This repo contains the materials for short course Julia Meets Mendel: Algorithms and Software for Modern Genomic Data at 2018 Joint Statistical Meeting (JSM), Vancouver, Canada.
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Janet Sinsheimer, Professor, Biomathematics, Biostatistics, Human Genetics, and Statistics, UCLA
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Eric Sobel, Professor, Human Genetics, UCLA
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Hua Zhou, Associate Professor, Biostatistics, UCLA
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Chris German, PhD student, UCLA
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Sarah Ji, PhD student, UCLA
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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.
The easiest way is to run Jupyter notebooks on a server dedicated to this course.
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Point your browser to http://35.233.157.190:8000/ (expired 07/31/2018).
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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 is
Joe Bruin
, then your username isjbruin
. Your password isjsmce18c
. Of course you can change password after you log in, e.g., bypasswd
command at Bash terminal. -
To transfer the course materials to your home directory on the server, click
Terminal
in JupyterLab and type command
git clone https://github.com/Hua-Zhou/JSM2018-CE18C.git
You should see the folder
JSM2018-CE18C
in the Files
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/lab
tohttp://35.233.157.190:8000/user/jbruin/tree
.
This is not 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, simply git 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.