Revised welcome lecture.

8f778b88 · Mihai · 6c116afd · 8f778b88 · 8f778b88
Commit 8f778b88 authored 7 years ago by Mihai
--- a/images/python_logo.svg
+++ b/images/python_logo.svg
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--- a/introduction/01_welcome.ipynb
+++ b/introduction/01_welcome.ipynb
@@ -12,7 +12,8 @@
    "===\n",
    "\n",
    "<br>\n",
-    "\n"
+    "\n",
+    "<img src=\"../images/python_logo.svg\" alt=\"Python Logo\">"
   ]
  },
  {
@@ -27,12 +28,36 @@
    "===\n",
    "\n",
    "* Aimed at PhD students, Postdocs, researchers, analysts, ...\n",
-    "* Programming as a tool to do your research.\n",
+    "* Focus on:\n",
-    "* Slightly focussed on bioinformatics.\n",
+    " - Basic understanding of Python.\n",
+    " - Programming as a tool to do your research.\n",
+    "    - Slightly biased on bioinformatics.\n",
+    "\n",
    "\n",
    "**Note:** This is its third session."
   ]
  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
+    "Hands on!\n",
+    "===\n",
+    "\n",
+    "**Programming is fun!**\n",
+    "* You only learn programming by doing it.\n",
+    "* Lecture format:\n",
+    "    - Blended teaching + exercising.\n",
+    "* Have your laptop open during the lessons.\n",
+    "* Repeat the code from the slides, play around with it.\n",
+    "* Do the session exercises.\n",
+    "* There will be a few assignments to submit."
+   ]
+  },
  {
   "cell_type": "markdown",
   "metadata": {
@@ -75,24 +100,37 @@
    "Program\n",
    "===\n",
    "\n",
-    "| Day             | Time  | Lesson                              | Teacher  | \n",
+    "| Day               | Time  | Lesson                              | Teacher  | \n",
-    "|-----------------|-------|------------------------------------ |----------|\n",
+    "|-------------------|-------|------------------------------------ |----------|\n",
-    "| Monday, 18/9    | 9-10  | Welcome, Introduction to Python (1) | Mihai    | \n",
+    "| **Monday, 18/9**  | 9 - 9:30  | Welcome, Setup                  | Mihai    | \n",
-    "|                 | 10-11 | Introduction to Python (2)          | Jeroen   |  \n",
+    "|                   | 9:30 - 10:30 |  Introduction to Python (1)  | Mihai    |\n",
-    "|                 | 11-12 | Introduction to Python (3)          | Mihai    | \n",
+    "|                   | 10:30 - 11:30 | Introduction to Python (2)  | Jeroen   |  \n",
-    "|                 | 12-13 | Practical help                      |          | \n",
+    "|                   | 11:30 - 12:30 | Introduction to Python (3)  | Mihai    | \n",
-    "| Tuesday, 19/9   | 9-10  | Assignments review                  |          |\n",
+    "|                   | 12:30 - 13:00 | Practical help              |          | \n",
-    "|                 | 10-11 | More Python Goodness (1)            | Mihai    | \n",
+    "| **Tuesday, 19/9** | 9-10  | Assignments review                  |          |\n",
-    "|                 | 11-12 | More Python Goodness (2)            | Mihai    | \n",
+    "|                   | 10-11 | More Python Goodness (1)            | Mihai    | \n",
-    "|                 | 12-13 | IPython Notebook                    | Mark     | \n",
+    "|                   | 11-12 | More Python Goodness (2)            | Mihai    | \n",
-    "| Wednesday, 20/9 | 9-10  | Assignments review                  |          | \n",
+    "|                   | 12-13 | IPython Notebook                    | Mark     | "
-    "|                 | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     | \n",
+   ]
-    "|                 | 11-12 | Data visualisation (1)              | Guy      | \n",
+  },
-    "|                 | 12-13 | Data visualisation (2)              | Guy      | \n",
+  {
-    "| Thursday, 21/9  | 9-10  | Assignments review                  |          | \n",
+   "cell_type": "markdown",
