https://github.com/cdcgov/microbetrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

https://github.com/cdcgov/microbetrace

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
  • .zenodo.json file
  • DOI references
    Found 2 DOI reference(s) in README
  • Academic publication links
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary

Keywords

bioinformatics cdc epidemiology genomic-data-analysis genomics genomics-visualization hiv network-visualization pathogens phylogenetic-trees phylogenetics phylogenomics phylogeny sequence-alignment
Last synced: 5 months ago · JSON representation

Repository

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Basic Info
  • Host: GitHub
  • Owner: CDCgov
  • License: apache-2.0
  • Language: TypeScript
  • Default Branch: master
  • Homepage: https://microbetrace.cdc.gov/
  • Size: 216 MB
Statistics
  • Stars: 94
  • Watchers: 16
  • Forks: 42
  • Open Issues: 72
  • Releases: 3
Fork of AABoyles/MicrobeTrace
Topics
bioinformatics cdc epidemiology genomic-data-analysis genomics genomics-visualization hiv network-visualization pathogens phylogenetic-trees phylogenetics phylogenomics phylogeny sequence-alignment
Created over 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Security

README.md

image

MicrobeTrace MicrobeTrace DOI

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Developed By (some folks at) CDC.

To Use MicrobeTrace:

To Spread the Word:

To Help Us Build:

Public Domain

This project constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This project is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this project will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License

The project utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

This program is free software: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

Privacy

This project contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Surveillance Platform Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/privacy.html.

Contributing

Anyone is encouraged to contribute to the project by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

Before you get started, please read the Developer's Guide to MicrobeTrace.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page are subject to the Presidential Records Act and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.

Records

This project is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.

Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.

Owner

  • Name: Centers for Disease Control and Prevention
  • Login: CDCgov
  • Kind: organization
  • Email: data@cdc.gov
  • Location: Atlanta, GA

CDC's collaborative software projects to protect America from health, safety, and security threats, both foreign and in the U.S.

GitHub Events

Total
  • Issues event: 216
  • Watch event: 4
  • Delete event: 33
  • Issue comment event: 204
  • Push event: 43
  • Gollum event: 45
  • Pull request event: 17
  • Fork event: 7
  • Create event: 6
Last Year
  • Issues event: 216
  • Watch event: 4
  • Delete event: 33
  • Issue comment event: 204
  • Push event: 43
  • Gollum event: 45
  • Pull request event: 17
  • Fork event: 7
  • Create event: 6

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 121
  • Total pull requests: 15
  • Average time to close issues: over 2 years
  • Average time to close pull requests: about 1 year
  • Total issue authors: 13
  • Total pull request authors: 6
  • Average comments per issue: 1.24
  • Average comments per pull request: 0.93
  • Merged pull requests: 4
  • Bot issues: 1
  • Bot pull requests: 6
Past Year
  • Issues: 75
  • Pull requests: 7
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 months
  • Issue authors: 7
  • Pull request authors: 4
  • Average comments per issue: 1.09
  • Average comments per pull request: 1.29
  • Merged pull requests: 1
  • Bot issues: 1
  • Bot pull requests: 1
Top Authors
Issue Authors
  • ikb6 (136)
  • roxycintron (20)
  • mossy426 (20)
  • AABoyles (18)
  • dacowan404 (10)
  • reagank (9)
  • JieH9 (2)
  • billswitzer2 (2)
  • frankambrosio3 (2)
  • liamxg (1)
  • mossy426-cdc (1)
  • dependabot[bot] (1)
  • newuser1971 (1)
  • mlarjim (1)
Pull Request Authors
  • dependabot[bot] (10)
  • AABoyles (6)
  • ikb6 (6)
  • roxycintron (2)
  • dacowan404 (1)
  • snyk-bot (1)
  • rob-caldwell (1)
  • mossy426 (1)
Top Labels
Issue Labels
[issue-type] bug (99) [issue-type] enhancement (50) high-priority (23) [issue-type] feedback (19) [issue-type] task (14) [effort] medium (6) [skill-level] beginner (5) [effort] large (4) help-wanted (4) [skill-level] intermediate (3) [effort] small (3) code.gov (3) [issue-type] user story (1) accessibility (1) dependencies (1) [skill-level] advanced (1) Epic (1) Support Request (1)
Pull Request Labels
dependencies (10) [issue-type] bug (4)

Dependencies

.github/workflows/codeql.yml actions
  • actions/checkout v3 composite
  • github/codeql-action/analyze v2 composite
  • github/codeql-action/autobuild v2 composite
  • github/codeql-action/init v2 composite
Dockerfile docker
  • node 14-slim build
package-lock.json npm
  • 911 dependencies
package.json npm
  • 3d-force-graph ^1.67.8 development
  • acorn ^6.4.2 development
  • alertifyjs ^1.13.1 development
  • alignment-viewer ^0.3.4 development
  • bioseq ^0.1.5 development
  • bootstrap ^4.6.0 development
  • browserslist ^4.16.5 development
  • chosen-js ^1.8.5 development
  • clipboard ^2.0.6 development
  • cssnano ^4.1.10 development
  • d3 ^5.16.0 development
  • d3-force-attract ^0.1.1 development
  • d3-polygon ^1.0.6 development
  • d3-symbol-extra ^0.1.0 development
  • devtools-detect ^3.0.1 development
  • file-saver ^2.0.5 development
  • fileto 0.1.0 development
  • glob-parent ^5.1.2 development
  • golden-layout ^1.5.9 development
  • html5sortable ^0.9.18 development
  • is-svg >=4.3.0 development
  • jquery ^3.5.1 development
  • jszip ^3.7.0 development
  • leaflet ^1.7.1 development
  • leaflet-image ^0.4.0 development
  • leaflet.markercluster ^1.4.1 development
  • localforage ^1.9.0 development
  • marked ^4.0.10 development
  • moment ^2.29.4 development
  • normalize-url ^4.5.1 development
  • nth-check >=2.0.1 development
  • open-iconic ^1.1.1 development
  • papaparse ^5.3.0 development
  • patristic ^0.5.6 development
  • pdfmake ^0.1.70 development
  • pixi-viewport ^4.21.0 development
  • pixi.js ^5.3.8 development
  • plotly.js ^1.58.4 development
  • popper.js ^1.16.1 development
  • postcss-cli ^7.1.2 development
  • puppeteer ^1.20.0 development
  • save-svg-as-png ^1.4.17 development
  • screenfull ^3.3.2 development
  • tabulator-tables ^4.9.3 development
  • tidytree ^0.5.8 development
  • tn93 ^0.3.2 development
  • xlsx ^0.17.0 development
  • xss ^1.0.8 development
  • express ^4.17.3
  • express-http-to-https ^1.1.4
  • express-static-gzip ^1.1.3
  • gzipper ^2.10.4
  • is-svg >=4.3.0
  • nth-check >=2.0.1