EMAN Wiki

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 (if I remember to do it every class :^/ )
• Homework assignments

A Note about the Book chapters The book chapters are excerpted from a book I've started writing. The book is incomplete at present, and the chapters are in rough-draft form. Additionally, the book is designed for eBook readers, and has multimedia content which doesn't come through in the PDF versions I'm passing to you. The book is not required reading, I'm providing it only to give those of you just starting with programming a little extra help.

(If you believe you will need an exception to something below, please ask BEFORE the class on Monday !)

Please follow these instructions exactly:

• Your class project MUST be submitted before 9 AM on Monday, Feb 25. No revisions will be accepted after this time.
• 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 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: Lastname_Firstname_project_2013.zip
• Email sludtke@bcm.edu with the subject “Class project submission”, and attach the .zip file

On Monday, Feb 25, we will meet at the usual location (check back here on Sunday to make sure there were no last minute changes):

• You will have up to 5 minutes (please practice this in advance) to:
  • Introduce what your software does
  • explain inputs/outputs
  • demonstrate that it works (live demo)
  • explain conceptually how the program was designed
• You will need to quickly connect your laptop to the projector. If you are worried that this might not work, you may wish to test it in advance sometime when the room is unoccupied (make sure to turn the projector off when done).
• We will try to get everyone in on the first day, but may have to have a second session.
• Everyone must be present, or risk a 0 for your project presentation
• I will ask for volunteers, and call people randomly when/if necessary
• We will try to get everyone in on the first day, and may run a little over-time to achieve this, assuming the room is not occupied. If you have somewhere to be immediately after class, I would suggest volunteering to go early.
• If you do not go on the first day, we will have a second session on Friday at the usual time. You will not be allowed to revise your submitted project, but, of course, can modify your presentation. Those who presented on day 1 are welcome, but not required to attend the second session if required.

Introduction to programming book draft - http://blake.bcm.edu/dl/EMAN2/Ludtke_book_draft_2013_01.pdf I'm making the entire current text of my book draft available to those in the class. It is very far from complete, and really only contains another 1 1/2 chapters beyond what I already made available. Since this website is publicly accessible, and I do intend to eventually finish the book, it is password protected. I will give you all the password to access it in class Friday, and I ask that you not circulate it outside the class. Thanks.

Auditors are welcome, but if possible (all students, and some others) please FORMALLY audit the class, rather than just showing up. A) this means you have at least a small commitment to actually attend and B) 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. It does not take much effort to audit formally.

Homework will be assigned each class, at least for the first 2/3 of the term, and is due via email to sludtke@bcm.edu , before the beginning of the following lecture. We will go over solutions to each homework assignment in-class. Homework is the reason for the strange schedule (M & Th). With this schedule you will always have at least two days for each homework assignment, and at least one day on which you can talk to me if you need help. Since the class is offered for credit, homework will be graded, but on a very lenient scale:

1. Homework turned in, but no reasonable attempt was made to complete the assignment 2. A good effort, but with very major flaws 3. Largely correct solution, but with some flaws 4. Program does what it should, with minimal flaws

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 even make an attempt at virtually every assignment will likely not achieve a B.

There will also be a class project in lieu of a final exam. 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 requirement for the program is that it do something useful. We will discuss more about the class projects later in the term.

• 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
• 96-well reader and calculator
• PCR Annealing Temperature Calculator
• One click identifier for PDF files
• Scraping and processing microarray data from the lab webpage