-    "|                 | 10-11 | Object-oriented programming         | Jonathan | \n",
+   "metadata": {
-    "|                 | 11-12 | Biopython                           | Guy      | \n",
+    "slideshow": {
-    "|                 | 12-13 | Putting everything together         | Jeroen   |\n",
+     "slide_type": "subslide"
+    }
+   },
+   "source": [
+    "| Day                 | Time  | Lesson                              | Teacher  | \n",
+    "|---------------------|-------|------------------------------------ |----------|\n",
+    "| **Wednesday, 20/9** | 9-10  | Assignments review                  |          | \n",
+    "|                     | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     | \n",
+    "|                     | 11-12 | Data visualisation (1)              | Guy      | \n",
+    "|                     | 12-13 | Data visualisation (2)              | Guy      | \n",
+    "| **Thursday, 21/9**  | 9-10  | Assignments review                  |          | \n",
+    "|                     | 10-11 | Object-oriented programming         | Jonathan | \n",
+    "|                     | 11-12 | Biopython                           | Guy      | \n",
+    "|                     | 12-13 | Putting everything together         | Jeroen   |\n",
    "\n",
    "All slides are linked as one-page documents from the course website: [https://git.lumc.nl/courses/programming-course](https://git.lumc.nl/courses/programming-course)"
   ]
@@ -108,12 +146,13 @@
    "Software requirements\n",
    "===\n",
    "\n",
-    "* Anaconda\n",
+    "* Anaconda:\n",
-    "    * Python 2.7\n",
+    "  * Python 2.7\n",
-    "    * NumPy, matplotlib, Biopython\n",
+    "  * Comes with all that's required:\n",
+    "    - NumPy, matplotlib, Biopython\n",
+    "  * [Installation instructions](https://docs.anaconda.com/anaconda/install/). \n",
    "* Git\n",
-    "\n",
+    "\n"
-    "Anaconda installation instructions [here](https://docs.anaconda.com/anaconda/install/)."
   ]
  },
  {
@@ -124,15 +163,14 @@
    }
   },
   "source": [
-    "Exercises\n",
+    "Assignments\n",
    "===\n",
    "\n",
-    "You only learn programming by doing it.\n",
+    "* We make use of GitHub Classroom:\n",
-    "\n",
+    "  - GitHub account required.\n",
-    "* Have your laptop open during the lessons.\n",
+    "  - Link with assignment repository.\n",
-    "* Repeat the code from the slides, play around with it.\n",
+    "  - Own forked repository to work on - automated by GitHub.\n",
-    "* Do the exercises.\n",
+    "  - Direct file upload to repository is possible."
-    "* There will be a few assignments to submit."
   ]
  },
  {
@@ -152,7 +190,7 @@
  },
  {
   "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
@@ -191,7 +229,7 @@
       "<IPython.core.display.HTML object>"
      ]
     },
-     "execution_count": 3,
+     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
@@ -217,6 +255,7 @@
  }
 ],
 "metadata": {
+  "celltoolbar": "Slideshow",
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",

 %% Cell type:markdown id: tags:
 <span style="font-size: 200%">Programming in Python</span>
 ===
 <br>
+<img src="../images/python_logo.svg" alt="Python Logo">
 %% Cell type:markdown id: tags:
 About the course
 ===
 * Aimed at PhD students, Postdocs, researchers, analysts, ...
-* Programming as a tool to do your research.
+* Focus on:
-* Slightly focussed on bioinformatics.
+ - Basic understanding of Python.
+ - Programming as a tool to do your research.
+    - Slightly biased on bioinformatics.
 **Note:** This is its third session.
 %% Cell type:markdown id: tags:
+Hands on!
+===
+**Programming is fun!**
+* You only learn programming by doing it.
+* Lecture format:
+    - Blended teaching + exercising.
+* Have your laptop open during the lessons.
+* Repeat the code from the slides, play around with it.
+* Do the session exercises.
+* There will be a few assignments to submit.
