auspice

Web app for visualizing pathogen evolution

https://github.com/nextstrain/auspice

Science Score: 54.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
8 of 79 committers (10.1%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.5%) to scientific vocabulary

Keywords from Contributors

sequences clade research virus strain sars-cov-2 rna nextstrain next-generation-sequencing neherlab

Last synced: 6 months ago · JSON representation ·

Repository

Web app for visualizing pathogen evolution

Basic Info

Host: GitHub
Owner: nextstrain
License: agpl-3.0
Language: JavaScript
Default Branch: master
Homepage: https://docs.nextstrain.org/projects/auspice/
Size: 20.2 MB

Statistics

Stars: 302
Watchers: 27
Forks: 169
Open Issues: 287
Releases: 0

Created almost 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

About Nextstrain

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response.

Resulting data and inferences are available live at the website nextstrain.org.

About Auspice

Definition: Observation by an augur, ie a prophetic sign.

Auspice is an open-source interactive web app for visualizing phylogenomic data. It may be used in tandem with nextstrain's bioinformatics toolkit augur or on its own. Auspice may be used to explore datasets locally or run as a server to share results.

Documentation

The main Nextstrain documentation is available at docs.nextstrain.org. This includes tutorials, how-to guides, and explanations of concepts to help you get started and answer common questions to achieve your goal(s) with Auspice and other Nextstrain tools.

When getting started with Auspice, it may be helpful to read our overview of how Auspice fits together with other Nextstrain tools.

For more detailed technical information how Auspice works and reference guides describing specific Auspice features, check out the Auspice reference-guide documentation at docs.nextstrain.org/projects/auspice.

Quickstart

Installation

See the relevant page on Auspice docs.

Obtain datasets to display

To get up & running, you'll need datasets to visualise. (Please see the nextstrain docs for tutorials on how to run your own analyses.)

If you've installed auspice from npm you may get datasets to display via:

bash mkdir data curl http://data.nextstrain.org/zika.json --compressed -o data/zika.json curl http://data.nextstrain.org/ncov.json --compressed -o data/ncov.json ...

