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<!DOCTYPE HTML>
<html lang="en">
<meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1">
<title>SBOL Visual CSS</title>
<xmp theme="simplex" style="display:none;">
# SBOL Visual CSS
SBOL Visual CSS is a pure-CSS library to easily display schematic DNA sequences
in the Visual SBOL standard:
<div class="sbol-visual centered">
<div class="sbolv promoter">p1</div>
<div class="sbolv cds">lac</div>
<div class="sbolv terminator">terminator</div>
</div>
While very light, SBOL Visual CSS is versatile enough to serve
as a generic SBOL visualizer for databases, web articles, etc.
It is distributed as <a href="dist/sbol-visual-standalone.css" download target="_blank">a self-contained CSS file</a>
(20kb) and is therefore fit for embedding into HTML emails.
Its features include inline SBOL (for instance
<span class="sbol-visual inline">
<span class="sbolv promoter"></span>
<span class="sbolv cds"></span>
<span class="sbolv terminator"></span>
</span>
) and combinatorial designs:
<div class="sbol-visual centered small">
<div class="sbolv insulator"></div>
<div class='combinatorial'>
<div class="sbol-visual">
<div class="sbolv promoter"></div>
<div class="sbolv cds"></div>
<div class="sbolv terminator"></div>
</div>
<div class="sbol-visual">
<div class="sbolv promoter"></div>
<div class="sbolv cds"></div>
<div class="sbolv terminator"></div>
</div>
<div class="sbolv user-defined">(bridge)</div>
</div>
<div class="sbolv promoter"></div>
<div class='combinatorial'>
<div class="sbolv cds"></div>
<div class="sbolv cds"></div>
</div>
<div class="sbolv terminator"></div>
</div>
## Some examples of SBOL Visual CSS in action
- [A drag-and-drop SBOLv editor](examples/drag_and_drop_construct_editor.html)
- [A text-based editor for combinatorial constructs](examples/text_based_construct_editor.html).
- [Advanced tooltips](examples/advanced_tooltips.html)
## Contribute !
SBOL-visual CSS was originally written at the <a href="http://genomefoundry.org/">Edinburgh Genome Foundry</a> by [Zulko](https://github.com/Zulko).
The code is released on [Github](https://github.com/Edinburgh-Genome-Foundry/SBOL-Visual-CSS) under the MIT Licence (Copyright Edinburgh Genome Foundry), everyone is welcome to contribute.
## Basic usage
Link <a href="dist/sbol-visual-standalone.css" download target="_blank">sbol-visual-standalone.css</a> to your html document:
```
<link rel="stylesheet" href="sbol-visual-standalone.css"></link>
```
Then in the body write a `sbol-visual` div with different `sbolv` elements:
```
<div class="sbol-visual">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds"><em>acs</em></div>
<div class="sbolv terminator"></div>
<div class="sbolv insulator"></div>
</div>
```
They will be displayed as follows:
<div class="sbol-visual">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds"><em>acs</em></div>
<div class="sbolv terminator"></div>
<div class="sbolv insulator"></div>
</div>
Note that the `sbolv` divs can contain any kind of html, for instance a link:
**Code:**
```
<div class="sbolv cds">
<a href="http://www.uniprot.org/uniprot/P0ACJ8">
Gene <em>crp</em>
</a>
</div>
```
**Result:**
<div class="sbolv cds">
<a href="http://www.uniprot.org/uniprot/P0ACJ8">
Gene <em>crp</em>
</a>
</div>
## Centering the symbols
An easy way to center the symbols is to add `centered` to the `sbol-visual` div.
Beware that all lines will be centered, even if they contain only a single symbol (which can happen at the end of a line wrap).
**Code:**
```
<div class="sbol-visual centered">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv cds">bla</div>
<div class="sbolv terminator">t2</div>
</div>
```
**Result:**
<div class="sbol-visual centered">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv cds">bla</div>
<div class="sbolv terminator">t2</div>
</div>
## Adaptive width and line break
Put any html you want into the `sbolv` divs, the SBOL symbols will stretch to make space:
**Code:**
```
<div class="sbol-visual centered">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds">some longer gene name</div>
<div class="sbolv terminator"></div>
</div>
```
**Result:**
<div class="sbol-visual centered">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds">some longer gene name</div>
<div class="sbolv terminator"></div>
</div>
If the caption is longer than `sbolv.max-width` (default is `200px`) the caption will be wrapped:
<div class="sbol-visual centered">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds">some really very long caption that you could have made shorter</div>
<div class="sbolv terminator"></div>
</div>
And if there the `sbolv` take too much place for one line only they are
automatically wrapped to the line (try changing your window's width and see how it responds):
<div class="sbol-visual">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds"><em>acs</em></div>
<div class="sbolv terminator"></div>
<div class="sbolv insulator"></div>
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds"><em>acs</em></div>
<div class="sbolv terminator"></div>
<div class="sbolv insulator"></div>
<div class="sbolv promoter"> P1 </div>
<div class="sbolv ribosome-entry-site"> rbs 1 </div>
<div class="sbolv cds"><em>acs</em></div>
<div class="sbolv terminator"></div>
<div class="sbolv insulator"></div>
</div>
## Changing the symbols' size
Since the symbols are vector graphics they will render well at any size.
