-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
[doc]build a more accessible mkdocs wiki website
- Loading branch information
1 parent
64aed5e
commit 744d9af
Showing
99 changed files
with
9,161 additions
and
6 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,28 @@ | ||
name: ci | ||
on: | ||
push: | ||
branches: | ||
- main | ||
permissions: | ||
contents: write | ||
jobs: | ||
deploy: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v4 | ||
- name: Configure Git Credentials | ||
run: | | ||
git config user.name github-actions[bot] | ||
git config user.email 41898282+github-actions[bot]@users.noreply.github.com | ||
- uses: actions/setup-python@v5 | ||
with: | ||
python-version: 3.x | ||
- run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV | ||
- uses: actions/cache@v4 | ||
with: | ||
key: mkdocs-material-${{ env.cache_id }} | ||
path: .cache | ||
restore-keys: | | ||
mkdocs-material- | ||
- run: pip install mkdocs-material | ||
- run: mkdocs gh-deploy --force |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -17,12 +17,12 @@ This software utilizes 2D averages and their corresponding alignment information | |
|
||
## Requirements | ||
|
||
* This software requires a GPU and CUDA acceleration, necessitating the installation of CUDA drivers and libraries, as well as the cupy library. | ||
* In some cases, [pyem](https://github.com/asarnow/pyem) is also needed to convert cryoSPARC’s `.cs` files to Relion’s `.star` format for processing. | ||
* This software requires a GPU and CUDA acceleration. So, the installation of CUDA drivers and libraries is necessary. | ||
* [pyem](https://github.com/asarnow/pyem) is also needed to convert cryoSPARC’s `.cs` files to Relion’s `.star` format for processing. | ||
|
||
## Installation | ||
|
||
For specific installation methods, please refer to the installation document: [[Installation Document]](./doc/en/Installation_en.md) [[安装文档]](./doc/zh-CN/Installation_zh-CN.md) | ||
For specific installation methods, please refer to the wiki installation section. | ||
|
||
## Usage | ||
|
||
|
@@ -34,15 +34,15 @@ MemXTerminator gui & | |
|
||
``` | ||
|
||
For detailed usage tutorials, please refer to the documentation: [[Usage Index]](./doc/index.md) | ||
For detailed usage tutorials, please refer to the wiki usage section. | ||
|
||
## License | ||
|
||
This software is licensed under GPL v3.0. | ||
|
||
## Acknowledgement | ||
|
||
Thanks to Jack Zhang@Yale MBB for his guidance. | ||
Thanks to Jack(Kai) Zhang@Yale MBB for his guidance. | ||
|
||
## Contributing | ||
|
||
|
@@ -52,4 +52,4 @@ I am still working on improving this software. More exciting features are on the | |
|
||
## Contact | ||
|
||
If you have any questions, please contact me: [email protected] | ||
If you have any questions, please contact me: [[email protected]](mailto:[email protected]) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,119 @@ | ||
site_name: MemXTerminator Wiki | ||
repo_url: https://github.com/ZhenHuangLab/MemXTerminator | ||
repo_name: MemXTerminator | ||
site_description: A simple and beautiful wiki for MemXTerminator | ||
site_author: Zhen Huang | ||
|
||
theme: | ||
name: material | ||
custom_dir: ./wiki/overrides | ||
language: en | ||
favicon: assets/icons/favicon.svg | ||
icon: | ||
logo: simple/gitbook | ||
font: | ||
text: "Roboto Slab" | ||
code: "Roboto Mono" | ||
palette: | ||
- media: "(prefers-color-scheme)" | ||
toggle: | ||
icon: material/brightness-auto | ||
name: Switch to dark mode | ||
|
||
# Palette toggle for light mode | ||
- media: "(prefers-color-scheme: light)" | ||
scheme: default | ||
toggle: | ||
icon: material/brightness-7 | ||
name: Switch to system preference | ||
|
||
# Palette toggle for dark mode | ||
- media: "(prefers-color-scheme: dark)" | ||
scheme: slate | ||
toggle: | ||
icon: material/brightness-4 | ||
name: Switch to light mode | ||
features: | ||
- navigation.instant | ||
- navigation.instant.progress | ||
- navigation.path | ||
- navigation.indexes | ||
- navigation.footer | ||
- announce.dismiss | ||
- toc.follow | ||
- content.code.copy | ||
- navigation.top | ||
- search.suggest | ||
- search.highlight | ||
- search.share | ||
|
||
docs_dir: ./wiki/docs | ||
site_dir: ./wiki/site | ||
|
||
plugins: | ||
- search | ||
|
||
markdown_extensions: | ||
