democapsid

Render viral capsids in the browser and export SVG.

Science Score: 67.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 13 DOI reference(s) in README
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Academic publication links
Links to: biorxiv.org
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (6.8%) to scientific vocabulary

Keywords

2d 3d biology capsid caspar-klug demoscene elongated figure graphics icosahedron lattice moody oblate perspective projection prolate publication render svg virus

Last synced: 6 months ago · JSON representation ·

Repository

Render viral capsids in the browser and export SVG.

Basic Info

Host: GitHub
Owner: dnanto
License: mit
Language: JavaScript
Default Branch: master
Homepage:
Size: 38.9 MB

Statistics

Stars: 12
Watchers: 2
Forks: 2
Open Issues: 0
Releases: 8

Topics

2d 3d biology capsid caspar-klug demoscene elongated figure graphics icosahedron lattice moody oblate perspective projection prolate publication render svg virus

Created over 5 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Abstract

This work implements Caspar-Klug Theory to generate high-quality, vectorized capsid cartoons in the browser and is the first online tool that provides comprehensive style customization, geometry, and SVG export of icosahedra and nets with different lattice structures.

Run

Run democapsid (v2.2.3): https://dnanto.github.io/democapsid/app.html.

build

bash npm run bump && \ npm run clean && \ npm run minify && \ npm run update && \ npm run zip && \ npm run tar && \ npm install

Paper

Negrón, D. A. (2021). Vectorized Capsid Rendering in the Browser with Capsid.js (p. 2020.12.02.408252). https://doi.org/10.1101/2020.12.02.408252
Negrón, D. A. (2021). Molecular Clock Analysis of Human Adenovirus [Ph.D., George Mason University]. In ProQuest Dissertations and Theses. http://www.proquest.com/docview/2572612100/abstract/9972F7D348C34013PQ/1

Poster

Demoscene

5th place at Demosplash 2021 for the combined demo/intro category (https://www.pouet.net/prod.php?which=90296)

Citation

Please comment on or cite the preprint at bioRxiv, which is Chapter 2 of the dissertation.
This work previously went by the name "capsid.js" and is now "democapsid".

Cited by

Hamann, M. V.; Beschorner, N.; Vu, X.-K.; Hauber, I.; Lange, U. C.; Traenkle, B.; Kaiser, P. D.; Foth, D.; Schneider, C.; Büning, H.; Rothbauer, U.; Hauber, J. Improved Targeting of Human CD4+ T Cells by Nanobody-Modified AAV2 Gene Therapy Vectors. PLOS ONE 2021, 16 (12), e0261269. https://doi.org/10.1371/journal.pone.0261269.

References

Twarock, R., & Luque, A. (2019). Structural puzzles in virology solved with an overarching icosahedral design principle. Nature Communications, 10(1), 4414. https://doi.org/10.1038/s41467-019-12367-3
Lehni, J., & Puckey, J. (2011). Paperjs/paper.js [JavaScript]. Paper.js. https://github.com/paperjs/paper.js
Luque, A., & Reguera, D. (2010). The Structure of Elongated Viral Capsids. Biophysical Journal, 98(12), 2993–3003. https://doi.org/10.1016/j.bpj.2010.02.051
Moody, M. F. (1965). The shape of the T-even bacteriophage head. Virology, 26(4), 567–576. https://doi.org/10.1016/0042-6822(65)90319-3
Caspar, D. L., & Klug, A. (1962). Physical principles in the construction of regular viruses. Cold Spring Harbor Symposia on Quantitative Biology, 27, 1–24. https://doi.org/10.1101/sqb.1962.027.001.005

License

MIT License

Owner

Name: Daniel Antonio Negrón
Login: dnanto
Kind: user

Website: https://dnanto.github.io/dnanto/
Repositories: 3
Profile: https://github.com/dnanto

𐂅𐂂 | 学者馬鹿

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
    democapsid
message: "If you use this software, please cite it as below."
type: software
authors:
    - given-names: Daniel
      family-names: Negrón
      email: dnegron2@gmu.edu
      affiliation: George Mason University
      orcid: "https://orcid.org/0000-0002-6123-2441"
identifiers:
    - type: doi
      value: 10.1101/2020.12.02.408252
      description: The bioRxiv preprint of the paper.
repository-code: "https://github.com/dnanto/democapsid"
url: "https://github.com/dnanto/democapsid/capsid.html"
abstract: >-
    This work implements Caspar-Klug Theory to
    generate high-quality, vectorized capsid cartoons 
    in the browser and is the first online tool that 
    provides comprehensive style customization,
     geometry, and SVG export of icosahedra and nets
    with different lattice structures.
keywords:
    - virus
    - capsid
    - caspar-klug
    - moody
    - icosahedron
    - prolate
    - oblate
    - elongated
    - lattice
    - 2D
    - 3D
    - svg
    - biology
    - graphics
    - render
    - projection
    - perspective
    - publication
    - figure
    - demoscene
license: MIT
preferred-citation:
    type: article
    authors:
        - given-names: Daniel
          family-names: Negrón
          email: dnegron2@gmu.edu
          affiliation: George Mason University
          orcid: "https://orcid.org/0000-0002-6123-2441"
    doi: 10.1101/2020.12.02.408252
    journal: bioRxiv
    abstract: >-
        This work implements Caspar-Klug Theory to
        generate high-quality, vectorized capsid cartoons 
        in the browser and is the first online tool that 
        provides comprehensive style customization,
         geometry, and SVG export of icosahedra and nets
        with different lattice structures.
        Motivation Few online services exist for rendering
        high-quality viral capsid figures compatible with
        common productivity software to develop effective
        infographics in the field of virology.


        Results The capsid.js library renders class I viral
        capsids within an online application that
        parameterizes style options, perspectives, and
        lattice patterns with SVG export.


        Availability This project is actively developed on
        GitHub (https://github.com/dnanto/capsid),
        distributed under the MIT License, hosted on GitHub
        Pages, and runs on modern browsers
        (https://dnanto.github.io/capsid/capsid.html).


        Supplementary information Supplementary data are
        available on GitHub.
    month: 12
    title: >-
        Vectorized Capsid Rendering in the Browser with
        Capsid.js
    year: 2021
    keywords:
        - 2D
        - 3D
        - biology
        - capsid
        - caspar-klug
        - demoscene
        - elongated
        - figure
        - graphics
        - icosahedron
        - lattice
        - oblate
        - perspective
        - projection
        - prolate
        - publication
        - render
        - svg
        - virology
        - virus

GitHub Events

Total

Release event: 2
Push event: 7
Pull request event: 6
Create event: 1

Last Year

Release event: 2
Push event: 7
Pull request event: 6
Create event: 1

Dependencies

.github/workflows/cffconvert.yml actions

actions/checkout v2 composite
citation-file-format/cffconvert-github-action 2.0.0 composite

package-lock.json npm

@jridgewell/gen-mapping 0.3.5 development
@jridgewell/resolve-uri 3.1.2 development
@jridgewell/set-array 1.2.1 development
@jridgewell/source-map 0.3.6 development
@jridgewell/sourcemap-codec 1.5.0 development
@jridgewell/trace-mapping 0.3.25 development
acorn 8.12.1 development
buffer-from 1.1.2 development
commander 2.20.3 development
source-map 0.6.1 development
source-map-support 0.5.21 development
terser 5.31.6 development
paper 0.12.18

package.json npm

terser ^5.31.6 development
paper ^0.12.18

ecosyste.ms

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