The size of the symbols is driven by the height of the `sbolv` divs.
To get smaller symbols you would first add CSS class `small` to `sbol-visual`:
```
.sbol-visual.small .sbolv {
height: 80px; /* default is 120px */
min-width: 35px; /* default is 50px */
}
```
Then add `small` to your div's classes:
**Code:**
```
<div class="sbol-visual small centered">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv cds">bla</div>
<div class="sbolv terminator">t2</div>
</div>
```
**Result:**
<div class="sbol-visual centered small">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv cds">bla</div>
<div class="sbolv terminator">t2</div>
</div>
<style>
.sbol-visual.small .sbolv {
height: 80px;
min-width: 35px;
}
</style>
## Combinatorial designs
Combinatorial designs (where several possibilities are given for some regions of the design) can be represented by grouping several symbols inside a div with class `combinatorial`.
**Code:**
```
<div class="sbol-visual centered small">
<div class="sbolv promoter">p1</div>
<div class='combinatorial'>
<div class="sbolv cds">gfp-mut2</div>
<div class="sbolv cds">gfp-mut3</div>
<div class="sbolv cds">yfp</div>
</div>
<div class='combinatorial'>
<div class="sbolv terminator">term1</div>
<div class="sbolv terminator">term2</div>
</div>
<div class="sbolv insulator">insulator</div>
</div>
**Result:**
```
<div class="sbol-visual centered small">
<div class="sbolv promoter">p1</div>
<div class='combinatorial'>
<div class="sbolv cds">gfp-mut2</div>
<div class="sbolv cds">gfp-mut3</div>
<div class="sbolv cds">yfp</div>
</div>
<div class='combinatorial'>
<div class="sbolv terminator">term1</div>
<div class="sbolv terminator">term2</div>
</div>
<div class="sbolv insulator">insulator</div>
</div>
You can also insert a `sbol-visual` div inside a `combinatorial` div to make more complex combinations:
**Code:**
```
<div class="sbol-visual centered small">
<div class="sbolv insulator"></div>
<div class='combinatorial'>
<div class="sbol-visual">
<div class="sbolv promoter"></div>
<div class="sbolv cds"></div>
<div class="sbolv terminator"></div>
</div>
<div class="sbol-visual">
<div class="sbolv promoter"></div>
<div class="sbolv cds"></div>
<div class="sbolv terminator"></div>
</div>
<div class="sbolv user-defined">(bridge)</div>
</div>
<div class="sbolv promoter"></div>
<div class='combinatorial'>
<div class="sbolv cds"></div>
<div class="sbolv cds"></div>
</div>
<div class="sbolv terminator"></div>
</div>
```
**Result:**
<div class="sbol-visual centered small">
<div class="sbolv insulator"></div>
<div class='combinatorial'>
<div class="sbol-visual">
<div class="sbolv promoter"></div>
<div class="sbolv cds"></div>
<div class="sbolv terminator"></div>
</div>
<div class="sbol-visual">
<div class="sbolv promoter"></div>
<div class="sbolv cds"></div>
<div class="sbolv terminator"></div>
</div>
<div class="sbolv user-defined">(bridge)</div>
</div>
<div class="sbolv promoter"></div>
<div class='combinatorial'>
<div class="sbolv cds"></div>
<div class="sbolv cds"></div>
</div>
<div class="sbolv terminator"></div>
</div>
And it is possible to nest combinatorial representations, to represent
combinatorial libraries obtained from two or more other combinatorial
libraries.
