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.

Class Projects

Your grade will be a combination of your presentation and your submitted project, and will count for 1/2 of your grade.

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 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

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:

1. Homework turned in, something attempted, but not functional
2. A good effort, but with major flaws
3. Largely correct solution, but with some flaws
4. 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 - 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.