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Vectorized Capsid Generation in the Browser with Capsid.js

Negron, D. A.

2020-12-03 bioinformatics
10.1101/2020.12.02.408252 bioRxiv
Show abstract

MotivationFew online services exist for rendering high-quality viral capsid figures compatible with common productivity software to develop effective infographics in the field of virology. ResultsThe capsid.js library renders class I viral capsids within an online application that parameterizes style options, perspectives, and lattice patterns with SVG export. AvailabilityThis 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 informationSupplementary data are available on GitHub.

Matching journals

The top 7 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 1%
18.5%
Similar papers in this journal
2
BMC Bioinformatics
○ 457 papers in training set
Top 1%
6.7%
Similar papers in this journal
3
PLOS ONE
● 5266 papers in training set
Top 24%
6.7%
Similar papers in this journal
4
Journal of Open Source Software
● 25 papers in training set
Top 0.1%
6.7%
Similar papers in this journal
5
PLOS Computational Biology
● 1863 papers in training set
Top 6%
6.3%
Similar papers in this journal
6
Acta Crystallographica Section D Structural Biology
● 59 papers in training set
Top 0.1%
4.0%
7
PeerJ
◐ 308 papers in training set
Top 2%
3.3%
50% of probability mass above
8
Viruses
○ 332 papers in training set
Top 2%
3.2%
9
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
3.2%
10
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.1%
2.4%
11
Virus Evolution
◐ 155 papers in training set
Top 0.7%
1.9%
12
Journal of Molecular Biology
○ 232 papers in training set
Top 2%
1.7%
13
Protein Science
○ 246 papers in training set
Top 2%
1.5%
14
F1000Research
○ 88 papers in training set
Top 2%
1.3%
15
Nucleic Acids Research
◐ 1281 papers in training set
Top 10%
1.3%
16
Gigabyte
● 62 papers in training set
Top 0.7%
1.3%
17
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 3%
1.1%
18
Nature Protocols
○ 33 papers in training set
Top 0.4%
1.1%
19
GigaScience
◐ 212 papers in training set
Top 3%
1.1%
20
eLife
● 5828 papers in training set
Top 62%
1.0%
21
Journal of Neuroscience Methods
○ 122 papers in training set
Top 2%
1.0%
22
Frontiers in Neuroinformatics
○ 41 papers in training set
Top 0.6%
0.9%
23
Frontiers in Genetics
○ 230 papers in training set
Top 5%
0.9%
24
mSystems
● 394 papers in training set
Top 6%
0.8%
25
ImmunoInformatics
○ 12 papers in training set
Top 0.2%
0.8%
26
Journal of Cell Science
● 393 papers in training set
Top 4%
0.8%
27
Frontiers in Bioinformatics
○ 49 papers in training set
Top 1%
0.8%
28
Frontiers in Immunology
○ 638 papers in training set
Top 9%
0.8%
29
Frontiers in Microbiology
○ 427 papers in training set
Top 9%
0.6%
30
Methods in Ecology and Evolution
○ 176 papers in training set
Top 2%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.