- Notifications
You must be signed in to change notification settings - Fork1
Short course "Julia Meets Mendel: Algorithms and Software for Modern Genomic Data" at 2018 Joint Statistical Meeting (JSM)
License
Hua-Zhou/JSM2018-CE18C
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
This repo contains the materials for short courseJulia Meets Mendel: Algorithms and Software for Modern Genomic Data at 2018 Joint Statistical Meeting (JSM), Vancouver, Canada.
Janet Sinsheimer, Professor, Biomathematics, Biostatistics, Human Genetics, and Statistics, UCLA
Eric Sobel, Professor, Human Genetics, UCLA
Hua Zhou, Associate Professor, Biostatistics, UCLA
Chris German, PhD student, UCLA
Sarah Ji, PhD student, UCLA
Juhyun Kim, PhD student, UCLA
| Time | Topic | Instructor |
|---|---|---|
| 8:30-9:00 | participants intro., OpenMendel [pdf] | Eric Sobel |
| 9:00-9:30 | Julia: intro. [ipynb], multiple dispatch/JIT/profiling [ipynb] | Hua Zhou |
| 9:30-10:15 | Julia: linear algebra [ipynb], optimization [ipynb] | Hua Zhou |
| 10:15-10:30 | coffee break | |
| 10:30-11:15 | Julia: GPU [ipynb], NNMF [ipynb], parallel computing [ipynb] | Hua Zhou |
| 11:15-noon | review of genetic and genomic concepts [pdf] | Janet Sinsheimer |
| noon-1:00 | lunch | |
| 1:00-1:30 | handling genetic data in OpenMendel [ipynb] | Hua Zhou |
| 1:30-2:30 | GWAS for population and genetic analysis [pdf,ipynb] | Eric Sobel |
| 2:30-3:15 | linear mixed models for genetic analysis [pdf,ipynb] | Janet Sinsheimer |
| 3:15-3:30 | coffee break | |
| 3:30-4:30 | mendelian randomization [pdf,ipynb] | Janet Sinsheimer |
| 4:30-5:00 | Course wrap-up [pdf] | Eric Sobel |
There are several ways to run Jupyter notebooks in this course.
Theeasiest way is to run Jupyter notebooks on a server dedicated to this course.
Point your browser tohttp://35.233.157.190:8000/ (expired 07/31/2018).
You'll be greeted by a JupyterHub login page:
Your username is initial of your first name + your last name. For example, if your name isJoe Bruin, then your username isjbruin. Your password isjsmce18c. Of course you can change password after you log in, e.g., bypasswdcommand at Bash terminal.After login, you will see the JupyterLab interface:
To transfer the course materials to your home directory on the server, click
Terminalin JupyterLab and type command
git clone https://github.com/Hua-Zhou/JSM2018-CE18C.git
You should see the folderJSM2018-CE18C in theFiles tab on the left of JupyterLab. Now you can open any Jupyter notebooks in that folder and run the examples.
- If you prefer the Jupyter Notebook interface instead of JupyterLab, change the address from
http://35.233.157.190:8000/user/jbruin/labtohttp://35.233.157.190:8000/user/jbruin/tree.
This isnot recommended during this short course, since your software environment (OS, Julia version, package versions, etc.) may be quite different from that assumed by the Jupyter notebooks. In case you want to run Jupyter notebooks on your own machine, simplygit clone https://github.com/Hua-Zhou/JSM2018-CE18C.git to sync the most recent course materials to your computer and install all needed Julia packages.