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Chaste

Chaste: Cancer, Heart and Soft Tissue Environment - Published in JOSS (2020)

https://github.com/chaste/chaste

Science Score: 95.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    48 of 78 committers (61.5%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

c-plus-plus cancer-research cell-based computational-biology developmental-biology electrophysiology hpc-applications mathematical-biology mathematical-modelling physiology
Last synced: 6 months ago · JSON representation

Repository

Chaste - Cancer Heart And Soft Tissue Environment - main public repository.

Basic Info
  • Host: GitHub
  • Owner: Chaste
  • License: other
  • Language: C++
  • Default Branch: develop
  • Homepage: https://chaste.github.io/
  • Size: 321 MB
Statistics
  • Stars: 139
  • Watchers: 17
  • Forks: 65
  • Open Issues: 62
  • Releases: 12
Topics
c-plus-plus cancer-research cell-based computational-biology developmental-biology electrophysiology hpc-applications mathematical-biology mathematical-modelling physiology
Created over 9 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

README.md

DOIBuild chaste/develop

Welcome to Chaste

If you are new to Chaste please see our Getting Started wiki page.

The files you have downloaded contain the source code for all Chaste functionality. Chaste makes use of a variety of external libraries and packages that need to be installed on your machine. The Install Guide webpage provides a comprehensive guide on how to install these external tools.

Chaste is distributed as open source software under the 3-clause BSD licence. For full details see the file Copying.pdf. Chaste uses various third party libraries which have their own licences. For details of these licences and the impact they may have on your use of Chaste please see Licences.html.

Chaste includes a complete test suite covering all the source code. The easiest way to use existing source codes is to create a test file which can call upon any of the source files.
The Chaste build system can build this file for you and handle all of the dependencies and library calls.

We suggest you use the projects directory in this manner to store your own source and test files if you do not wish to modify the Chaste source code. For more information, see the User Projects webpage.

For more information please refer to the Chaste website at: https://chaste.github.io

Information on changes in this release can be found on the release notes webpage.

Tutorial examples for this release are available at: https://chaste.github.io/releases/2024.2/user-tutorials/

API documentation generated from the code by Doxygen is available at: https://chaste.github.io/doxygen-releases/release_2024.2

Chaste welcomes contributions from the community. For information on how to contribute to Chaste, and for support and bug reports, please see the file CONTRIBUTING.md.

A number of external libraries have been created that build on the Chaste trunk code. These include the following: * Microvessel Chaste (https://jmsgrogan.github.io/MicrovesselChaste/) * ChemChaste (https://github.com/OSS-Lab/ChemChaste)

Note that, while Chaste developers may have been contributed to the development of these external libraries, we are unable to offer any support in their maintenance, testing or usage. If you have any questions about one of these external libraries, please contact that library's lead developer directly.

Owner

  • Name: Chaste - Cancer Heart and Soft Tissue Environment
  • Login: Chaste
  • Kind: organization
  • Email: chaste-users@maillist.ox.ac.uk
  • Location: United Kingdom

C++ library for computational biology and physiology simulations

JOSS Publication

Chaste: Cancer, Heart and Soft Tissue Environment
Published
March 13, 2020
DOI
Volume 5, Issue 47, Page 1848
Authors
Fergus R. Cooper ORCID
Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
Ruth E. Baker ORCID
Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
Miguel O. Bernabeu ORCID
Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
Rafel Bordas ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Louise Bowler ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Alfonso Bueno-Orovio ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Helen M. Byrne ORCID
Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
Valentina Carapella ORCID
Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
Louie Cardone-Noott
Department of Computer Science, University of Oxford, Oxford, UK
Jonathan Cooper ORCID
Research IT Services, University College London, London, UK
Sara Dutta
Department of Computer Science, University of Oxford, Oxford, UK
Benjamin D. Evans ORCID
Centre for Biomedical Modelling and Analysis, Living Systems Institute, University of Exeter, Exeter, UK, School of Psychological Science, University of Bristol, Bristol, UK
Alexander G. Fletcher ORCID
School of Mathematics & Statistics, University of Sheffield, Sheffield, UK, Bateson Centre, University of Sheffield, Sheffield, UK
James A. Grogan
Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
Wenxian Guo ORCID
Department of Computer Science, University of Saskatchewan, Canada
Daniel G. Harvey
Department of Computer Science, University of Oxford, Oxford, UK
Maurice Hendrix ORCID
Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK, Digital Research Service, University of Nottingham, Nottingham, UK
David Kay ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Jochen Kursawe ORCID
Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
Philip K. Maini ORCID
Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
Beth McMillan ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Gary R. Mirams ORCID
Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
James M. Osborne ORCID
School of Mathematics and Statistics, University of Melbourne, Victoria, Australia
Pras Pathmanathan ORCID
Office of Science and Engineering Laboratories (OSEL), Center for Devices and Radiological Health (CDRH), U.S. Food and Drug Administration (FDA), Silver Spring, MD 20993, USA
Joe M. Pitt-Francis ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Martin Robinson ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Blanca Rodriguez ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Raymond J. Spiteri
Department of Computer Science, University of Saskatchewan, Canada
David J. Gavaghan ORCID
Department of Computer Science, University of Oxford, Oxford, UK
Editor
Marie E. Rognes ORCID
Tags
C++ cardiac electrophysiology monodomain bidomain simulation cancer heart lung cell-based
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 42
  • Release event: 1
  • Issues event: 77
  • Watch event: 13
  • Delete event: 29
  • Issue comment event: 170
  • Push event: 140
  • Pull request review comment event: 21
  • Pull request review event: 69
  • Pull request event: 73
  • Fork event: 9
Last Year
  • Create event: 42
  • Release event: 1
  • Issues event: 77
  • Watch event: 13
  • Delete event: 29
  • Issue comment event: 170
  • Push event: 140
  • Pull request review comment event: 21
  • Pull request review event: 69
  • Pull request event: 73
  • Fork event: 9