# Python Markdown | ||
- abbr | ||
- admonition | ||
- attr_list | ||
- pymdownx.emoji: | ||
emoji_index: !!python/name:material.extensions.emoji.twemoji | ||
emoji_generator: !!python/name:material.extensions.emoji.to_svg | ||
- def_list | ||
- footnotes | ||
- md_in_html | ||
- toc: | ||
permalink: true | ||
|
||
# Python Markdown Extensions | ||
- pymdownx.arithmatex: | ||
generic: true | ||
- pymdownx.betterem: | ||
smart_enable: all | ||
- pymdownx.caret | ||
- pymdownx.critic | ||
- pymdownx.details | ||
- pymdownx.highlight | ||
- pymdownx.inlinehilite | ||
- pymdownx.keys | ||
- pymdownx.mark | ||
- pymdownx.smartsymbols | ||
- pymdownx.superfences | ||
- pymdownx.tabbed: | ||
alternate_style: true | ||
- pymdownx.tasklist: | ||
custom_checkbox: true | ||
- pymdownx.tilde | ||
|
||
extra_javascript: | ||
- javascripts/mathjax.js | ||
- javascripts/katex.js | ||
- javascripts/extra.js | ||
- https://polyfill.io/v3/polyfill.min.js?features=es6 | ||
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js | ||
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js | ||
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js | ||
|
||
extra_css: | ||
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css | ||
- stylesheets/extra.css | ||
nav: | ||
- Home: index.md | ||
- Installation: ./tutorials/installation.md | ||
- Usage: ./tutorials/usage.md | ||
- Tutorials: | ||
- "Basic workflow": ./tutorials/basic-workflow.md | ||
- "Preprocessing": ./tutorials/preprocessing.md | ||
- Radonfit: | ||
- ./tutorials/radonfit-tutorials/index.md | ||
- Particle Membrane Analysis: ./tutorials/radonfit-tutorials/radonfit-mem-analysis.md | ||
- Particle Membrane Subtraction: ./tutorials/radonfit-tutorials/radonfit-particle-mem-subtraction.md | ||
- Micrograph Membrane Subtraction: ./tutorials/radonfit-tutorials/radonfit-mms.md | ||
- Bezierfit: | ||
- ./tutorials/bezierfit-tutorials/index.md | ||
- Particle Membrane Analysis: ./tutorials/bezierfit-tutorials/bezierfit-mem-analysis.md | ||
- Particle Membrane Subtraction: ./tutorials/bezierfit-tutorials/bezierfit-particle-mem-subtraction.md | ||
- Micrograph Membrane Subtraction: ./tutorials/bezierfit-tutorials/bezierfit-mms.md | ||
- Frequently Asked Questions: ./tutorials/faq.md |
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Oops, something went wrong.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,59 @@ | ||
--- | ||
comments: true | ||
--- | ||
# Welcome to MemXTerminator Wiki! | ||
|
||
A software for membrane analysis and subtraction in cryo-EM. | ||
|
||
![MemXTerminator](./assets/images/0-1.png) | ||
<span class="caption">MemXTerminator</span> | ||
|
||
## Overview | ||
|
||
This software utilizes 2D averages and their corresponding alignment information, employing methods such as Radon transformation, cross-correlation, L1 norm, Bezier curves, Monte Carlo simulations, and genetic algorithms. It analyzes and subtracts membranes of any shape in cryo-EM, ultimately producing particle stacks and micrographs with membrane signals removed, suitable for subsequent membrane protein analysis. | ||
|
||
## Features | ||
|
||
* Capable of analyzing biological membranes of any shape, including simple lines and arcs, as well as more complex shapes like S or W curves; | ||
* Accurately locates and subtracts biological membrane signals; | ||
* Utilizes GPU and CUDA acceleration to enhance computational speed; | ||
* Features a user-friendly GUI for ease of use. | ||
|
||
## Requirements | ||
|
||
* This software requires a GPU and CUDA acceleration. So, the installation of CUDA drivers and libraries is necessary. | ||
* [pyem](https://github.com/asarnow/pyem) is also needed to convert cryoSPARC’s `.cs` files to Relion’s `.star` format for processing. | ||
|
||
## Installation | ||
|
||
For specific installation methods, please refer to the installation section. | ||
|
||
## Usage | ||
|
||
This software has a user-friendly GUI. To use this software, simply type: | ||
|
||
```bash | ||
|
||
MemXTerminator gui & | ||
|
||
``` | ||
|
||
For detailed usage tutorials, please refer to the usage section. | ||
|
||
## License | ||
|
||
This software is licensed under GPL v3.0. | ||
|
||
## Acknowledgement | ||
|
||
Thanks to Jack(Kai) Zhang@Yale MBB for his guidance. | ||
|
||
## Contributing | ||
|
||