**Code:**
```
<div class="sbol-visual centered small">
<div class='combinatorial'>
<div class="sbol-visual">
<div class='combinatorial'>
<div class="sbolv promoter">Pr1</div>
<div class="sbolv promoter">Pr2</div>
</div>
<div class="sbolv cds"><em>acs</em></div>
</div>
<div class="sbol-visual">
<div class='combinatorial'>
<div class="sbolv promoter">PrA</div>
<div class="sbolv promoter">PrB</div>
</div>
<div class="sbolv cds"><em>bla</em></div>
</div>
</div>
<div class="sbolv terminator"></div>
</div>
```
**Result:**
<div class="sbol-visual centered small">
<div class='combinatorial'>
<div class="sbol-visual">
<div class='combinatorial'>
<div class="sbolv promoter">Pr1</div>
<div class="sbolv promoter">Pr2</div>
</div>
<div class="sbolv cds"><em>acs</em></div>
</div>
<div class="sbol-visual">
<div class='combinatorial'>
<div class="sbolv promoter">PrA</div>
<div class="sbolv promoter">PrB</div>
</div>
<div class="sbolv cds"><em>bla</em></div>
</div>
</div>
<div class="sbolv terminator"></div>
</div>
## Antisense symbols
**Code:**
```
<div class="sbol-visual centered small">
<div class="sbolv antisense terminator"></div>
<div class="sbolv antisense cds">cds 1</div>
<div class="sbolv antisense promoter"></div>
<div class="sbolv promoter"></div>
<div class="sbolv cds">cds 2</div>
</div>
```
**Result:**
<div class="sbol-visual centered small">
<div class="sbolv antisense terminator"></div>
<div class="sbolv antisense cds">cds 1</div>
<div class="sbolv antisense promoter"></div>
<div class="sbolv promoter"></div>
<div class="sbolv cds">cds 2</div>
</div>
If you don't fancy the inverted text of the antisense
symbol labels, place the label inside an `antisense` div:
**Code:**
```
<div class="sbol-visual centered small">
<div class="sbolv antisense terminator"></div>
<div class="sbolv antisense cds">
<div class="antisense">cds 1</div>
</div>
<div class="sbolv antisense promoter"></div>
</div>
```
**Result:**
<div class="sbol-visual centered small">
<div class="sbolv antisense terminator"></div>
<div class="sbolv antisense cds">
<div class="antisense">cds 1</div>
</div>
<div class="sbolv antisense promoter"></div>
</div>
Also note that is is possible to invert a whole block at once
making the block antisense:
**Code:**
```
<div class="sbol-visual centered small antisense">
<div class="sbolv promoter"></div>
<div class="sbolv cds">
<div class="antisense">cds</div>
</div>
<div class="sbolv terminator"></div>
</div>
```
**Result:**
<div class="sbol-visual centered small antisense">
<div class="sbolv promoter"></div>
<div class="sbolv cds">
<div class="antisense">cds</div>
</div>
<div class="sbolv terminator"></div>
</div>
## Inline symbols
Inline symbols use a `span` and the `inline` class:
```
To make an expression unit you need
a promoter (<span class="sbolv inline promoter"></span>)
a CDS (<span class="sbolv inline cds"></span>)
and a terminator (<span class="sbolv inline terminator"></span>).
The final result looks like this:
<span class="sbol-visual inline">
<span class="sbolv promoter"></span>
<span class="sbolv cds"></span>
<span class="sbolv terminator"></span>
</span>.
```
To make an expression unit you need
a promoter (<span class="sbolv inline promoter"></span>)
a CDS (<span class="sbolv inline cds"></span>)
and a terminator (<span class="sbolv inline terminator"></span>).
The final result looks like this:
<span class="sbol-visual inline">
<span class="sbolv promoter"></span>
<span class="sbolv cds"></span>
<span class="sbolv terminator"></span>
</span>.
## Changing the color of the symbols
For the moment there is no easy way to change the color of the symbols - apart
from modifying the SVG files. However it is possible to invert all colors of the
`sbolv` elements with the `inverted` class. The symbols and caption appear then white.
```
<div style="background:black; padding-top:20px;">
<div class="sbol-visual centered inverted">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv cds">bla</div>
<div class="sbolv terminator">t2</div>
</div>
</div>
```
<div style="background:black; padding-top:20px;">
<div class="sbol-visual centered inverted">
<div class="sbolv promoter"> P1 </div>
<div class="sbolv cds">bla</div>
<div class="sbolv terminator">t2</div>
</div>
</div>
## Using SBOL Visual CSS in an email
To send an email featuring SBOLv symbols, SBOL Visual CSS must be embedded into
the HTML of the email (see [this Python script](examples/embed_SBOLv_in_html_email.py)).
