EMAN Wiki

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===== Practical Introduction to Programming for Scientists =====
==== Spring 2015 ====
=== Mondays & Fridays, 9am - 10:30  N315 ===

Since some of you don't have Blackboard access, this Wiki page will host all class material, including:

  * Lecture notes
  * Screen-capture video of each lecture
  * Homework assignments

Please note that we will use Python 2.7.X for this class. While Python 3.X is available, it remains much less widely used than Python 2, and most important features for purposes of this class have been back-ported to Python 2.7.

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||Lecture ||Notes ||Video ||Homework || Other ||
||1 - Introduction ||[[http://blake.bcm.edu/dl/EMAN2/lecture_1.pdf]]\\ [[http://blake.bcm.edu/dl/EMAN2/terminal_1.txt]] ||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture1.mp4|Lecture Video]]|| 1. Take this survey: http://goo.gl/forms/fHCmTavj1c \\ 2. Email passport style photo to sludtke@bcm.edu\\ 3. Get Python 2.7.X working on your computer || ||
||2 - Program Flow ||[[http://blake.bcm.edu/dl/EMAN2/lecture_2.pdf]]\\ [[http://blake.bcm.edu/dl/EMAN2/terminal_2.txt]] ||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture2.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/homework_1.pdf]] || [[http://blake.bcm.edu/dl/EMAN2/practice_soln_1.pdf]] ||
||3 - Lab 1 ||[[http://blake.bcm.edu/dl/EMAN2/lecture_3.pdf]]\\ [[http://blake.bcm.edu/dl/EMAN2/terminal_3.txt]] ||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture3.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/Lab1.pdf]]\\ [[http://blake.bcm.edu/dl/EMAN2/translate_orig.py]] || ||
||4 - More Basics ||[[http://blake.bcm.edu/dl/EMAN2/lecture_4.pdf]]\\ [[http://blake.bcm.edu/dl/EMAN2/terminal_4.txt]] ||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture4.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/homework_2.pdf]] ||[[http://blake.bcm.edu/dl/EMAN2/extra_practice_2.pdf]] ||
||5 - Loops and Modules ||[[http://blake.bcm.edu/dl/EMAN2/lecture_5.pdf]]\\ [[http://blake.bcm.edu/dl/EMAN2/terminal_5.txt]] ||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture5.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/homework_3.pdf]] || http://anandology.com/python-practice-book/index.html ||
||6 - Lab 2 (BioPython) ||[[http://blake.bcm.edu/dl/EMAN2/lecture_6.pdf]] ||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture6.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/lab_2.pdf]]||[[http://blake.bcm.edu/dl/EMAN2/pubmed.py]] ||
||7 - Numerical Computing ||[[http://blake.bcm.edu/dl/EMAN2/lecture_7.pdf]] \\ [[http://blake.bcm.edu/dl/EMAN2/terminal_7.txt]]||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture7.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/homework_4.pdf]] || ||
||8 - Lab 3 (NumPy & Matplotlib) ||[[http://blake.bcm.edu/dl/EMAN2/lecture_8.pdf]]||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture8.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/lab3_hw4.pdf]] ||[[http://blake.bcm.edu/dl/EMAN2/plot.py]] \\  [[http://blake.bcm.edu/dl/EMAN2/sample1.txt]] \\  [[http://blake.bcm.edu/dl/EMAN2/sample2.txt]] ||
||9 - Image Processing and Networking ||[[http://blake.bcm.edu/dl/EMAN2/lecture_9.pdf]] \\ [[http://blake.bcm.edu/dl/EMAN2/terminal_9.txt]]||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture9.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/homework_5.pdf]] || ||
||10 - Lab 4 (Network Programming) ||[[http://blake.bcm.edu/dl/EMAN2/lecture_10.pdf]]||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture10.mp4|Lecture Video]]|| [[http://blake.bcm.edu/dl/EMAN2/tcp_send_file.py]] ||[[http://blake.bcm.edu/dl/EMAN2/udp_chat.py]]\\ [[http://blake.bcm.edu/dl/EMAN2/tcp_send.py]]\\ [[http://blake.bcm.edu/dl/EMAN2/tcp_receive.py]] ||
||11 - PIL and GUI Programming ||[[http://blake.bcm.edu/dl/EMAN2/lecture_11.pdf]]||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture11.mp4|Lecture Video]]|| || [[http://blake.bcm.edu/dl/EMAN2/extra_practice_11.pdf]] ||
||12 - OOP, Debugging and the Real World ||[[http://blake.bcm.edu/dl/EMAN2/lecture_12.pdf]]||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture12.mp4|Lecture Video]]|| Before lab next monday, install:\\ Follow instructions under "The fast way":\\ [[https://learn.adafruit.com/introducing-pro-trinket/setting-up-arduino-ide]]\\ [[https://github.com/adafruit/Adafruit_NeoPixel]] ||
||13 - Lab 5 (Arduino) || No Lecture || [[LectureVideo/ArduinoLab|Arduino Lab]] || || ||
||14 - Compression and Databases ||[[http://blake.bcm.edu/dl/EMAN2/lecture_14.pdf]]||[[http://blake.grid.bcm.edu/dl/Intro_Programming_15/Lecture14.mp4|Lecture Video]]|| || ||


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===== Important Instructions for Class Projects =====

If you believe you will need an exception to something below, please ask by Feb 27 (the final lecture !)

