Biochemistry laboratories - 201
Jean-Yves Sgro -jsgro@wisc.edu
Find this document here (short URL) today: http://go.wisc.edu/418lui
*Note*: To see as slides click on **"Gift icon"** at the top right. To revert back to page view click on **"book icon"** when on the first slide.
Hand-outs are in HTML format:
Note: other tutorials are at https://bcrf.biochem.wisc.edu/
material at http://swcarpentry.github.io/python-novice-inflammation/
If you are using a different computer you may need to download the data to be analysed again. Skip if done previously !
python-novice-inflammation
.data
.anaconda-navigator
(the correct answer will likely appear before you type it all!return
keyLaunch
for the jupyter notebookIf the navigator starts and closes the set-up is not correct. The work-around to launching jupyter notebook via Terminal is explained in the next slide/section.
IF Starting the Anaconda Navigator does not work launch the exercise notebook by Terminal line command as detailed below.
Terminal
return
keyWithin the Terminal type the following commands after the $ prompt and press return. The first command places the working directory to the area where the data files are located:
$ cd ~/Desktop/python-novice-inflammation/data
$ jupyter notebook
This will start your default web browser (Safari on the iMacs) and list the data files.
Start a new notebook from the top right pull-down menu "New"
The Default or Root options will both start a Python 3.6 session.
Start a new notebook from the top right pull-down menu "New"
The Default or Root options will both start a Python 3.5 session.
By default the new notebook will be called "Untitled".
Use the menu File > Rename..." to change the name of your notebook of your choosing.
Note: Notebooks are "autosaved" on a regular basis. To save "maually" click on the little disk icon below the word File at the top left.
By default each cell in the notebook is python code
which can be annotated by simple comments with lines starting with the symbol #
.
However, a whole cell can be used to annotate the research we are doing by using the markdown simple formatting language, creating a richer text with header levels, bold and italics or *both, and even tables. To make a cell a markdown* cell use the pull-down menu of the notebook to change from the default code
to Markdown
.
The following code is one way to create Headings
levels:
# Heading 1
## Heading 2
### Heading 3
#### Heading 4
After processing they become:
Normal text is simply typed and paragraphs are created with an empty line in between.
For example the following text (placed here in a mode that does not process)
This is some text that
will become one line when processed.
A blank line will make a new
paragraph to continue the story.
will be processed as:
This is some text that will become one line when processed.
A blank line will make a new paragraph to continue the story.
Bold is accomplished by **
(two stars) or __
(two underscores) before and after the word:
This word is **bold** and this one is __bold__ too.
This word is bold and this one is bold too.
Italics are accomplished by *
or _
before and after the word:
This word is *italic* and this one is _italic_ too.
This word is italic and this one is italic too.
To get both we can combine:
This word is ***both*** and this one is _**both**_ too.
This word is *both* and this one is both too.
Italic | Bold | *Both* | |
---|---|---|---|
Using * |
*italic* italic |
**bold** bold |
***both*** *both* |
Using _ |
_italic_ italic |
__bold__ bold |
___both___ ___both___ |
Combining * and _ |
_**both**_ both |
Table: Summary Table
While the above is mostly sufficient for annotating a notebook, there are more markdown options detailed on web pages such as:
And many more resources exist.
For annotating today's notebook, headings, text, bold and italics should suffice!