+%% Cell type:markdown id: tags:
 Teachers
 ===
 * Jeroen Laros<br>
  [j.f.j.laros@lumc.nl](mailto:j.f.j.laros@lumc.nl)
 * Mihai Lefter<br>
  [m.lefter@lumc.nl](mailto:m.lefter@lumc.nl)
 * Jonathan Vis<br>
  [j.k.vis@lumc.nl](mailto:j.k.vis@lumc.nl)
 * Mark Santcroos<br>
  [m.a.santcroos@lumc.nl](mailto:m.a.santcroos@lumc.nl)
 * Guy Allard<br>
  [w.g.Allard@lumc.nl](mailto:w.g.allard@lumc.nl)
 %% Cell type:markdown id: tags:
 Program
 ===
-| Day             | Time  | Lesson                              | Teacher  |
+| Day               | Time  | Lesson                              | Teacher  |
-|-----------------|-------|------------------------------------ |----------|
+|-------------------|-------|------------------------------------ |----------|
-| Monday, 18/9    | 9-10  | Welcome, Introduction to Python (1) | Mihai    |
+| **Monday, 18/9**  | 9 - 9:30  | Welcome, Setup                  | Mihai    |
-|                 | 10-11 | Introduction to Python (2)          | Jeroen   |
+|                   | 9:30 - 10:30 |  Introduction to Python (1)  | Mihai    |
-|                 | 11-12 | Introduction to Python (3)          | Mihai    |
+|                   | 10:30 - 11:30 | Introduction to Python (2)  | Jeroen   |
-|                 | 12-13 | Practical help                      |          |
+|                   | 11:30 - 12:30 | Introduction to Python (3)  | Mihai    |
-| Tuesday, 19/9   | 9-10  | Assignments review                  |          |
+|                   | 12:30 - 13:00 | Practical help              |          |
-|                 | 10-11 | More Python Goodness (1)            | Mihai    |
+| **Tuesday, 19/9** | 9-10  | Assignments review                  |          |
-|                 | 11-12 | More Python Goodness (2)            | Mihai    |
+|                   | 10-11 | More Python Goodness (1)            | Mihai    |
-|                 | 12-13 | IPython Notebook                    | Mark     |
+|                   | 11-12 | More Python Goodness (2)            | Mihai    |
-| Wednesday, 20/9 | 9-10  | Assignments review                  |          |
+|                   | 12-13 | IPython Notebook                    | Mark     |
-|                 | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     |
-|                 | 11-12 | Data visualisation (1)              | Guy      |
+%% Cell type:markdown id: tags:
-|                 | 12-13 | Data visualisation (2)              | Guy      |
-| Thursday, 21/9  | 9-10  | Assignments review                  |          |
+| Day                 | Time  | Lesson                              | Teacher  |
-|                 | 10-11 | Object-oriented programming         | Jonathan |
+|---------------------|-------|------------------------------------ |----------|
-|                 | 11-12 | Biopython                           | Guy      |
+| **Wednesday, 20/9** | 9-10  | Assignments review                  |          |
-|                 | 12-13 | Putting everything together         | Jeroen   |
+|                     | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     |
+|                     | 11-12 | Data visualisation (1)              | Guy      |
+|                     | 12-13 | Data visualisation (2)              | Guy      |
+| **Thursday, 21/9**  | 9-10  | Assignments review                  |          |
+|                     | 10-11 | Object-oriented programming         | Jonathan |
+|                     | 11-12 | Biopython                           | Guy      |
+|                     | 12-13 | Putting everything together         | Jeroen   |
 All slides are linked as one-page documents from the course website: [https://git.lumc.nl/courses/programming-course](https://git.lumc.nl/courses/programming-course)
 %% Cell type:markdown id: tags:
 Software requirements
 ===
-* Anaconda
+* Anaconda:
-    * Python 2.7
+  * Python 2.7
-    * NumPy, matplotlib, Biopython
+  * Comes with all that's required:
+    - NumPy, matplotlib, Biopython
+  * [Installation instructions](https://docs.anaconda.com/anaconda/install/).
 * Git
-Anaconda installation instructions [here](https://docs.anaconda.com/anaconda/install/).
 %% Cell type:markdown id: tags:
-Exercises
+Assignments
 ===
-You only learn programming by doing it.
+* We make use of GitHub Classroom:
+  - GitHub account required.
-* Have your laptop open during the lessons.
+  - Link with assignment repository.
-* Repeat the code from the slides, play around with it.
+  - Own forked repository to work on - automated by GitHub.
-* Do the exercises.
+  - Direct file upload to repository is possible.
-* There will be a few assignments to submit.
 %% Cell type:markdown id: tags:
 Getting help
 ===
 * Ask a teacher.
 * If it's private, mail one of the teachers.
 %% Cell type:code id: tags:
 ``` python
 from IPython.display import HTML
 def css_styling():
    styles = open('../styles/custom.css', 'r').read()
    return HTML('<style>' + styles + '</style>')
 css_styling()
 ```
 %% Output
    <IPython.core.display.HTML object>
 %% Cell type:markdown id: tags:
 License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)