Adds directions for slides, tidies up a few more things

Author: dleehr

2016-python.ipynb

@@ -30,17 +30,16 @@
     }
    },
    "source": [
-    "## 01-Warmup: Python & Notebook"
+    "## Python & Notebook"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "- Explain the notebook. Environment for using python that's great for teaching and exploring\n",
-    "- Rename our untitled notebook\n",
-    "- save it\n",
-    "- cells"
+    "- Rename our untitled notebook and save it\n",
+    "- Explore cells"
    ]
   },
   {
@@ -81,13 +80,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 10,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "SyntaxError",
+     "evalue": "invalid syntax (<ipython-input-10-b9f0e0801bac>, line 1)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-10-b9f0e0801bac>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    print Hello world\u001b[0m\n\u001b[0m                    ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
+     ]
+    }
+   ],
    "source": [
-    "# print Hello world"
+    "print Hello world"
    ]
   },
   {
@@ -309,6 +317,13 @@
     "9.0 / 10.0 # Make sure we divide with floats, otherwise we get integers"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Summary slide in presentation**"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -470,6 +485,13 @@
     "'a' not in name"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Summary slide in presentation**"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -634,6 +656,13 @@
     "This isn't surprising if you think of the program as just a list of steps, but if you expect it to behave like a spreadsheet, it may be surprising."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Summary slide in presentation**"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -734,13 +763,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 11,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'r3' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-11-fbfbf23cf48f>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mr3\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'G'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m: name 'r3' is not defined"
+     ]
+    }
+   ],
    "source": [
-    "# r3[2] = 'G'"
+    "r3[2] = 'G'"
    ]
   },
   {
@@ -791,14 +832,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let's quickly take stock of what we know. \n",
-    "\n",
-    "1. Our DNA sequence is represented as a string, and has a variable name\n",
-    "2. Strings are sequences of characters, each character at a numbered position (starting from 0)\n",
-    "3. We can access characters with the `[ ]` square brackets and the position number\n",
-    "4. We can combine characters back into strings with the `+` (plus sign)\n",
-    "\n",
-    "So, we can pull out characters in any order we want, and combine them into a new sequence by adding them together:"
+    "** slide in presentation**"
    ]
   },
   {
@@ -947,6 +981,13 @@
     "Now, I think we're ready to reverse the sequence. Let's make this a hands-on exercise to write some code that reverses the sequence in `seq10` and puts it in a variable called `rev10`. Remember, you can add strings together and the order is important!"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Exercise in presentation**"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 32,
@@ -969,6 +1010,20 @@
     "print rev10"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Summary slide in presentation**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Intro Dictionaries slide in presentation**"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -980,14 +1035,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now that we've got reverse figured out, we can tackle complementing. To do that, we need to look up the complementary base for base, and build a new sequence:\n",
-    "\n",
-    "    A -> T\n",
-    "    C -> G\n",
-    "    G -> C\n",
-    "    T -> A\n",
-    "\n",
-    "Python has a data type called a dictionary that's great for looking things up. It works like a dictionary - you have a key (e.g. the word you're looking up) and a value (e.g. the definition). Each key can only be in the dictionary once, but the values may be repeated."
+    "Python has a data type called a dictionary that's great for looking things up. It associates pairs of things together: a key and a value."
    ]
   },
   {
@@ -1415,7 +1463,14 @@
    },
    "outputs": [],
    "source": [
-    "# sequence_types[1] = 'dna'"
+    "sequence_types[1] = 'dna'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Summary slide in presentation**"
    ]
   },
   {
@@ -1468,25 +1523,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can have multiple conditions we check too, and to demonstrate that, I want to calculate the **GC-content percentage** of the sequence.\n",
-    "\n",
-    "(G + C) / (A + T + G + C)\n",
-    "        "
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "So to approach this, we're going to loop over the sequence and total up the G's and C's. We also need to total up The A's and T's\n",
-    "\n",
-    "The general algorithm here will be\n",
-    "\n",
-    "- Loop over each item in the sequence\n",
-    "    - If it's a `G` or a `C`, increment our GC counter\n",
-    "    - For all items, increment our ATGC counter\n",
-    "    \n",
-    "We know how to write a loop, and we know how to write a counter and incrment it. And we just saw `if`, but we haven't used it in our loop, so let's write that"
+    "**Instruction slide in presentation**"
    ]
   },
   {
@@ -1586,6 +1623,13 @@
     "    print 'High'"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Summary slide in presentation**"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1758,7 +1802,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Exercise: Split, upper, and reverse"
+    "**Exercise slide in presentation**"
    ]
   },
   {
@@ -2165,40 +2209,16 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Exercise: I found out that you can reverse a string (or a list) by using the slice notation `[::-1]`. Update the reverse function to use this and see if anything changes with `reverse_complement`"
+    "**Exercise slide in presentation**"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 75,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "cba\n"
-     ]
-    }
-   ],
-   "source": [
-    "s = 'abc'\n",
-    "r = s[::-1]\n",
-    "print r"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 76,
+   "cell_type": "markdown",
    "metadata": {
     "collapsed": true
    },
-   "outputs": [],
    "source": [
-    "def double(x):\n",
-    "    return x * 2"
+    "**Summary slide in presentation**"
    ]
   },
   {
@@ -2525,6 +2545,13 @@
     "        exit(1)\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Summary slide in presentation**"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},