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  1. Article ; Online: dot-app

    Braxton Fitts / Ziran Zhang / Massoud Maher / Barry Demchak

    F1000Research, Vol

    a Graphviz-Cytoscape conversion plug-in [version 2; referees: 3 approved, 1 approved with reservations]

    2017  Volume 5

    Abstract: 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 ... ...

    Abstract 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 available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not have as many styling options as the Graphviz software suite. dot-app enables the interchange of networks between Cytoscape and DOT-compatible applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.
    Keywords Bioinformatics ; Medicine ; R ; Science ; Q
    Subject code 005
    Language English
    Publishing date 2017-07-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  2. Article ; Online: Porting and using PanGIA for Cytoscape 3

    David Welker / Barry Demchak

    F1000Research, Vol

    challenges and solutions [v1; ref status: indexed, http://f1000r.es/3r3]

    2014  Volume 3

    Abstract: Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon ... ...

    Abstract Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which plugins relied changed, requiring a significant porting effort for plugins to work as Cytoscape 3 apps. PanGIA is a Cytoscape add-on (http://apps.cytoscape.org/apps/pangia) designed to analyze and visualize genetic interaction data in light of physical interaction data. In order to convert the PanGIA plugin to an app, various challenges, including those related to a transformed data model, concurrency, and randomization had to be overcome. In the process, the ability to control randomization was added to the GUI, a feature which was not only integral to the porting process, but which also ensures more easily reproducible scientific analysis for PanGIA users. Most authors of Cytoscape 2 plugins will face similar challenges porting their software to work with Cytoscape 3, and this paper gives details of how the PanGIA port addressed them.
    Keywords Bioinformatics ; Medicine ; R ; Science ; Q
    Language English
    Publishing date 2014-07-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: aMatReader

    Brett Settle / David Otasek / John H Morris / Barry Demchak

    F1000Research, Vol

    Importing adjacency matrices via Cytoscape Automation [version 2; referees: 2 approved]

    2018  Volume 7

    Abstract: Adjacency matrices are useful for storing pairwise interaction data, such as correlations between gene pairs in a pathway or similarities between genes and conditions. The aMatReader app enables users to import one or multiple adjacency matrix files into ...

    Abstract Adjacency matrices are useful for storing pairwise interaction data, such as correlations between gene pairs in a pathway or similarities between genes and conditions. The aMatReader app enables users to import one or multiple adjacency matrix files into Cytoscape, where each file represents an edge attribute in a network. Our goal was to import the diverse adjacency matrix formats produced by existing scripts and libraries written in R, MATLAB, and Python, and facilitate importing that data into Cytoscape. To accelerate the import process, aMatReader attempts to predict matrix import parameters by analyzing the first two lines of the file. We also exposed CyREST endpoints to allow researchers to import network matrix data directly into Cytoscape from their language of choice. Many analysis tools deal with networks in the form of an adjacency matrix, and exposing the aMatReader API to automation users enables scripts to transfer those networks directly into Cytoscape with little effort.
    Keywords Medicine ; R ; Science ; Q
    Subject code 005
    Language English
    Publishing date 2018-08-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Copycat Layout

    Brett Settle / David Otasek / John H Morris / Barry Demchak

    F1000Research, Vol

    Network layout alignment via Cytoscape Automation [version 2; referees: 2 approved]

    2018  Volume 7

    Abstract: 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 ...

    Abstract 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), researchers can utilize the Copycat layout and its output in workflows written in their language of choice by using only a few simple REST calls. Copycat enables researchers to visually compare groups of homologous genes, generate network comparison images for publications, and quickly identify differences between similar networks at a glance without leaving their script. With a few extra REST calls, scripts can discover nodes present in one network but not in the other, which can feed into more complex analyses (e.g., modifying mismatched nodes based on new data, then re-running the layout to highlight additional network changes).
    Keywords Medicine ; R ; Science ; Q
    Subject code 000
    Language English
    Publishing date 2018-08-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  5. Article ; Online: Copycat Layout

    Brett Settle / David Otasek / John H Morris / Barry Demchak

    F1000Research, Vol

    Network layout alignment via Cytoscape Automation [version 1; referees: 2 approved]

    2018  Volume 7

    Abstract: 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 ...