For your class presentation, your first slide should have:
  * Your name (so other students who may not know you can vote for you)
  * Your department/program
  * Descriptive title of your project
  * You may wish to say something very briefly about your previous programming experience
  * We will be on a tight schedule, so I will have to enforce the 5 minute timeline pretty rigorously. Please practice in advance !

**Please follow these instructions exactly:**

  * Your class project MUST be submitted by 11:59 PM on Sat, Feb 28. No revisions will be accepted after this time. You can use Sunday to prepare your oral presentation :^)
  * Your submission should consist of:
    * one or more .py files (should have sufficient comments to figure out how they work)
    * any necessary additional files to demonstrate that the program works
    * A PDF file with a brief description of your program, what inputs the program takes, what outputs the program produces, and what it is supposed to do.
    * The final item in the PDF should be a command-line to use in running the program, and any necessary instructions to demonstrate that it works.
  * Combine all files into a .zip file named:  Familyname_Givenname_project_2015.zip
  * Email sludtke@bcm.edu with the subject "Class project submission", and attach the .zip file

//Note:// If your project requires data files too large to email (even for a basic demonstration), you can share the extra files with me via BigFile, DropBox or Google Drive. If you need to do this, prepare the files in advance, and include the download instructions in the PDF in the .zip file.

===== Class Project Overview =====

The class project will count for 1/2 of your grade in the class, and will be scored on both your presentation and the program itself. You will likely have only ~5 minutes to present your projects when the time comes, but that shouldn't limit their complexity or your ambitions. It is a good idea to select a project which is somewhat ambitious but has some fallback positions in case you don't succeed in everything you had planned to do. Your initial project plan will not be a factor in your final grade. If the program meets the criteria below, even if it's very different than your original aim, you will still receive full credit.

Each person will, over the course of the term, write a program, and briefly present it at a special class at the end of the term. The sole requirements for the program are: 
 1. It must do something useful not easily completed with existing freely available tools
 2. Not be completely trivial. The complexity of your project is expected to correspond somewhat to your level of past programming experience. 

==== Examples of past class projects ====
  * Analysis of DNA capture targets that failed during sequencing
  * Calculating the probabilities of different discrete distributions
  * A Candidate Gene Searcher
  * Calculating dN/dS automatically from pairs of orthologs by pipelining clustal and paml
  * Pubmed search tool
  * Identify evolutionarily conserved water molecules in structure
  * 96-well reader and calculator
  * PCR Annealing Temperature Calculator
  * One click identifier for PDF files
  * Scraping and processing microarray data from the lab webpage

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This class attracts people with widely varying backgrounds and skill levels. Since the course is supposed to be accessible to people with little to no programming experience, the bar for achieving an acceptable grade (B) in the class is set fairly low. If you make a reasonable attempt at all of the homework assignments, even if not completely successful, and complete a class project of some sort, you can expect to get at least a B in the class. This does not mean you can slip through without making an effort at all. Particularly if you have no programming experience at all, the class WILL take a significant effort on your part. Those who don't make a reasonable attempt at virtually every assignment may  not achieve a B. Turning in something incomplete is better than turning in nothing.


**Homework will be assigned each Friday, due before class the following Friday**, at least for the first 2/3 of the term, and is handed in via email to the class TA, Amanda Koire <koire@bcm.edu> with a cc to sludtke@bcm.edu. We will go over solutions to homework assignments in-class. Since the class is offered for credit, homework will be graded, but on a lenient scale:

 3. Homework turned in, something attempted, but not functional
 4. A good effort, but with major flaws
 5. Largely correct solution, but with some flaws
 6. Program does what it should, with minimal flaws

**Auditors are welcome**, but if possible (all students, and some others) please formally audit the class, rather than just showing up. 1) this means you have at least a small commitment to actually attend and 2) if you don't formally audit, the GS has no record of your interest and they may give me a very small room to teach in next time. 

**Introduction to programming book draft** - [[http://blake.bcm.edu/dl/EMAN2/Ludtke_book_draft_2015_01.pdf]]  I started writing a programming book a couple of years ago, but like many such projects, it is far from complete. Since this website is publicly accessible, and I do hope to eventually finish the book, it is password protected. I provided the password in-class, and I ask that you not circulate it outside the class. Thanks.  Note that the book is not required reading. It is there as an additional resource.