If you've installed auspice from source, we have a helper script to download a number of datasets for testing:

```bash

from the auspice src directory

npm run get-data ```

Obtain narratives to view locally

This repository contains a number of "test narratives" which serve both to provide examples of the capability of narratives, as well as being used to test functionality and fix bugs. These should work out of the box, assuming you have obtained the necessary datasets via the above script.

If you wish to view the nextstrain-maintained narratives, then this can be done by checking out the nextstrain/narratives github repo and telling auspice to look for narratives there via the --narrativeDir argument.

Run auspice

bash auspice view --datasetDir data

And view auspice in the browser at localhost:4000

If you are editing source code, running the following command will allow hot-reloading.

bash auspice develop --datasetDir data

Environment variables

The client looks for some environment variables. All are optional.

[!NOTE] This is an incomplete list. For other variables, search for process.env. in the codebase.

SKIP_REDUX_CHECKS: Set this to a truthy value to improve dev server responsiveness. Useful when you see a console warning like this:

ImmutableStateInvariantMiddleware took 200ms, which is more than the warning threshold of 32ms. If your state or actions are very large, you may want to disable the middleware as it might cause too much of a slowdown in development mode.

CLI (Command Line Interface)

Run auspice --help or auspice view --help to see all the available command line options.

Contributor Information

We have received a number of generous offers to contribute developer effort to nextstrain (and auspice) following our work on hCoV-19. We welcome contributions! To get started, please review these resources before submitting a pull request:

This project strictly adheres to the Contributor Covenant Code of Conduct.

License and copyright

Source code to Nextstrain is made available under the terms of the GNU Affero General Public License (AGPL). Nextstrain 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 GNU Affero General Public License for more details.

Owner

Name: Nextstrain
Login: nextstrain
Kind: organization

Website: https://nextstrain.org
Twitter: nextstrain
Repositories: 84
Profile: https://github.com/nextstrain

Real-time tracking of pathogen evolution

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."

preferred-citation:
  type: article
  title: "Nextstrain: real-time tracking of pathogen evolution"
  doi: "10.1093/bioinformatics/bty407"
  journal: "Bioinformatics"
  year: 2018
  month: 5
  volume: 34
  issue: 23
  start: 4121
  end: 4123

  authors:
    - family-names: Hadfield
      given-names:  James

    - family-names: Megill
      given-names:  Colin

    - family-names: Bell
      given-names:  Sidney M.

    - family-names: Huddleston
      given-names:  John

    - family-names: Potter
      given-names:  Barney

    - family-names: Callender
      given-names:  Charlton

    - family-names: Sagulenko
      given-names:  Pavel

    - family-names: Bedford
      given-names:  Trevor

    - family-names: Neher
      given-names:  Richard A.

Committers

Last synced: 9 months ago

All Time

Total Commits: 4,474
Total Committers: 79
Avg Commits per committer: 56.633
Development Distribution Score (DDS): 0.533

Past Year

Commits: 347
Committers: 11
Avg Commits per committer: 31.545
Development Distribution Score (DDS): 0.646

Top Committers

Name	Email	Commits
James Hadfield	j**2@s**k	2,090
Trevor Bedford	t**r@b**o	512
Colin Megill	c**l@g**m	500
Victor Lin	1****n	353
Jover	j**1@g**m	260
Richard Neher	r**r@t**e	172
Thomas Sibley	t**y@f**g	75
Emma Hodcroft	e**t@g**m	66
Kairsten Fay	k**y@g**m	56
eharkins	e**s@g**m	54
salvatore-fxpig	s**e@f**m	42
Richard Neher	r**r@u**h	37
sidneymbell	s**b@u**u	20
Chris Wilcox	c**x@g**m	14
max	m**x@z**o	12
Rick Leir	r**r@l**m	10
joachimschmidt557	j**7@o**m	10
John Huddleston	h**j@g**m	10
ivan-aksamentov	i**v@g**m	9
John SJ Anderson	j**4@f**g	9
Cameron Devine	c**n@g**m	9
Anouar	a**1@g**m	8
mingir2	m**2@i**u	6
lukas	6****u	6
Marc Aaron	m**r@g**m	6
Cameron Yick	c**k@d**m	6
clint	c**t@b**l	5
Slava	u**r@g**m	5
evogytis	g**s@g**m	5
dependabot[bot]	4****]	5
and 49 more...

Committer Domains (Top 20 + Academic)

fredhutch.org: 3 google.com: 3 salesforce.com: 2 uw.edu: 2 sanger.ac.uk: 1 bedford.io: 1 tuebingen.mpg.de: 1 fxpig.com: 1 unibas.ch: 1 zimon.co: 1 leirtech.com: 1 illinois.edu: 1 datadoghq.com: 1 indigoag.com: 1 apsis.io: 1 mapmeld.com: 1 argon.mcb.uj.edu.pl: 1 walter.gd: 1 chanzuckerberg.com: 1 dreamofsky.com: 1 iastate.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 236
Total pull requests: 299
Average time to close issues: about 1 year
Average time to close pull requests: 4 months
Total issue authors: 37
Total pull request authors: 17
Average comments per issue: 2.5
Average comments per pull request: 1.19
Merged pull requests: 193
Bot issues: 0
Bot pull requests: 55

Past Year

Issues: 60
Pull requests: 121
Average time to close issues: 16 days
Average time to close pull requests: 15 days
Issue authors: 11
Pull request authors: 8
Average comments per issue: 1.22
Average comments per pull request: 1.01
Merged pull requests: 87
Bot issues: 0
Bot pull requests: 11

View more stats

Top Authors

Issue Authors

jameshadfield (80)
corneliusroemer (35)
joverlee521 (28)
victorlin (28)
huddlej (17)
genehack (7)
trvrb (5)
emmahodcroft (5)
kvargha (3)
sidneymbell (3)
