformatics 36, no. 8 (2019): 2632–33. http://dx.doi.org/10.1093/bioinformatics/btz968.

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Abstract Summary Multiple databases provide valuable information about curated pathways and other resources that can be used to build and analyze networks. OmniPath combines 61 (and continuously growing) network resources into a comprehensive collection, with over 120 000 interactions. We present here the OmniPath App, a Cytoscape plugin to flexibly import data from OmniPath via a simple and intuitive interface. Thus, it makes possible to directly access the large body of high-quality knowledge provided by OmniPath within Cytoscape for inspection and further use with other tools. Availability

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Kutmon, Martina, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, and Susan L. Coort. "CyTargetLinker app update: A flexible solution for network extension in Cytoscape." F1000Research 7 (June 14, 2018): 743. http://dx.doi.org/10.12688/f1000research.14613.1.

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Here, we present an update of the open-source CyTargetLinker app for Cytoscape (http://apps.cytoscape.org/apps/cytargetlinker) that introduces new automation features. CyTargetLinker provides a simple interface to extend networks with links to relevant data and/or knowledge extracted from so-called linksets. The linksets are provided on the CyTargetLinker website or can be custom-made for specific use cases. The new automation feature enables users to programmatically execute the app’s functionality in Cytoscape (command line tool) and with external tools (e.g. R, Jupyter, Python, etc). This a

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Kutmon, Martina, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, and Susan L. Coort. "CyTargetLinker app update: A flexible solution for network extension in Cytoscape." F1000Research 7 (August 13, 2019): 743. http://dx.doi.org/10.12688/f1000research.14613.2.

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Here, we present an update of the open-source CyTargetLinker app for Cytoscape (http://apps.cytoscape.org/apps/cytargetlinker) that introduces new automation features. CyTargetLinker provides a simple interface to extend networks with links to relevant data and/or knowledge extracted from so-called linksets. The linksets are provided on the CyTargetLinker website (https://cytargetlinker.github.io/) or can be custom-made for specific use cases. The new automation feature enables users to programmatically execute the app’s functionality in Cytoscape (command line tool) and with external tools (e

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Micale, Giovanni, Andrea Continella, Alfredo Ferro, Rosalba Giugno, and Alfredo Pulvirenti. "GASOLINE: a Cytoscape app for multiple local alignment of PPI networks." F1000Research 3 (September 23, 2014): 140. http://dx.doi.org/10.12688/f1000research.4537.2.

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Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithm. GASOLINE starts with the identification of sets of similar nodes, called seeds of the alignment. Alignments are then extended in a greedy manner and finally refined. Both the identification of seeds and the extension of alignments are performed through

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Settle, Brett, David Otasek, John H. Morris, and Barry Demchak. "Copycat Layout: Network layout alignment via Cytoscape Automation." F1000Research 7 (June 21, 2018): 822. http://dx.doi.org/10.12688/f1000research.15144.1.

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The copycatLayout app is a network-based visual differential analysis tool that improves upon the existing layoutSaver app and is delivered pre-installed with Cytoscape, beginning with v3.6.0. LayoutSaver cloned a network layout by mapping node locations from one network to another based on node attribute values, but failed to clone view scale and location, and provided no means of identifying which nodes were successfully mapped between networks. Copycat addresses these issues and provides additional layout options. With the advent of Cytoscape Automation (packaged in Cytoscape v3.6.0), resea

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Settle, Brett, David Otasek, John H. Morris, and Barry Demchak. "Copycat Layout: Network layout alignment via Cytoscape Automation." F1000Research 7 (August 10, 2018): 822. http://dx.doi.org/10.12688/f1000research.15144.2.

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The copycatLayout app is a network-based visual differential analysis tool that improves upon the existing layoutSaver app and is delivered pre-installed with Cytoscape, beginning with v3.6.0. LayoutSaver cloned a network layout by mapping node locations from one network to another based on node attribute values, but failed to clone view scale and location, and provided no means of identifying which nodes were successfully mapped between networks. Copycat addresses these issues and provides additional layout options. With the advent of Cytoscape Automation (packaged in Cytoscape v3.6.0), resea

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Wu, Guanming, Eric Dawson, Adrian Duong, Robin Haw, and Lincoln Stein. "ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis." F1000Research 3 (September 12, 2014): 146. http://dx.doi.org/10.12688/f1000research.4431.2.

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High-throughput experiments are routinely performed in modern biological studies. However, extracting meaningful results from massive experimental data sets is a challenging task for biologists. Projecting data onto pathway and network contexts is a powerful way to unravel patterns embedded in seemingly scattered large data sets and assist knowledge discovery related to cancer and other complex diseases. We have developed a Cytoscape app called “ReactomeFIViz”, which utilizes a highly reliable gene functional interaction network combined with human curated pathways derived from Reactome and ot

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Piñero, Janet, Josep Saüch, Ferran Sanz, and Laura I. Furlong. "The DisGeNET cytoscape app: Exploring and visualizing disease genomics data." Computational and Structural Biotechnology Journal 19 (2021): 2960–67. http://dx.doi.org/10.1016/j.csbj.2021.05.015.

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Wang, Jianxin, Jiancheng Zhong, Gang Chen, Min Li, Fang-xiang Wu, and Yi Pan. "ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network." IEEE/ACM Transactions on Computational Biology and Bioinformatics 12, no. 4 (2015): 815–22. http://dx.doi.org/10.1109/tcbb.2014.2361348.

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Kofia, Victor, Ruth Isserlin, Alison M. J. Buchan, and Gary D. Bader. "Social Network: a Cytoscape app for visualizing co-publication networks." F1000Research 4 (August 5, 2015): 481. http://dx.doi.org/10.12688/f1000research.6804.1.

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Networks that represent connections between individuals can be valuable analytic tools. The Social Network Cytoscape app is capable of creating a visual summary of connected individuals automatically. It does this by representing relationships as networks where each node denotes an individual and an edge linking two individuals represents a connection. The app focuses on creating visual summaries of individuals connected by co-publication links in academia, created from bibliographic databases like PubMed, Scopus and InCites. The resulting co-publication networks can be visualized and analyzed

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Kofia, Victor, Ruth Isserlin, Alison M. J. Buchan, and Gary D. Bader. "Social Network: a Cytoscape app for visualizing co-authorship networks." F1000Research 4 (October 8, 2015): 481. http://dx.doi.org/10.12688/f1000research.6804.2.

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Networks that represent connections between individuals can be valuable analytic tools. The Social Network Cytoscape app is capable of creating a visual summary of connected individuals automatically. It does this by representing relationships as networks where each node denotes an individual and an edge linking two individuals represents a connection. The app focuses on creating visual summaries of individuals connected by co-authorship links in academia, created from bibliographic databases like PubMed, Scopus and InCites. The resulting co-authorship networks can be visualized and analyzed t

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Kofia, Victor, Ruth Isserlin, Alison M. J. Buchan, and Gary D. Bader. "Social Network: a Cytoscape app for visualizing co-authorship networks." F1000Research 4 (December 23, 2015): 481. http://dx.doi.org/10.12688/f1000research.6804.3.

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Networks that represent connections between individuals can be valuable analytic tools. The Social Network Cytoscape app is capable of creating a visual summary of connected individuals automatically. It does this by representing relationships as networks where each node denotes an individual and an edge linking two individuals represents a connection. The app focuses on creating visual summaries of individuals connected by co-authorship links in academia, created from bibliographic databases like PubMed, Scopus and InCites. The resulting co-authorship networks can be visualized and analyzed t

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