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 6,913
  • Total Committers: 78
  • Avg Commits per committer: 88.628
  • Development Distribution Score (DDS): 0.855
Past Year
  • Commits: 246
  • Committers: 8
  • Avg Commits per committer: 30.75
  • Development Distribution Score (DDS): 0.589
Top Committers
Name Email Commits
Joe Pitt-Francis j****f@c****k 1,005
Gary Mirams g****s@g****m 819
Jonathan Cooper j****r@c****k 718
Fergus Cooper f****2@g****m 588
Fergus Cooper c****r@m****k 507
James Osborne j****o@c****k 501
Alex Fletcher f****r@m****k 467
Dan Harvey d****y@d****k 231
MauriceHendrix m****x@n****k 219
Alexander Fletcher a****r@s****k 191
James Osborne j****e@g****m 163
fcooper f****r@b****5 160
Pras Pathmanathan p****s@c****k 156
Rafel Bordas r****b@c****k 135
Martin Robinson m****n@m****k 122
Louie Cardone-Noott l****t@l****k 105
Matthew Leach m****h@h****k 102
Kwabena N Amponsah k****m@y****m 79
Ben Evans b****s@g****m 54
Aydar u****d@g****m 50
Jochen Kursawe k****e@m****k 44
b3008711 b****1@1****k 44
Martin Robinson m****s@g****m 43
Twin hi@t****m 40
Kevin Hoellring k****g@f****e 38
Yohan Davit d****t@m****k 28
Jack 4****l 26
Alberto Corrias a****o@n****g 26
Thomas Pak t****k@l****k 25
Maurice Hendrix u****2@p****k 21
and 48 more...
Committer Domains (Top 20 + Academic)
maths.ox.ac.uk: 10 cs.ox.ac.uk: 9 dtc.ox.ac.uk: 4 nottingham.ac.uk: 2 sheffield.ac.uk: 2 linacre.ox.ac.uk: 2 pmlapgmi01.nottingham.ac.uk: 2 student.unimelb.edu.au: 2 hotmail.co.uk: 1 19scompl029.ncl.ac.uk: 1 twin.uk.com: 1 fau.de: 1 nus.edu.sg: 1 ucl.ac.uk: 1 balliol.ox.ac.uk: 1 wofford.edu: 1 some.ox.ac.uk: 1 jmsgrogan.com: 1 usask.ca: 1 maastrichtuniversity.nl: 1 sjc.ox.ac.uk: 1 tumbler.cs.ox.ac.uk: 1 keble.ox.ac.uk: 1 merton.ox.ac.uk: 1 victorchang.edu.au: 1 dizzy.cs.ox.ac.uk: 1 luin68386.ad.nottingham.ac.uk: 1 trix.cs.ox.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 93
  • Total pull requests: 88
  • Average time to close issues: 3 months
  • Average time to close pull requests: 22 days
  • Total issue authors: 14
  • Total pull request authors: 10
  • Average comments per issue: 2.67
  • Average comments per pull request: 0.7
  • Merged pull requests: 62
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 57
  • Pull requests: 82
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 15 days
  • Issue authors: 9
  • Pull request authors: 9
  • Average comments per issue: 1.53
  • Average comments per pull request: 0.59
  • Merged pull requests: 60
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • fcooper8472 (50)
  • kwabenantim (18)
  • mirams (16)
  • jmpf (11)
  • jmosborne (8)
  • ptheywood (8)
  • MILeach (5)
  • AlexFletcher (4)
  • BJackal (2)
  • MauriceHendrix (2)
  • bdevans (2)
  • fieldofnodes (1)
  • MichaelClerx (1)
  • Mobinati (1)
  • mobinat (1)
Pull Request Authors
  • fcooper8472 (49)
  • kwabenantim (27)
  • mirams (26)
  • jmpf (9)
  • MILeach (7)
  • jmosborne (7)
  • bdevans (5)
  • ptheywood (5)
  • jonc125 (2)
  • Reshief (2)
  • BJackal (1)
  • MauriceHendrix (1)
Top Labels
Issue Labels
component: infrastructure (44) component: cell_based (23) bug (19) enhancement (17) priority: normal (16) component: core (14) priority: low (12) priority: breaks build (9) good-first-issue (7) priority: high (7) component: heart (6) documentation (3) component: lung (2) help wanted (1)
Pull Request Labels
component: infrastructure (10) ci:off (5) component: cell_based (5) enhancement (5) priority: high (5) priority: normal (4) component: pychaste (1) component: core (1) good-first-issue (1)

Dependencies

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pychaste/src/py/pyproject.toml pypi
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