Welcome lecture assignments and software.

3a2d0891 · Mihai Lefter · 3998f10f · 3a2d0891 · 3998f10f
Commit 3a2d0891 authored 7 years ago by Mihai Lefter
--- a/introduction/01_welcome.ipynb
+++ b/introduction/01_welcome.ipynb
@@ -11,9 +11,7 @@
    "<span style=\"font-size: 200%\">Programming in Python</span>\n",
    "===\n",
    "\n",
-    "<br>\n",
-    "\n",
-    "<img src=\"python_logo.svg\" alt=\"Python Logo\">"
+    "<br>"
   ]
  },
  {
@@ -149,7 +147,9 @@
    "* Anaconda:\n",
    "  * Python 2.7\n",
    "  * Comes with all that's required:\n",
-    "    - NumPy, matplotlib, Biopython\n",
+    "    - Python interpreter, Jupyter Notebook.\n",
+    "    - Libraries:\n",
+    "      - NumPy, Panda, matplotlib, Bokeh, Biopython, ...\n",
    "  * [Installation instructions](https://docs.anaconda.com/anaconda/install/). \n",
    "* Git\n",
    "\n"
@@ -166,11 +166,14 @@
    "Assignments\n",
    "===\n",
    "\n",
-    "* We make use of GitHub Classroom:\n",
-    "  - GitHub account required.\n",
-    "  - Link with assignment repository.\n",
-    "  - Own forked repository to work on - automated by GitHub.\n",
-    "  - Direct file upload to repository is possible."
+    "* We make use of GitHub Classroom.\n",
+    "* GitHub account required.\n",
+    "* Receive link with assignment repository.\n",
+    "* Own forked repository to work on.\n",
+    "  - Clone it.\n",
+    "  - Code.\n",
+    "  - Push it.\n",
+    "* Direct file upload to repository is also possible."
   ]
  },
  {
@@ -246,7 +249,7 @@
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
-     "slide_type": "slide"
+     "slide_type": "-"
    }
   },
   "source": [

 %% Cell type:markdown id: tags:

 <span style="font-size: 200%">Programming in Python</span>
 ===

 <br>

-<img src="python_logo.svg" alt="Python Logo">
-
 %% Cell type:markdown id: tags:

 About the course
 ===

 * Aimed at PhD students, Postdocs, researchers, analysts, ...
 * Focus on:
 - 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  |
 |-------------------|-------|------------------------------------ |----------|
 | **Monday, 18/9**  | 9 - 9:30  | Welcome, Setup                  | Mihai    |
 |                   | 9:30 - 10:30 |  Introduction to Python (1)  | Mihai    |
 |                   | 10:30 - 11:30 | Introduction to Python (2)  | Jeroen   |
 |                   | 11:30 - 12:30 | Introduction to Python (3)  | Mihai    |
 |                   | 12:30 - 13:00 | Practical help              |          |
 | **Tuesday, 19/9** | 9-10  | Assignments review                  |          |
 |                   | 10-11 | More Python Goodness (1)            | Mihai    |
 |                   | 11-12 | More Python Goodness (2)            | Mihai    |
 |                   | 12-13 | IPython Notebook                    | Mark     |

 %% Cell type:markdown id: tags:

 | Day                 | Time  | Lesson                              | Teacher  |
 |---------------------|-------|------------------------------------ |----------|
 | **Wednesday, 20/9** | 9-10  | Assignments review                  |          |
 |                     | 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:
  * Python 2.7
  * Comes with all that's required:
-    - NumPy, matplotlib, Biopython
+    - Python interpreter, Jupyter Notebook.
+    - Libraries:
+      - NumPy, Panda, matplotlib, Bokeh, Biopython, ...
  * [Installation instructions](https://docs.anaconda.com/anaconda/install/).
 * Git


 %% Cell type:markdown id: tags:

 Assignments
 ===

-* We make use of GitHub Classroom:
-  - GitHub account required.
-  - Link with assignment repository.
-  - Own forked repository to work on - automated by GitHub.
-  - Direct file upload to repository is possible.
+* We make use of GitHub Classroom.
+* GitHub account required.
+* Receive link with assignment repository.
+* Own forked repository to work on.
+  - Clone it.
+  - Code.
+  - Push it.
+* Direct file upload to repository is also possible.

 %% 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)

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