## Generating a PNG
It is possible to convert SBOLv images to PDF, PNG, etc. using any modern HTML
renderer. For instance [this Python script](examples/render_png_with_wkHTMLtoImage.py)
uses [wkHTMLtoPDF](http://wkhtmltopdf.org/) to generate PNGs from a list of elements.
It implements the practical function `render_sbolv` which is used as follows:
```
render_sbolv(
sbolv_elements=[
("promoter", "P1"),
("cds", "my favourite gene with a super long name"),
("terminator", "Tr. 1"),
("promoter", "P2"),
("cds", "<em>acs</em>"),
("terminator", "Tr. 2")
],
outfile="rendered_sbolv.png",
css_stylesheets=["../dist/sbol-visual-standalone.css"]
)
```
<img src="examples/rendered_sbolv.png" class="centered-image"/>
## Reference
Here are the different `sbolv` classes supported, in alphabetical order:
<table>
<tr>
<th>`sbolv` class</th>
<th>Symbol</th>
</tr>
<tr><td>`blunt-restriction-site`</td><td><div class="sbolv blunt-restriction-site"></div></td></tr>
<tr><td>`cds`</td><td><div class="sbolv cds"></div></td></tr>
<tr><td>`five-prime-overhang`</td><td><div class="sbolv five-prime-overhang"></div></td></tr>
<tr><td>`five-prime-sticky-restriction-site`</td><td><div class="sbolv five-prime-sticky-restriction-site"></div></td></tr>
<tr><td>`insulator`</td><td><div class="sbolv insulator"></div></td></tr>
<tr><td>`primer-binding-site`</td><td><div class="sbolv primer-binding-site"></div></td></tr>
<tr><td>`origin-of-replication`</td><td><div class="sbolv origin-of-replication"></div></td></tr>
<tr><td>`operator`</td><td><div class="sbolv operator"></div></td></tr>
<tr><td>`promoter`</td><td><div class="sbolv promoter"></div></td></tr>
<tr><td>`protease-site`</td><td><div class="sbolv protease-site"></div></td></tr>
<tr><td>`protein-stability-element`</td><td><div class="sbolv protein-stability-element"></div></td></tr>
<tr><td>`restriction-enzyme-recognition-site`</td><td><div class="sbolv restriction-enzyme-recognition-site"></div></td></tr>
<tr><td>`ribonuclease-site`</td><td><div class="sbolv ribonuclease-site"></div></td></tr>
<tr><td>`ribosome-entry-site`</td><td><div class="sbolv ribosome-entry-site"></div></td></tr>
<tr><td>`rna-stability-element`</td><td><div class="sbolv rna-stability-element"></div></td></tr>
<tr><td>`signature`</td><td><div class="sbolv signature"></div></td></tr>
<tr><td>`terminator`</td><td><div class="sbolv terminator"></div></td></tr>
<tr><td>`three-prime-overhang`</td><td><div class="sbolv three-prime-overhang"></div></td></tr>
<tr><td>`three-prime-sticky-restriction-site`</td><td><div class="sbolv three-prime-sticky-restriction-site"></div></td></tr>
<tr><td>`user-defined`</td><td><div class="sbolv user-defined"></div></td></tr>
</table>
<a href="https://github.com/Edinburgh-Genome-Foundry/SBOL-Visual-CSS">
<img style="position: absolute; top: 0; right: 0; border: 0; z-index: 1000; margin: 0;"
src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png" alt="Fork me on GitHub">
</a>
</xmp>
<!-- <script src="http://strapdownjs.com/v/0.2/strapdown.js"></script> -->
<script src="https://cdn.rawgit.com/arturadib/strapdown/gh-pages/v/0.2/strapdown.js"></script>
<link rel="stylesheet" href="dist/sbol-visual-standalone.css"></link>
<style language="css" type="text/css">
@import url(https://fonts.googleapis.com/css?family=Raleway);
h1 {
font-size: 50px;
text-align: center;
margin-bottom:30px
}
h2 {
margin-top: 35px;
}
body{
}
#content {
font-family: "Raleway";
font-size: 16px;
max-width: 700px;
}
code, pre {
font-size:16px;
}
.sbol-visual.big .sbolv {
height: 150px;
min-width: 60px;
}
table {
margin:auto;
}
th, td {
text-align: center !important;
vertical-align: middle !important;
}
#headline {
padding-left:50px;
background: url("EGF-logo.svg") no-repeat;
background-size: 40px;
}
.centered-image {
display: block;
margin-left: auto;
margin-right: auto
}
</style>
</html>