**Always welcome!** This software may still has room for improvement such as updating the usage documentation, improving the GUI design, and enhancing the software's usability. | ||
|
||
I am still working on improving this software. More exciting features are on the way! | ||
|
||
## Contact | ||
|
||
If you have any questions, please contact me: [[email protected]](mailto:[email protected]) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,37 @@ | ||
document.addEventListener('DOMContentLoaded', (event) => { | ||
|
||
const overlay = document.createElement('div'); | ||
overlay.style.cssText = 'position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: rgba(0, 0, 0, 0.8); display: none; align-items: center; justify-content: center; z-index: 1000; transition: opacity 0.5s;'; | ||
overlay.style.cursor = 'zoom-out'; | ||
document.body.appendChild(overlay); | ||
|
||
const overlayImg = document.createElement('img'); | ||
overlayImg.style.cssText = 'max-width: 90%; max-height: 90%; transition: transform 0.3s;'; | ||
overlay.appendChild(overlayImg); | ||
|
||
document.body.addEventListener('click', function (e) { | ||
if (e.target.tagName === 'IMG') { | ||
e.target.style.cursor = 'zoom-in'; | ||
overlayImg.src = e.target.src; | ||
overlayImg.style.transform = 'scale(0)'; | ||
overlay.style.display = 'flex'; | ||
overlayImg.style.cursor = 'zoom-out'; | ||
setTimeout(() => { | ||
overlay.style.opacity = '1'; | ||
overlayImg.style.transform = 'scale(1)'; | ||
}, 0); | ||
} | ||
}); | ||
|
||
const closeOverlay = () => { | ||
overlay.style.opacity = '0'; | ||
setTimeout(() => { | ||
overlayImg.style.transform = 'scale(0)'; | ||
}, 50); | ||
setTimeout(() => { overlay.style.display = 'none'; }, 500); | ||
}; | ||
|
||
overlay.addEventListener('click', function () { | ||
closeOverlay(); | ||
}); | ||
}); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,10 @@ | ||
document$.subscribe(({ body }) => { | ||
renderMathInElement(body, { | ||
delimiters: [ | ||
{ left: "$$", right: "$$", display: true }, | ||
{ left: "$", right: "$", display: false }, | ||
{ left: "\\(", right: "\\)", display: false }, | ||
{ left: "\\[", right: "\\]", display: true } | ||
], | ||
}) | ||
}) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,16 @@ | ||
window.MathJax = { | ||
tex: { | ||
inlineMath: [["\\(", "\\)"]], | ||
displayMath: [["\\[", "\\]"]], | ||
processEscapes: true, | ||
processEnvironments: true | ||
}, | ||
options: { | ||
ignoreHtmlClass: ".*|", | ||
processHtmlClass: "arithmatex" | ||
} | ||
}; | ||
|
||
document$.subscribe(() => { | ||
MathJax.typesetPromise() | ||
}) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,64 @@ | ||
/* 使用黑幕,只要<span class="heimu" title="你知道的太多了">输入你想加的文字</span>即可 */ | ||
|
||
span.heimu a.external, | ||
span.heimu a.external:visited, | ||
span.heimu a.extiw, | ||
span.heimu a.extiw:visited { | ||
color: #252525; | ||
} | ||
.heimu, | ||
.heimu a, | ||
a .heimu, | ||
.heimu a.new { | ||
background-color: #252525; | ||
color: #252525; | ||
text-shadow: none; | ||
} | ||
body:not(.heimu_toggle_on) .heimu:hover, | ||
body:not(.heimu_toggle_on) .heimu:active, | ||
body:not(.heimu_toggle_on) .heimu.off { | ||
transition: color .13s linear; | ||
color: white; | ||
} | ||
body:not(.heimu_toggle_on) .heimu:hover a, | ||
body:not(.heimu_toggle_on) a:hover .heimu, | ||
body:not(.heimu_toggle_on) .heimu.off a, | ||
body:not(.heimu_toggle_on) a:hover .heimu.off { | ||
transition: color .13s linear; | ||
color: lightblue; | ||
} | ||
body:not(.heimu_toggle_on) .heimu.off .new, | ||
body:not(.heimu_toggle_on) .heimu.off .new:hover, | ||
body:not(.heimu_toggle_on) .new:hover .heimu.off, | ||
body:not(.heimu_toggle_on) .heimu.off .new, | ||
body:not(.heimu_toggle_on) .heimu.off .new:hover, | ||
body:not(.heimu_toggle_on) .new:hover .heimu.off { | ||
transition: color .13s linear; | ||
color: #BA0000; | ||
} | ||
|
||
/* 使用黑幕 */ | ||
|
||
.overlay-img { | ||
transition: transform 0.25s; | ||
} | ||
|
||
.overlay { | ||
transition: opacity 0.25s; | ||
} | ||
|
||
.small { | ||
display: block; | ||
margin: 0 auto; | ||
width: 60%; | ||
} | ||
|
||
/* 添加图片说明,只要<span class="caption">输入你想加的文字</span>即可 */ | ||
|
||
.caption { | ||
font-style: italic; | ||
font-size: 0.8em; | ||
color: #666; | ||
display: block; | ||
text-align: center; | ||
} |
Oops, something went wrong.