9/2/2015 BCHB524 - 2015 - Edwards

Bioinformatics Computing

BCHB5242015

Lecture 0

9/2/2015 BCHB524 - 2015 - Edwards

Where to find me?

http://grg.tn/edwards

>> Teaching >> Bioinformatics Computing

http://grg.tn/bchb524

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9/2/2015 BCHB524 - 2015 - Edwards

Where to find me?

Room 1217, 3300 Whitehaven St, NW3

9/2/2015 BCHB524 - 2015 - Edwards

Where to find me?

Basic Science Wisconsin Ave Shuttle4

9/2/2015 BCHB524 - 2015 - 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.

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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.

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9/2/2015 BCHB524 - 2015 - 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.

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9/2/2015 BCHB524 - 2015 - 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!

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9/2/2015 BCHB524 - 2015 - 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.

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9/2/2015 BCHB524 - 2015 - 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

9/2/2015 BCHB524 - 2015 - Edwards

You are responsible for your own learning!

You must

Do the homework!

Get help when you need it!

Work smart!

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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!

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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!

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