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Bioinformatics Computing

Bioinformatics Computing. BCHB524 Lecture 0. Where to find me?. http://grg.tn/edwards >> Teaching >> Bioinformatics Computing http://grg.tn/bchb524. Where to find me?. Room 1217, Harris Building, 3300 Whitehaven St, NW. Where to find me?. Wisconsin Ave Shuttle. Room 235, Basic Science.

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Bioinformatics Computing

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  1. Bioinformatics Computing BCHB524Lecture 0 BCHB524 - Edwards

  2. Where to find me? • http://grg.tn/edwards>> Teaching >> Bioinformatics Computing • http://grg.tn/bchb524 BCHB524 - Edwards

  3. Where to find me? BCHB524 - Edwards Room 1217, Harris Building, 3300 Whitehaven St, NW

  4. Where to find me? BCHB524 - Edwards Wisconsin Ave Shuttle Room 235, Basic Science

  5. 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. BCHB524 - Edwards

  6. What about this course? • Lecture • Monday, 1:15pm – 2:45pm, BSB 341 • Wednesday, 1:15pm – 2:45pm, BSB 341 • 1-2 homework exercises at end of each lecture • Computer-lab: • Friday, 10am-12pm, Harris 1300 • Required, for 5 credit students (Recommended regardless) • Get help, work on homework, brainstorm with others • Weekly programming homework (60%) • Submit on Monday by noon, using canvas. • Term project (40%) • Significant bioinformatics analysis or software project • Presentation at end of semester. BCHB524 - Edwards

  7. 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. BCHB524 - Edwards

  8. Homework • Due date is Monday at noon. • Solutions posted on Monday before class. • ...so no credit for late homework! • Submit homework electronically to blackboard... • ...canvas marks late submissions! • You may help each other and discuss, but no copy-and-paste! • No eyes on the screen! BCHB524 - Edwards

  9. 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. BCHB524 - Edwards

  10. 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. BCHB524 - Edwards

  11. You are responsible for your own learning! You must • Do the homework! • Get help when you need it! • Work smart! BCHB524 - Edwards

  12. 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! BCHB524 - Edwards

  13. 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! BCHB524 - Edwards

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