schedule & assignments
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class: MW 1-2:15 in 133 SMI
office hours: M 10-11 & T 3-4, 1208 Medical Sciences Center
- guest lecture by Mike Cammilleri: Job scheduling and Resource Allocation on the Statistics High Performance Computing Cluster
- see here for a (possibly outdated) reference, and julia example
- homework for 12/12: peer review and group project contributions
- distributed computing in julia
- create new types & julia packages with unit tests
- please fill out evaluations: your voice is important
- send group project contributions: see Canvas
- peer review of final project: see Canvas for instructions, github issues for providing & receiving comments. If you didn’t get the github email: go to github, login, click on “issues” on the top bar, then click on “mentioned” to see all the issues that you were tagged on.
- guest lecture by Professor Doug Bates: Julia for GWAS (genome-wide association studies) and Mixed Models
- homework: final project submission (via a github issue) due R 12/6 11:59pm
- julia intro continued
- intro to julia
- group work in class (final project due R 12/6)
- homework for M 11/26: install julia
final project (due R 12/6): group work in class
- final project: group work in class
- homework for M 11/19: peer-review of hw 2
- python classes and methods
- description of final project
- homework for M 11/19: peer-review of hw 2
- python list comprehension, running external programs, classes and methods
- for Sunday 11/11: homework 2. hard deadline! peer review assignments will be made M 11/12
- for M 11/19: peer-review of hw 2 due
- week of 11/19: the final project will be assigned
- more with python: working with files and directories, break and continue loops, dictionaries
- homework for W 11/7: homework 2 (link on Canvas) individually or in groups of 2
- python functions & scripts continued: we will finish our script / module and make it use arguments
- for M 11/5: submit your “binomial” python code on your github course note repo; if this is group work, submit to one of your repositories and indicate all student names in the github issue
- for W 11/7: do homework 2, in groups of 1 or 2: see link on Canvas.
- python functions
- homework for W 10/31:
- python’s tuples and lists and regular expressions
- homework for M 10/31:
- python’s basic types, syntax, loops, lists
- homework for W 10/24: python scw
- intro to python
- homework for M 10/22:
- python scw: finish section 1 analyzing patient data and do section 2 repeating actions with loops
- git branch exercise:
- pair up with one other student in the class
- decide which git repository to work on: class notes repo from one or the other student, say student A
- student A goes to her/his own repository, clicks on “Settings” then “Collaborator” (github might ask for your password) then enters the gihub user name for student B, then click “Add collaborator”: to give push access to student B
- student A: start a new branch “A”, add something to it, push the branch to github
- student B: clone the repo on her/his laptop, start new branch “B”, add changes or new file to it, push the branch to github
- student A: pull branch B, add changes to it, push to github
- student B: pull branch A, add changes to it, push to github
- student A and B: each checkout master branch, merge his/her own branch into master, push to github. The second student doing this will need to pull first.
- both students: check the branches and merge on the repo’s network: click on “Insights” then “Network”; there should be at least 1 merge commit and labels for at least 3 branches: master, A and B.
- open a github issue with a link to the url with the “network” view; tag the instructor & TA on this issue, give both student names.
- awk, curl & wget
- homework for M 10/15: peer reviews. Both reviewers will be given access and will be tagged on the github issue Check your issues here and click on the “Mentioned” tab to see the list of issues where you were tagged (provided that you have read access to the repo).
- shell scripts: if, arguments
- for Wed 10/10 8pm: exercise 3 of homework assignment 1, including submission via github issue
- for M 10/15: peer reviews
- back to shell tools: e.g.
- homework for W 10/3:
- git and github for collaboration
- homework for M 10/1:
- finish to create your own github repo for your course notes, and to push your local repo there, if not done in class already
- open an issue on your github course note repo, where you tag the instructor + TA, with a comment on one particular thing that you learned in the course so far; use at least 1 markdown syntax feature when you write this github issue.
- do shell scripts from the software carpentry: how to pass arguments to a script
- do “tracking a species”
from the software carpentry: combines
cut, pipes and script arguments usage.
- reflexions on hw 1.1: one solution, and video on Unix by Gary Bernhardt
- git for version control
- homework for W 9/26:
do the exercise in this recap section
include as many markdown syntax features as you can within your local repo
- more practice with grep
- project management & markdown format
- homework for M 9/24: exercise 2 of homework assignment 1
- less and man
- search with regular expressions, grep and find
- for W 9/19: finish finding things except for “tracking a species”
- for M 9/24: exercise 2 of homework assignment 1
- pipes, shell loops, and more on redirection, processes, controls.
- homework for M 9/17:
- auditors: email me to be added to the course mailing list (canvas)
- everyone: turn on your canvas notifications
- shell basics
- homework for W 9/12:
- course intro: why should we learn these things? expectations? logistics?
- best practices
- intro to the Unix shell
- homework for M 9/10: