EMAN Wiki

Practical Introduction to Programming for Scientists

Spring 2017

Mondays & Fridays, 9am - 10:30 N315

For several reasons I use this site rather than Blackboard, this Wiki page will host all class material, including:

Lecture notes
Screen-capture video of each lecture
Homework assignments
http://blake.bcm.edu/dl/EMAN2/GS-SB-406.pdf (Syllabus, note - subject to change)

I started writing an introduction to programming book some years ago, and while I haven't gotten around to finishing it, some other classes have found it a useful supplement to the class lectures, particularly for people just starting with programming. For that reason I'm making the current (very incomplete) draft of the book available to you:

http://blake.bcm.edu/dl/EMAN2/Intro_Programming_01_17.ibooks - Multimedia version of book (iPad/Mac iBooks only)
http://blake.bcm.edu/dl/EMAN2/Intro_Programming_01_17.pdf - PDF version of book, missing some material

Note that this class now uses Python 3.5 via a free distribution called Anaconda available for Linux, Max and Windows. By using a common environment, it is easier to deal with the differences between Python on different platforms. The default Python available on Linux and Mac is still Python 2.7. Please make sure you set up Anaconda 3.5 and use that instead.

Lecture	Notes	Video	Homework	Other
1 - Introduction	http://blake.bcm.edu/dl/EMAN2/lecture_1.pdf	Lecture Video	1. Take this survey: https://goo.gl/forms/irr7VmrQhaxEUYQp1 2. Email passport style photo to sludtke@bcm.edu 3. Get Anaconda Python 3.5 set up on your laptop
2 - Conditionals and Loops	http://blake.bcm.edu/dl/EMAN2/lecture_2.pdf http://blake.bcm.edu/dl/EMAN2/Lecture_2.ipynb	Lecture Video	See last page of class notes	http://blake.bcm.edu/dl/EMAN2/practice_soln_1.pdf
3 - Writing Programs	http://blake.bcm.edu/dl/EMAN2/lecture_3.pdf http://blake.bcm.edu/dl/EMAN2/translate.py	Lecture Video	See last page of class notes
4 - Standard Libraries and Miscellany	http://blake.bcm.edu/dl/EMAN2/lecture_4.pdf http://blake.bcm.edu/dl/EMAN2/Lecture4.ipynb	Lecture Video	See last page of class notes	http://blake.bcm.edu/dl/EMAN2/two_column.txt
5 - Biopython and Numpy	http://blake.bcm.edu/dl/EMAN2/lecture_5.pdf http://blake.bcm.edu/dl/EMAN2/Lecture5.ipynb	Lecture Video	See last page of class notes	http://blake.bcm.edu/dl/EMAN2/reference.py
6 - OOP, XML and Networking	http://blake.bcm.edu/dl/EMAN2/lecture_6.pdf http://blake.bcm.edu/dl/EMAN2/Lecture6a.ipynb http://blake.bcm.edu/dl/EMAN2/Lecture6b.ipynb	Lecture Video	See last page of class notes
7 - Debugging and GUI Intro	http://blake.bcm.edu/dl/EMAN2/lecture_7.pdf http://blake.bcm.edu/dl/EMAN2/Lecture7.ipynb	Lecture Video	See last page of class notes
8 - Image Processing	http://blake.bcm.edu/dl/EMAN2/lecture_8.pdf	Lecture Video	See last page of class notes
9 - Databases and Data Compression	http://blake.bcm.edu/dl/EMAN2/lecture_9.pdf	Lecture Video	Install SSH client (if necessary)
10 - Recursion, Parsing, Qt4	http://blake.bcm.edu/dl/EMAN2/lecture_10.pdf	Lecture Video		http://blake.bcm.edu/dl/EMAN2/scrabble_recur.py http://blake.bcm.edu/dl/EMAN2/scrabble_enum.py http://blake.bcm.edu/dl/EMAN2/scrabble_check.py
11 - Network Programming, Javascript, Making	http://blake.bcm.edu/dl/EMAN2/lecture_11.pdf	Lecture Video	Suggestions for Final Lecture	IN CLASS MINI-LAB THIS FRIDAY http://blake.bcm.edu/dl/EMAN2/udp_chat.py
12 - The outside world + Mini-lab	http://blake.bcm.edu/dl/EMAN2/lecture_12.pdf			http://blake.bcm.edu/dl/EMAN2/lab_neopixel.pdf http://blake.bcm.edu/dl/EMAN2/lab_sensehat.pdf http://blake.bcm.edu/dl/EMAN2/lab_camera.pdf
13 - Linux clusters	http://blake.bcm.edu/dl/EMAN2/lecture_13.pdf	Lecture Video