9/2/2015BCHB Edwards Bioinformatics Computing BCHB Lecture 0

9/2/2015BCHB Edwards Where to find me? >> Teaching >> Bioinformatics Computing 2

9/2/2015BCHB Edwards Where to find me? Room 1217, 3300 Whitehaven St, NW 3

9/2/2015BCHB Edwards Where to find me? Basic ScienceWisconsin Ave Shuttle 4

9/2/2015BCHB Edwards What about this course? Learn by doing. Confront initial steep learning curve head-on. Learn by imitation. Change working programs for new functionality. Learn by observation. See cause-and-effect of program changes. Learn by example. Demonstrate with common, useful tasks. Learn by idiom. Use common programming abstractions. 5

What about this course? Lecture Monday, 1:15pm – 2:45pm Wednesday, 1:15pm – 2:45pm 1-2 homework exercises at end of each lecture Computer-lab: Friday, 10am-12pm, Harris 1300 Required, for 5 credit students (Recommended) Get help, work on homework, brainstorm with others Weekly programming homework (60%) Submit on Monday by noon, using blackboard. Term project (40%) Significant bioinformatics analysis or software project Presentation and report at end of semester. 9/2/2015BCHB Edwards6

9/2/2015BCHB Edwards Lectures Slides are posted to the web before each lecture, Lectures will be recorded and available after lecture. You must make sure you understand and can reproduce the examples I demonstrate in lecture… …the homework presumes you’ll use the lecture examples as a starting point. Go back over the material as soon as the lecture is over! Predict how changes to the code will change the result. 7

9/2/2015BCHB Edwards Homework Due date is Monday at noon. Solutions posted on Monday before class....so no credit for late homework! Submit homework electronically to blackboard......blackboard marks late submissions! You may help each other and discuss, but no copy-and-paste! No eyes on the screen! 8

9/2/2015BCHB Edwards Homework Write each exercise up as a mini-experiment. Provide the result (the code). Describe the method used and any tricky details. Discuss the strengths and weaknesses of the solution. Clarity, correctness, robustness, speed, other? Document what you learned by carrying out the experiment. 9

9/2/2015BCHB Edwards Homework Make sure you understand and can execute all of the examples from the lecture… …otherwise, seek assistance. Homework is strongly tied to the content of each lecture. If you don't understand how, stop and think! Learn from the solutions and critiques If you don't understand the solutions or critiques, seek assistance. 10

9/2/2015BCHB Edwards You are responsible for your own learning! You must Do the homework! Get help when you need it! Work smart! 11

Virtual Machines We will use a virtual machine as our programming environment Consistent look and feel (Guest) Regardless of your laptop / desktop (Host) Get comfortable with VirtualBox Use of Shared Folders View options Good bullet-point for your CV! 9/2/2015BCHB Edwards12

Linux Platform We will use a Linux guest virtual machine as our programming environment Free operating-system Modest resource requirements Our virtual machine is CentOS 5.11 based: 512Mb memory, 24Gb hard-drive Common in bioinformatics and other scientific computing disciplines Gain familiarity with command-line Good bullet-point for your CV! 9/2/2015BCHB Edwards13