    Abstract 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), researchers can utilize the Copycat layout and its output in workflows written in their language of choice by using only a few simple REST calls. Copycat enables researchers to visually compare groups of homologous genes, generate network comparison images for publications, and quickly identify differences between similar networks at a glance without leaving their script. With a few extra REST calls, scripts can discover nodes present in one network but not in the other, which can feed into more complex analyses (e.g., modifying mismatched nodes based on new data, then re-running the layout to highlight additional network changes).
    Keywords Medicine ; R ; Science ; Q
    Subject code 000
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: aMatReader

    Brett Settle / David Otasek / John H Morris / Barry Demchak

    F1000Research, Vol

    Importing adjacency matrices via Cytoscape Automation [version 1; referees: 2 approved]

    2018  Volume 7

    Abstract: Adjacency matrices are useful for storing pairwise interaction data, such as correlations between gene pairs in a pathway or similarities between genes and conditions. The aMatReader app enables users to import one or multiple adjacency matrix files into ...

    Abstract Adjacency matrices are useful for storing pairwise interaction data, such as correlations between gene pairs in a pathway or similarities between genes and conditions. The aMatReader app enables users to import one or multiple adjacency matrix files into Cytoscape, where each file represents an edge attribute in a network. Our goal was to import the diverse adjacency matrix formats produced by existing scripts and libraries written in R, MATLAB, and Python, and facilitate importing that data into Cytoscape. To accelerate the import process, aMatReader attempts to predict matrix import parameters by analyzing the first two lines of the file. We also exposed CyREST endpoints to allow researchers to import network matrix data directly into Cytoscape from their language of choice. Many analysis tools deal with networks in the form of an adjacency matrix, and exposing the aMatReader API to automation users enables scripts to transfer those networks directly into Cytoscape with little effort.
    Keywords Medicine ; R ; Science ; Q
    Subject code 005
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: dot-app

    Braxton Fitts / Ziran Zhang / Massoud Maher / Barry Demchak

    F1000Research, Vol

    a Graphviz-Cytoscape conversion plug-in [version 1; referees: 1 approved, 2 approved with reservations]

    2016  Volume 5

    Abstract: 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 ... ...

    Abstract 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 functions available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not offer all of the styling options that DOT-based applications (particularly GraphViz) do. dot-app enables the interchange of networks between Cytoscape and DOT-based applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.
    Keywords Bioinformatics ; Medicine ; R ; Science ; Q
    Subject code 005
    Language English
    Publishing date 2016-10-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: RCy3

    Julia A. Gustavsen / Shraddha Pai / Ruth Isserlin / Barry Demchak / Alexander R. Pico

    F1000Research, Vol

    Network biology using Cytoscape from within R [version 3; peer review: 3 approved]

    2019  Volume 8

    Abstract: RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future ... ...

    Abstract RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.
    Keywords Medicine ; R ; Science ; Q
    Subject code 020
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: RCy3

    Julia A. Gustavsen / Shraddha Pai / Ruth Isserlin / Barry Demchak / Alexander R. Pico

    F1000Research, Vol

    Network biology using Cytoscape from within R [version 1; peer review: 2 approved]

    2019  Volume 8

    Abstract: RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future ... ...

    Abstract RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.
    Keywords Medicine ; R ; Science ; Q
    Subject code 020
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  10. Article ; Online: Cytoscape Automation

    David Otasek / John H. Morris / Jorge Bouças / Alexander R. Pico / Barry Demchak

    Genome Biology, Vol 20, Iss 1, Pp 1-

    empowering workflow-based network analysis

    2019  Volume 15

    Abstract: Abstract Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation ( ...

    Abstract Abstract Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio. We expose over 270 Cytoscape core functions and 34 Cytoscape apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation. Independent projects to create and publish Python/R native CA interface libraries have reached an advanced stage, and a number of automation workflows are already published.
    Keywords Workflow ; Reproducibility ; Cytoscape ; Interoperability ; REST ; Microservice ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2019-09-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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