ivan-aksamentov (2)
YasirKusay (2)
AngieHinrichs (2)
rleir (2)
rneher (2)

Pull Request Authors

victorlin (131)
jameshadfield (101)
dependabot[bot] (86)
joverlee521 (35)
genehack (13)
tsibley (5)
trvrb (4)
ivan-aksamentov (3)
corneliusroemer (3)
CameronDevine (2)
zhangmengjie-amy (2)
j23414 (2)
huddlej (2)
sagar-pathak (2)
bcoe (2)

Top Labels

Issue Labels

bug (86) enhancement (75) please take this issue (15) performance improvement (11) streamtrees (9) documentation (6) request for comments (6) good first issue (4) narratives (4) revisit sometime (4) source: office hours (4) source: discussion forum (3) priority: high (2) regression (2) browser-specific (2) office-hours (1) priority: low (1) blocked (1) priority: moderate (1) dependencies (1) javascript (1) proposal (1)

Pull Request Labels

dependencies (86) preview on nextstrain.org (63) javascript (44) preview on auspice.us (27) experiment (10) performance improvement (7) github_actions (2) bug (2) revisit sometime (2) enhancement (2) streamtrees (2) priority: high (1) proposal (1) documentation (1)

Packages

Total packages: 2
Total downloads:
- npm 2,031 last-month

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 6
(may contain duplicates)
Total versions: 183
Total maintainers: 4

npmjs.org: auspice

Web app for visualizing pathogen evolution

Homepage: https://www.npmjs.com/package/auspice
License: AGPL-3.0-only
Latest release: 2.65.0
published 6 months ago

Versions: 179
Dependent Packages: 2
Dependent Repositories: 6
Downloads: 2,029 Last month

Rankings

Downloads: 1.5%

Forks count: 2.5%

Stargazers count: 3.7%

Dependent repos count: 4.8%

Average: 6.7%

Dependent packages count: 21.1%

Maintainers (3)

jameshadfield nextstrain-bot trvrb

Last synced: 6 months ago

npmjs.org: @khaitd0340/auspice

Web app for visualizing pathogen evolution

Homepage: https://www.npmjs.com/package/auspice
License: AGPL-3.0-only
Latest release: 2.59.5
published over 1 year ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 2 Last month

Rankings

Dependent repos count: 25.6%

Average: 31.4%

Dependent packages count: 37.1%

Maintainers (1)

khaitd0340

Last synced: 6 months ago

Dependencies

.github/workflows/ci.yaml actions

actions/checkout v2 composite
actions/setup-node v2 composite

.github/workflows/make_pr_for_downstream_repo.yaml actions

actions/checkout v2 composite
actions/setup-node v2 composite
peter-evans/create-pull-request v3 composite

package-lock.json npm

1283 dependencies

package.json npm

@babel/eslint-parser ^7.16.3 development
bundlesize ^0.18.1 development
chai ^4.1.2 development
chai-http ^4.0.0 development
eslint ^7.5.0 development
eslint-config-airbnb ^18.2.0 development
eslint-plugin-import ^2.13.0 development
eslint-plugin-jsx-a11y ^6.3.0 development
eslint-plugin-react ^7.2.1 development
eslint-plugin-react-hooks ^4.0.1 development
jest ^25.1.0 development
jest-circus ^25.3.0 development
jest-image-snapshot ^3.0.1 development
jest-puppeteer ^4.4.0 development
puppeteer ^2.1.1 development
quoted-printable ^1.0.1 development
start-server-and-test ^1.14.0 development
@babel/core ^7.3.4
@babel/plugin-proposal-class-properties ^7.3.4
@babel/plugin-proposal-decorators ^7.3.0
@babel/plugin-syntax-dynamic-import ^7.8.3
@babel/plugin-transform-runtime ^7.8.3
@babel/preset-env ^7.9.6
@babel/preset-react ^7.0.0
@hot-loader/react-dom ^16.13.0
argparse ^1.0.10
babel-loader ^8.0.4
babel-plugin-lodash ^3.3.4
babel-plugin-strip-function-call ^1.0.2
babel-plugin-styled-components ^1.10.0
binomial ^0.2.0
buffer ^6.0.3
chalk ^2.4.1
clean-webpack-plugin ^4.0.0
compression ^1.7.3
compression-webpack-plugin ^3.1.0
core-js ^3.6.5
create-react-class ^15.7.0
css-loader ^3.4.0
css.escape ^1.5.1
d3-array ^2.2.0
d3-axis ^1.0.6
d3-brush ^1.0.4
d3-color ^1.0.3
d3-ease ^1.0.3
d3-format ^1.3.0
d3-interpolate ^1.1.5
d3-scale ^1.0.5
d3-selection ^1.1.0
d3-shape ^1.2.0
d3-timer ^1.0.7
d3-transition ^1.2.0
d3-zoom ^1.1.3
dom-to-image ^2.6.0
dompurify ^2.3.3
express ^4.16.3
express-naked-redirect ^0.1.9
express-static-gzip ^0.2.2
html-webpack-plugin ^4.5.2
i18next ^19.3.2
leaflet 1.7.1
leaflet-gesture-handling 1.2.1
linspace ^1.0.0
lodash ^4.17.21
lodash-webpack-plugin ^0.11.6
marked ^0.7.0
mousetrap ^1.6.2
node-fetch ^2.6.1
null-loader ^4.0.0
outer-product 0.0.4
papaparse ^5.3.1
prop-types ^15.6.0
query-string ^4.2.3
react ^16.8.6
react-collapsible ^2.8.4
react-dom ^16.8.6
react-ga ^2.2.0
react-helmet ^5.2.1
react-hot-loader ^4.8.4
react-i18next ^11.3.3
react-icons ^3.9.0
react-redux ^7.2.6
react-select ^5.2.2
react-tooltip ^4.2.10
react-transition-group ^1.2.1
react-virtualized ^9.22.3
redux ^4.0.1
redux-thunk ^2.3.0
regenerator-runtime ^0.13.5
style-loader ^0.13.2
styled-components ^4.0.3
typeface-lato ^0.0.75
webpack ^5.74.0
webpack-bundle-analyzer ^3.9.0
webpack-dev-middleware ^3.7.3
webpack-hot-middleware ^2.25.2
whatwg-fetch ^0.10.1
xlsx ^0.17.1
yaml-front-matter ^4.0.0

docs/environment.yml conda

make
pip
recommonmark
sphinx

auspice

Science Score: 54.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

About Nextstrain

About Auspice

Documentation

Quickstart

Installation

Obtain datasets to display

from the auspice src directory

Obtain narratives to view locally

Run auspice

Environment variables

CLI (Command Line Interface)

Contributor Information

License and copyright

Owner

Citation (CITATION.cff)

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

npmjs.org: auspice

Rankings

Maintainers (3)

npmjs.org: @khaitd0340/auspice

Rankings

Maintainers (1)

Dependencies