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https://github.com/cytoscape/cytoscape-automation

Collection of scripts that include programmatic io and control of Cytoscape

https://github.com/cytoscape/cytoscape-automation

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
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    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.3%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Collection of scripts that include programmatic io and control of Cytoscape

Basic Info
  • Host: GitHub
  • Owner: cytoscape
  • License: cc0-1.0
  • Language: HTML
  • Default Branch: master
  • Size: 754 MB
Statistics
  • Stars: 88
  • Watchers: 28
  • Forks: 59
  • Open Issues: 23
  • Releases: 1
Created about 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License

README.md

Cytoscape Automation Overview

Visit automation.cytoscape.org for a curated set of automation examples.

What is Cytoscape Automation

Cytoscape is a desktop-based tool that focuses on user-initiated operations for generating user-consumable results. Cytoscape Automation enables users to create workflows executed entirely within Cytoscape or by external tools (e.g., Jupyter, R, GenomeSpace, etc), and whose results are reproducible. This enables Cytoscape to scale to large collections of datasets and to larger more complex workflows than is practical via keyboard and mouse.

Cytoscape Automation exists in two skins the Commands interface and the Functions interface. Both can accomplish similar results, but are focused on different usage styles. Commands reprise user-initiated interactions (e.g., open session, import data, export image), whereas the Functions interface enables programmers to manipulate and operate on networks as internal Cytoscape data. Both Commands and Functions are available via a REST interface.

To learn more about Cytoscape Automation, visit our FAQ.

Also see our repo directories for Script Writers and for App Developers.

Owner

  • Name: Cytoscape Consortium
  • Login: cytoscape
  • Kind: organization

GitHub Events

Total
  • Watch event: 7
  • Issue comment event: 2
  • Push event: 12
  • Pull request event: 4
  • Fork event: 2
Last Year
  • Watch event: 7
  • Issue comment event: 2
  • Push event: 12
  • Pull request event: 4
  • Fork event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 30 days
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 30 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Kreijstal (1)
Pull Request Authors
  • GeneCodeSavvy (1)
Top Labels
Issue Labels
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Dependencies

binder/environment.yml conda
  • pandas
  • py2cytoscape
for-app-developers/cy-automation-cy-rest-basic-sample/pom.xml maven
  • io.swagger:swagger-annotations 1.5.7 provided
  • javax.ws.rs:javax.ws.rs-api 2.0 provided
  • org.cytoscape:service-api [3.5.0,3.5.1] provided
  • org.cytoscape:swing-application-api [3.5.0,3.5.1] provided
  • org.cytoscape:work-api [3.5.0,3.5.1] provided
  • org.osgi:org.osgi.core 4.2.0
  • junit:junit 4.8.2 test
  • org.cytoscape:service-api [3.5.0,3.5.1] test
  • org.mockito:mockito-all 1.8.5 test
  • org.ops4j.pax.logging:pax-logging-api 1.5.2 test
for-app-developers/cy-automation-cy-rest-best-practices-sample/pom.xml maven
  • io.swagger:swagger-annotations 1.5.7 provided
  • javax.ws.rs:javax.ws.rs-api 2.0 provided
  • org.cytoscape:service-api [3.5.0,3.5.1] provided
  • org.cytoscape:swing-application-api [3.5.0,3.5.1] provided
  • org.cytoscape:work-api [3.5.0,3.5.1] provided
  • org.osgi:org.osgi.core 4.2.0
  • junit:junit 4.8.2 test
  • org.cytoscape:service-api [3.5.0,3.5.1] test
  • org.mockito:mockito-all 1.8.5 test
  • org.ops4j.pax.logging:pax-logging-api 1.5.2 test
for-app-developers/cy-automation-cy-rest-json-util-sample/pom.xml maven
  • com.fasterxml.jackson.core:jackson-databind 2.9.10.1 provided
  • com.google.code.gson:gson 2.3 provided
  • io.swagger:swagger-annotations 1.5.7 provided
  • javax.ws.rs:javax.ws.rs-api 2.0 provided
  • org.cytoscape:ci-api 3.6.0 provided
  • org.cytoscape:util-api 3.6.0 provided
  • org.ops4j.pax.logging:pax-logging-api 1.5.3 provided
  • org.ops4j.pax.logging:pax-logging-service 1.5.3 provided
  • org.cxio:cxio 1.1.0
  • org.cytoscape:core-task-api 3.6.0
  • org.cytoscape:model-api 3.6.0
  • org.cytoscape:service-api 3.6.0
  • org.cytoscape:swing-application-api 3.6.0
  • org.cytoscape:work-api 3.6.0
  • org.osgi:org.osgi.core 4.2.0
  • junit:junit 4.8.2 test
  • org.cytoscape:service-api 3.6.0 test
  • org.mockito:mockito-all 1.8.5 test
for-app-developers/cy-automation-taskfactory-json-sample/pom.xml maven
  • org.cytoscape:service-api 3.6.0 provided
  • org.cytoscape:swing-application-api 3.6.0 provided
  • org.cytoscape:work-api 3.6.0 provided
  • org.ops4j.pax.logging:pax-logging-api 1.5.3 provided
  • org.ops4j.pax.logging:pax-logging-service 1.5.3 provided
  • org.osgi:org.osgi.compendium 4.2.0 provided
  • com.google.code.gson:gson 2.3
  • org.osgi:org.osgi.core 4.2.0
  • junit:junit 4.8.2 test
  • org.cytoscape:service-api 3.6.0 test
  • org.mockito:mockito-all 1.8.5 test
for-app-developers/cy-automation-taskfactory-sample/pom.xml maven
  • org.cytoscape:service-api [3.5.0,3.5.1] provided
  • org.cytoscape:swing-application-api [3.5.0,3.5.1] provided
  • org.cytoscape:work-api [3.5.0,3.5.1] provided
  • org.ops4j.pax.logging:pax-logging-api 1.5.3 provided
  • org.ops4j.pax.logging:pax-logging-service 1.5.3 provided
  • org.osgi:org.osgi.compendium 4.2.0 provided
  • org.osgi:org.osgi.core 4.2.0
  • junit:junit 4.8.2 test
  • org.cytoscape:service-api [3.5.0,3.5.1] test
  • org.mockito:mockito-all 1.8.5 test
for-scripters/JavaScript/basic-workflow/package.json npm
  • biojs-io-mitab latest
  • biojs-rest-psicquic latest
  • bionode-ncbi latest
  • cytoscape ^2.3.1
  • request latest
  • underscore latest