Jupyter notebooks are a way that you can have code, text, images, and math all live together in harmony. This concept can be called "Literate Proramming", where all code that is written also has comments or an explanation of why it was written (which is not always obvious). In particular, the Jupyter notebook allows you to write some code, run (evaluate) it, and see the output all in once. This is called a "read-eval-print loop" or REPL.
By the end of this notebook, you will have...
Clone the biom262 repository (click here to get the HTTPS URL for cloning: https://github.com/biom262/biom262-2016) to ~/code
or c:\code
.
In your Jupyter notebook
To edit the type of any cell, select it, then use the dropdown menu at the top of the screen.
To insert a new cell, use the Insert option in the toolbar.
To edit any cell, double-click on it.
To execute the contents of any cell (or visualize markdown language), hit the "execute" button in the toolbar (play/pause symbol): Or, press "Shift+Enter" to run the cell and create a new one underneath. "Ctrl+Enter" runs the current cell and doesn't make a new one.
Check out "Help > Keyboard Shortcuts" to get all the possible keyboard shortcuts. Here's an online list of keyboard shortcuts as of April 2015.
Markdown does not automatically hard-wrp carriage returns.
Italics = 1 "*" or "_"
Bold = 2 "**" or "__"
monospace
text (for code) is initiated by a prepending '`' character
Use "" or a preceeding tab to remove formatting issues caused by markdown language syntax.
\- This is not a list
\-- When I do this
example
subexample
Normal link example:
[Class Website](http://en.wikipedia.org "Class Website")
Minimal example:
SampleID|GeneID|ExpressionValue
-|-|-|-
A|ACTB|40
B|ACTB|9500
C|ACTB|0
SampleID | GeneID | ExpressionValue | |
---|---|---|---|
A | ACTB | 40 | |
B | ACTB | 9500 | |
C | ACTB | 0 |
\${a \choose a_1,a_2} $
${a \choose a_1,a_2}$.
Note: If you're getting an error with a red \mathchoice
then you need to upgrade your Jupyter notebook to 4.1. See this issue.
![Example image](http://icons.iconarchive.com/icons/icons-land/medical/256/Body-DNA-icon.png "Example image")
Jupyter notebook allows for test executions for over 50 programming languages within the browser. See the full list of supported tools here: https://github.com/ipython/ipython/wiki/IPython-kernels-for-other-languages
a = "Hello World"
print(a)
Hello World
%%bash
echo "Hello World"
Hello World
%%perl
use strict;
use warnings;
my $a = "Hello World";
print "$a\n";
Hello World
%%bash
and %%perl
magics were used to enter those particular kernels.?
: help command? hat
or ?? hat
!
: run as system shell! pwd
(prints present working directory)%%bash
%magic
pastebin
( Source )%pastebin 3 18-20 ~1/1-5