EMAN Wiki

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

• Lecture notes
• Recordings of most lectures
• Homework assignments

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If you believe you will need an exception to something below, please ask by Feb 23 (the final lecture !)

For your class presentation, your first slide should have:

• Your name
• 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 10 minute timeline pretty rigorously
• Test your laptop with the projector in this room BEFORE Feb 26! You may use the network-based connection if you like, but note that it is laggy.

Please follow these instructions exactly:

• Your class project MUST be submitted by 11:59 PM on Sat, Feb 24. 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 (email me to discuss in advance if the files are >20 MB)
  • 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_2016.zip
• Email sludtke42@gmail.com with the subject “Class project submission”, and attach the .zip file. If the zip file is too large, feel free to use Box, Dropbox or Goodle Drive to send the attachment.

• A laptop computer is required to take this class, and it should be brought to class for in-class team learning exercises
• Homework is generally found on the last page of the lecture handout, and completed homework should be emailed to both TAs and myself
• If you miss a lecture review the material on this page at least 1 day before the next lecture, as there may be an assignment!
• Course TA's are Michael Bell jmbell@bcm.edu and Muyuan Chen Muyuan.Chen@bcm.edu. They both sit in N420
• I don't have formal office hours, but can be found in my office, N420.01 most mornings. The later in the day the busier I get. Email at any time sludtke@bcm.edu
• This class uses Python 3.6 via a free distribution called Anaconda available for Linux, Macs 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.X. Please do not try to make-do with some other Python installation on your machine. If you are knowledgeable enough to know of other distributions, you are also knowledgeable enough to install Anaconda side-by-side with your other tools.

Anaconda is available here: https://www.anaconda.com/download (you want the Python 3.6 version of Anaconda 5)

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

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 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.

• 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

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, 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 at all.

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 (not that we need N315).