BIOE591: Preliminary Assessment

This course is targeted at graduate students who plan to work with high-throughput, short-read DNA sequence data. I therefore assume a solid background in genetics as relates to your chosen field. I further assume some proficiency in using the computer, and prior exposure (even if limited) to the basics of scientific programming in R or Python. To help me adjust my instruction to your needs and current skillset, I would like you to answer the following questions in a separate document and email me the answers. (This will not be graded, but will count towards your participation grade.)

Genetics

  1. What is the Central Dogma?

  2. What is DNA? What are the four nucleotides?

  3. What is RNA? What are the four ribonucleotides?

  4. Where do you find DNA in an organisms?

  5. What is an allele, and what is an allele frequency? How would you calculate an allele frequency with DNA sequence data?

  6. What is a genetic marker?

  7. Where does genetic variation come from?

  8. What forces impact patterns of genetic variation?

  9. What is a genome?

  10. How big is a mammal genome (to an order of magnitude)?

  11. What is ploidy? Are humans diploid, haploid, or tetraploid?

  12. What is recombination?

  13. What is linkage disequilibrium?

  14. What are three types of mutations?

  15. What is population genetic stucture / population subdivision?

Computer Skills

  1. What kind of computer do you have, and what operating system does it run?

  2. What is memory? How much memory does your computer have?

  3. What is storage? How much storage space does your computer have?

  4. Create a folder (or directory) for this course and provide its path below.

  5. Pick a recent research project, class assignment, or work task that required you to create a directory. How did you structure its contents?

  6. Have you ever used the command line?

  7. What is a computing cluster, and have you ever used one?

  8. What programming languages have you used, if any?

  9. What is a package (or library)?

  10. Have you ever written a function?

  11. What is version control?

  12. Have you used Git or GitHub?

  13. What does it mean for an analysis to be reproducible?

  14. Have you ever archived data?

  15. What is open source software?

Open

  1. What are you hoping to get out of this class?

  2. Do you have your own dataset, or will you be working with an example?

  3. What kind of questions do you want to address with data?

  4. What are you worried about in this class, if anything?

  5. Is there anything else I should know to help you have a good semester?