Programming

Module Leaders:
Alison Maxwell - DeGrado Lab (alison.maxwell@ucsf.edu)
Greyson Lewis - Marshall Lab (greyson.lewis@ucsf.edu)
Jack Stevenson - Shokat lab (jack.stevenson@ucsf.edu)
Taylor Cavazos - Witte lab (taylor.cavazos@ucsf.edu)
Jenna Pellegrino - Fraser lab (jenna.pellegrino@ucsf.edu)
Snow Naing - Krogan and Li labs (snow.naing@ucsf.edu)


Schedule:
Day 1 (9/4, 1 pm - 5 pm)  (Joint with CCB):
  • Getting friendly with the Command Line (Taylor)
  • Pair-review the summer Ramachandran projects
    • How did you structure your code?
    • What sorts of methods did you write?
    • What are the best parts of your code?
    • What are the worst parts of your code? How could you improve it?
    • How do you know if your code is efficient?
    • How does your coding style differ from your partner's?
    • If you could do this again, what would you do differently?

Day 2 (9/6, 9 am - 4 pm):

Day 3 (9/13, 1 pm - 5 pm):
  • Complete data structures activity
  • Review data structures activity
  • Special topics
    • Parallel computing (Greyson)
      • using pool (for slow functions): notebook
      • stackoverflow for tighter control: here
    • Regular expressions (Jack)
    • Plotting in Python (Taylor): Jupyter Notebook
    • Discuss and present Rosalind solutions
      • Trie
      • Super string merging
      • Dynamic programming

Extra fun:
For those of you looking for more PDB fun: 10000+ structures to play with.

Rosalind also has a ton of problems if you want to keep challenging yourself! 


Useful links:
ċ
20180906_MyFirstNotebook.ipynb
(69k)
Greyson Lewis,
Sep 6, 2018, 2:18 PM
ċ
20180913_MultiprocessingTutorial.ipynb
(3k)
Greyson Lewis,
Sep 13, 2018, 4:45 PM
ĉ
Greyson Lewis,
Sep 4, 2018, 3:08 PM
ċ
GitHub_presentation_2018.key
(1186k)
Alison Maxwell,
Sep 5, 2018, 10:31 PM
ċ
Pandas_Bootcamp_2018.ipynb
(339k)
Greyson Lewis,
Sep 6, 2018, 11:10 AM
ą
Greyson Lewis,
Sep 6, 2018, 11:10 AM
ć
Greyson Lewis,
Sep 11, 2018, 4:07 PM
Ĉ
Greyson Lewis,
Sep 6, 2018, 11:10 AM
Ċ
Alison Maxwell,
Sep 6, 2018, 8:55 AM
ċ
plotting_tutorial.ipynb
(9k)
Greyson Lewis,
Sep 12, 2018, 12:19 PM