From 7e0b649848d2f9c9788d09151ef0308779effaa7 Mon Sep 17 00:00:00 2001
From: Michiel van Galen <m.van_galen@lumc.nl>
Date: Thu, 10 Jul 2014 14:17:40 +0200
Subject: [PATCH] Some additions
---
notebook.ipynb | 91 +++++++++++++++++++++++++++++++++++++++-----------
1 file changed, 71 insertions(+), 20 deletions(-)
diff --git a/notebook.ipynb b/notebook.ipynb
index 0cb4c87..f77eefb 100644
--- a/notebook.ipynb
+++ b/notebook.ipynb
@@ -1,7 +1,7 @@
{
"metadata": {
"name": "",
- "signature": "sha256:50f0011df38c64a61f87d0fd5e0bd41496c221072c1ed80168340a42e699384e"
+ "signature": "sha256:ffac64912e6dd086a01e7335bc70811bb3d120474fe85a1a87e60f80994db347"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -305,7 +305,9 @@
"- Add elegant explanatory text\n",
"- Direct output of computations\n",
"- Add figures and video\n",
- "- Integration in Git"
+ "- Integration in Git\n",
+ "- Export your notebooks to PDF or HTML (nbconvert)\n",
+ "- Share notebooks easily with nbviewer"
]
},
{
@@ -376,6 +378,7 @@
" \n",
" \n",
"- Remotely, Shark cluster LUMC\n",
+ " - Connect to shark\n",
" - Type 'notebook' and click the given URL"
]
},
@@ -384,7 +387,7 @@
"level": 1,
"metadata": {},
"source": [
- "The user interface"
+ "The notebook user interface"
]
},
{
@@ -556,7 +559,7 @@
"level": 1,
"metadata": {},
"source": [
- "Two mayor cell types"
+ "Two different cell types"
]
},
{
@@ -585,7 +588,15 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "This is a markdown cell which allows to format your document nicely and add context to code cells."
+ "- Markdown cell\n",
+ " - Format your notebook\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "This is a markdown cell which allows to format your document **nicely** and add *context* to code cells."
]
},
{
@@ -609,7 +620,14 @@
"level": 1,
"metadata": {},
"source": [
- "Running python code"
+ "Code cells"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Mainly contain Python code"
]
},
{
@@ -617,7 +635,15 @@
"level": 4,
"metadata": {},
"source": [
- "All of the python goodness works!"
+ "All of the python goodness works inside code cells!"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Running cells\n"
]
},
{
@@ -819,7 +845,7 @@
"level": 1,
"metadata": {},
"source": [
- "\u00a7 Excercise : My first Notebook"
+ "\u00a7 Excercise : My first Notebook (1)"
]
},
{
@@ -837,7 +863,7 @@
" - Remember the keyboard shortcuts or the help function ('h')\n",
"\n",
"\n",
- "Notice the laste cell produced output! We will continue to develop this notebook later this session."
+ "Notice the last cell produced output! We will continue to develop this notebook later this session."
]
},
{
@@ -900,7 +926,7 @@
"level": 4,
"metadata": {},
"source": [
- "Show some output and use it into another function"
+ "Example: Show some output and use it into another function"
]
},
{
@@ -1129,7 +1155,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "Since markdown is a subset of HTML, this will also work"
+ "Since markdown is a superset of HTML, this will also work"
]
},
{
@@ -1232,7 +1258,7 @@
"metadata": {},
"source": [
"<br></br><br></br>\n",
- "Some final examples:"
+ "Some other examples:"
]
},
{
@@ -1320,7 +1346,7 @@
"level": 1,
"metadata": {},
"source": [
- "\u00a7 Excercise : My first Notebook"
+ "\u00a7 Excercise : My first Notebook (2)"
]
},
{
@@ -1330,9 +1356,9 @@
"Let's add some markdown cells to the notebook you created earlier:\n",
" - Select the top code cell\n",
" - Press ESC to go into command mode\n",
- " - Press 'b', this will add a cell above the selected cell\n",
+ " - Press 'a', this will add a cell above the selected cell\n",
" - Notice the focus is on the new cell\n",
- " - Now press 'm' to set the celltype to Markdown\n",
+ " - Now press 'm' to set the celltype to 'Markdown'\n",
" - Press ENTER and add some code (see below for example)\n",
" - Run the cell and see if it worked\n"
]
@@ -1424,23 +1450,48 @@
],
"prompt_number": 46
},
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "\u00a7 Excercise : My first Notebook (3)\n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "A palindromic sequence is a nucleic acid sequence (DNA or RNA) that is the same whether read 5' (five-prime) to 3' (three prime) on one strand or 5' to 3' on the complementary strand with which it forms a double helix. Palindromic sequences play an important role in molecular biology:\n",
+ "\n",
+ "http://en.wikipedia.org/wiki/Palindromic_sequence\n"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "Palindromic sequences play an important role in molecular biology:\n",
"\n",
- "http://en.wikipedia.org/wiki/Palindromic_sequence"
+ "<a href=\"url\"><img src=\"http://upload.wikimedia.org/wikipedia/commons/thumb/7/75/DNA_palindrome.svg/1590px-DNA_palindrome.svg.png\" align=\"center\" width=\"500\" ></a>\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Take some time to develop your notebook further and add the following features to your notebook:\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "Add the following features to your notebook:\n",
- " - Think of function which can test if a seqeunce is palindromic\n",
+ " - Think of function which can test if a sequence is palindromic\n",
+ " - Use the functions 'translate' and 'reverse'\n",
" - Nicely formatted mardown cell(s) explaining the notebook\n",
- " - Add links as references like above"
+ " - Add links as references like the one above\n"
]
},
{
--
GitLab