coral

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

https://github.com/jmchandonia/coral

Science Score: 67.0%

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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
Links to: ncbi.nlm.nih.gov
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Low similarity (8.6%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

Basic Info

Host: GitHub
Owner: jmchandonia
License: agpl-3.0
Language: Python
Default Branch: main
Size: 7.89 MB

Statistics

Stars: 7
Watchers: 2
Forks: 3
Open Issues: 2
Releases: 4

Created about 5 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

CORAL

CORAL (Contextual Ontology-based Repository Analysis Library) is a framework for rigorous self-validated data modeling and integrative, reproducible data analysis.

This software was developed at the Berkeley Lab by Pavel S. Novichkov, John-Marc Chandonia, Charles DeVilholm, and Adam P. Arkin.

CORAL Prototype Implementation (CORAL) Copyright (c) 2021-2023, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

This software is available under the GNU Affero General Public License ("AGPL") or a separate commercial use license. If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at IPO@lbl.gov. If you would like more information about obtaining this software under the terms of the commercial use license rather than the AGPL, please contact Berkeley Lab's Intellectual Property Office at IPO@lbl.gov.

NOTICE. U.S. Government Rights. The Software was developed under funding from the U.S. Government. During a period of commercialization granted to Berkeley Lab by the U.S. Department of Energy, the U.S. Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly, by or on behalf of the U.S. Government. Subsequent to that period, the U.S. Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

This work by ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) (http://enigma.lbl.gov), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory, is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, under contract number DE-AC02-05CH11231.

Citation

Novichkov PS^*, Chandonia JM^*, Arkin AP. 2022. CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis. Gigascience 2022 Oct 17;11:giac089. [PubMed]|[PDF]

^* Joint first authors

Note that a lot of documentation, including an overview of the software, is in the Supplemental PDF, also called "giac089_Supplemental_File" on the journal's website.

Installation

Follow the installation instructions in back_end, then the instructions in front_end.

Owner

Name: John-Marc Chandonia
Login: jmchandonia
Kind: user
Location: berkeley, ca
Company: Berkeley National Lab

Website: https://www.strgen.org/~jmc/
Repositories: 47
Profile: https://github.com/jmchandonia

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use CORAL, please cite the Gigascience publication, from 'preferred-citation'"
repository-code: "https://github.com/jmchandonia/CORAL"
title: "CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis"
authors:
  -
    given-names: "Pavel S"
    family-names: "Novichkov"
    affiliation: "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"
    orcid: https://orcid.org/0000-0002-1102-007X
  -
    given-names: "John-Marc"
    family-names: "Chandonia"
    affiliation: "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"
    orcid: https://orcid.org/0000-0002-5153-9079
  -
    given-names: "Charles"
    family-names: "DeVilholm"
    affiliation: "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"
  -
    given-names: "Adam P"
    family-names: "Arkin"
    affiliation: "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and Department of Bioengineering, University of California, Berkeley, CA 94720, USA"
    orcid: https://orcid.org/0000-0002-4999-2931
preferred-citation:
  title: "CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis"
  journal: "Gigascience"
  doi: "10.1093/gigascience/giac089"
  year: 2022
  type: article
  notes: "Pavel S. Novichkov and John-Marc Chandonia are joint first authors; John-Marc Chandonia and Adam P. Arkin are corresponding authors"
  authors:
    -
      given-names: "Pavel S"
      family-names: "Novichkov"
      affiliation: "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"
      orcid: https://orcid.org/0000-0002-1102-007X
    -
      given-names: "John-Marc"
      family-names: "Chandonia"
      affiliation: "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"
      orcid: https://orcid.org/0000-0002-5153-9079
      email: JMChandonia@lbl.gov
    -
      given-names: "Adam P"
      family-names: "Arkin"
      affiliation: "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and Department of Bioengineering, University of California, Berkeley, CA 94720, USA"
      orcid: https://orcid.org/0000-0002-4999-2931
      email: APArkin@lbl.gov

GitHub Events

Total

Issues event: 1
Watch event: 2
Push event: 32

Last Year

Issues event: 1
Watch event: 2
Push event: 32

Dependencies

front_end/package-lock.json npm

1750 dependencies

front_end/package.json npm

@angular-devkit/build-angular ^0.1102.8 development
@angular/cli ^11.2.8 development
@angular/compiler-cli ~11.2.9 development
@angular/language-service ~11.2.9 development
@ngneat/spectator ^5.9.0 development
@types/datatables.net ^1.10.19 development
@types/googlemaps 3.39.12 development
@types/jasmine ~2.8.8 development
@types/jasminewd2 ^2.0.8 development
@types/node ^12.11.1 development
codelyzer ^6.0.1 development
copy-webpack-plugin ^5.1.1 development
jasmine-core ~3.5.0 development
jasmine-spec-reporter ~5.0.0 development
karma ~6.3.2 development
karma-chrome-launcher ~3.1.0 development
karma-coverage-istanbul-reporter ~3.0.2 development
karma-jasmine ~4.0.0 development
karma-jasmine-html-reporter ^1.5.0 development
ng-mocks ^11.10.1 development
protractor ~7.0.0 development
ts-node ~7.0.0 development
tslint ~6.1.0 development
typescript ~4.0.7 development
@agm/core ^3.0.0-beta.0
@angular-devkit/schematics ^11.2.8
@angular-slider/ngx-slider ^2.0.3
@angular/animations ~11.2.9
@angular/common ~11.2.9
@angular/compiler ~11.2.9
@angular/core ~11.2.9
@angular/forms ~11.2.9
@angular/platform-browser ~11.2.9
@angular/platform-browser-dynamic ~11.2.9
@angular/router ~11.2.9
@auth0/angular-jwt ^3.0.1
@ng-select/ng-select ^6.1.0
@swimlane/ngx-datatable ^18.0.0
@types/d3 ^5.7.2
@types/jquery ^3.3.38
angular-plotly.js 1.4.0
angular-resizable-element ^3.3.3
angular-tree-component ^8.5.6
bootstrap 4.0.0-beta.2
class-transformer ^0.2.3
core-js ^2.6.11
d3 ^5.16.0
datatables.net ^1.10.22
datatables.net-bs4 ^1.10.22
jquery ^3.5.1
lodash-es ^4.17.21
ngx-bootstrap ^5.6.1
ngx-spinner ^11.0.1
plotly.js ^1.54.5
rxjs ~6.5.5
sse.js ^0.5.0
terser-webpack-plugin ^2.3.7
tslib ^2.0.0
vis-data ^6.6.1
vis-network ^8.3.1
vis-util ^4.3.3
visjs-network ^4.24.11
zone.js ~0.10.2

back_end/python/setup.py pypi

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