Bioinformatics Computing BINF 524 Lecture 0 BINF 524

Bioinformatics Computing BINF 524 Lecture 0 BINF 524 - Edwards

Where to find me? l l l Email: nje 5@georgetown. edu My Homepage l http: //grg. tn/edwards l http: //edwardslab. bmcb. georgetown. edu/ BINF 524 Homepage l l l http: //grg. tn/binf 524 http: //edwardslab. bmcb. georgetown. edu/teaching/binf 524/2020/ Homepage >> Teaching >> Bioinformatics Computing BINF 524 - Edwards

What about this course? l Learn by doing. l l Learn by imitation. l l See cause-and-effect of program changes. Learn by example. l l Change working programs for new functionality. Learn by observation. l l Confront initial steep learning curve head-on. Demonstrate with common, useful tasks. Learn by idiom. l Use common programming abstractions. BINF 524 - Edwards

What about this course? l Lecture l l Computer-lab: l l Friday, 10 am-12 pm, Zoom (synchronous) Required, for 5 credit students (Recommended regardless) Get help, work on homework, brainstorm with others Weekly programming homework (60%) l l Monday, 1: 15 pm – 2: 45 pm, Zoom (synchronous) Wednesday, 1: 15 pm – 2: 45 pm, Zoom (synchronous) 1 -2 homework exercises at end of each lecture Submit on Monday by noon, using canvas. Term project (40%) l l Significant bioinformatics analysis or software project Presentation at end of semester. BINF 524 - Edwards

Virtual Learning Methodology Lectures: l l l Zoom, synchronous, recorded Recommended, not required. Cameras on when possible! Speak up, interrupt, and use the chat! Zoom recording (does not capture cameras or chat) Lab: l l Zoom, synchronous, not recorded. One student per breakout room. Share your screen I will join each breakout room on request via chat or in rotation. Zoom: l Zoom meeting links will be password protected (see canvas…) BINF 524 - Edwards

Lectures l l l Slides are posted to the web before each lecture, Lectures will be recorded and available after lecture. You must make sure you understand can reproduce the examples I demonstrate in lecture… l l l …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. BINF 524 - Edwards

Homework l l Due date is Monday at noon. Solutions posted on Monday before class. l l Submit homework electronically to blackboard. . . l l . . . so no credit for late homework!. . . canvas marks late submissions! You may talk each other and discuss, but no copy-and-paste! l l No eyes on others’ screens! No copy and paste! BINF 524 - Edwards

Homework l l Write each exercise up as a mini-experiment. Provide the result (the code). Describe the method used any tricky details. Discuss the strengths and weaknesses of the solution. l l Clarity, correctness, robustness, speed, other? Document what you learned by carrying out the experiment. BINF 524 - Edwards

Homework l Make sure you understand can execute all of the examples from the lecture… l l Homework is strongly tied to the content of each lecture. l l …otherwise, seek assistance. If you don't understand how, stop and think! Learn from the solutions and critiques l If you don't understand the solutions or critiques, seek assistance. BINF 524 - Edwards

You are responsible for your own learning! You must l Do the homework! l Get help when you need it! l Work smart! BINF 524 - Edwards

Virtual Machines l We will use a virtual machine as our programming environment l l l Get comfortable with Virtual. Box l l l Consistent look and feel (Guest) Regardless of your laptop / desktop (Host) Use of Shared Folders View options Good bullet-point for your CV! BINF 524 - Edwards

Linux Platform l We will use a Linux guest virtual machine as our programming environment l l l Our virtual machine is Cent. OS 7. 8 based: l l 2 Gb memory, 32 Gb hard-drive Common in bioinformatics and other scientific computing disciplines l l Free operating-system Modest resource requirements Gain familiarity with command-line Good bullet-point for your CV! BINF 524 - Edwards