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Text Formatting with Markdown

MolMeth uses a markup language called Markdown that transforms raw text into nicely formatted documents in html or pdf. The syntax is designed to be intuitive and resemble the common way to write when no formatting is available, a style that is often used to write e-mails. MolMeth also supports some custom features and has it's own syntax in some cases.

Markdown is supported in most places where user inputed text is shown with some restrictions. Naturally single line attributes like names or notes does not support tables and other large block elements.

An example

The following unformatted text will generate the visualisation output below.

**Lorem ipsum**

Lorem ipsum dolor sit amet, consectetuer adipiscing
elit.Etiam laoreet convallis lectus. Maecenas faucibus
velit sed sapien. Vestibulum ante ipsum *primis* in
faucibus orci luctus et ultrices posuere cubilia Curae;
Aenean molestie.

* Nullam iaculis sodales mi.
* Mauris rutrum eros sed lacus.
* Ut ultrices lectus eget lorem.

Duis mauris arcu, commodo pulvinar, facilisis sed,
tincidunt eleifend, augue. Morbi nunc. Suspendisse
feugiat velit id elit.

Text styles

Bold and italic type is used with stars as described below.

Sub- or superscript is entered with _ or ^ and cancelled with another _, ^ or space character. Html and therefore also markdown does not support sub- and superscripting at the same time e.g. dubble indices in mathematical forumlae.

Paragraph with normal text.

*Emphasized text*, also known as *italic*.

**Strongly emphasized text**, also known as **bold**.

Super^1 script^23^, sub_456 script_7890_.

Nesting is also possible A^B_C_D^_E^F^G_H

MolMeth uses unicode encoding for all text storage so any character inputted in a form will appear correctly on the page.

In case you do not know how to type certain symbol you can click the character palette link in the header and copy them from there. An example is show in this sections header.

I can speak ελληνικά!

Links

Use this syntax to make a URL into a clickable link. Do not leave out the protocol part or else markdown will not render it (as in the last example).

<mail@domain.com>

<http://www.website.com>

<www.anothersite.com> <-- Invalid

All e-mail addresses published on MolMeth are obfuscated to prevent them from getting caught by spambots. However, even though we are using a front line technique for this it is not impossible to beat it.

Lists

Standard Markdown supports both numbered and unnumbered lists at multiple levels. Unnumbered list items are defined with - + or * characters. Numbered list items can be defined with any number and dot but will always result in a numbering of 1, 2, 3, 4 … etc.

When nesting lists make sure indent the items in steps of 3 spaces. Other indent sizes can also work but sometimes causes Markdown's parser to misinterpret.

Unnumbered list:

- Paul
- Whiteman

Numbered list:

1. Eddie
2. Cantor

Nested lists:

- Bix
   1. Spiritus
   2. Et
      * Lasse
      * Dahlquist
         6. Hilmer
         7. Borgeling
   3. Artibus
- Beiderbecke

Tables

Tables are a bit cumbersome and tedious to write but please endure it as this is the most intuitive and simple representation.

Header elements are defined by surrounding the text with '#' characters.

Left or right alignment is defined by positioning the text to the left or right in the cell, at most one whitespace or # from border. Center alignment is achieved by having two or more whitespaces or # between the text and both cell borders.

|# Left header ##|### Centered header ###|## Right header #|
|       Cell 1,1 | C_el_l 1,2            | Cell 1,3        |
|       Cell 2,1 |      TIMING: aaa      | Cell 2,3        |
| Cell 3,1       | Cell 3,2              | Cell 3,3        |

However, if you are lazy and do not care about having proper syntax Markdown will still understand what you mean (as long as the first '|' on every line have the same indentation). This is not recommended but is still possible.

|# Left header #|## Centered header ##|## Right header #|
|# Cell 1,1#|C_el_l 1,2|Cell 1,3|
|##Cell 2,1#|  TIMING: aaa  |#Cell 2,3#|
|#Cell 3,1#| Cell 3,2|Cell 3,3|

Figures and Images

Images are added to protocols in the following way.

1. Click "Documents" in the "Resources" menu on the left side of the page. Create a new document and upload the file when filling out the form.
2. Go to the protocol and add the document as an attachment (click the "Add" link in the protocol's attachment section).
3. When selecting a document for the attachment a default embed key will be generated. Generally it will be a pretty long string so it is advisable to change it into something simpler that is easier to use. The key can then be used to incorporate the image in the protocol's description or in a step in the following way:

Markdown	FIGURE: example_diagram If you leave out the description here you will automatically get the document's description instead.
html	Example Diagram If you leave out the description here you will automatically get the document's description instead. Full size

Quick tips

The keyword IMAGE has the same function as FIGURE.

The title is taken from the document. The description can either be written in place or will be taken from the document if left out.

What happens if the original document is modified?

All updates will automatically apply to all protocols using the document. However, the attachment's key is never changed automatically to avoid having to update the protocol's code manually.

Including non-image files

Non-image files are included in the same way as images and will appear in similar box but without the thumbnail.

Attention Marks

MolMeth supports a way to highlight certain paragraphs in a protocol that are of special importance. Currently there are four kinds of attention marks (shown below) and we suggest you use them whenever possible to make sure the reader does not miss important information and give an quick overview of the protocol's waiting points.

TIMING: Incubate on ice for 20 minutes.

CRITICAL: The temperature must never go above 40°C.

CAUTION: Keep the beaker inside a fume
hood until all reagent has dissolved.

NOTE: This step can in some cases be modified and
included together with step 4 in order to save time.
For description of the modified protocol see step 5.