bio386, 20151117Tue

Bio386, computing survey

Computing project

Review student presentations.

*** bio386, Gordon exercise 20151105Thu

Gordon, file transfer

Procedure to transfer bio386.tar archives from QIN's directory to student directory: 

You can loginto Gordon using ssh or Putty directly

$ ssh username@gordon.sdsc.xsede.org

Then go to your file directory:  

$ cd /oasis/scratch/username/temp_project/

Then copy bio386.tar to your file directory

$  cp /oasis/scratch/hongqin/temp_project/bio386.tar . 

Then 

$ tar xvf bio386.tar 

Then

$ cd Slim-network-aging-bio386-fall-2015

Then 

$ nano -w  20151101-net-sim-ginppi.R

Inside of nano, you should change the username in the following line: 

mydir = '/oasis/scratch/username/temp_project/Slim-network-aging-bio386-fall-2015'

Then control-X save and exit nano

Now, we can need to change the working directory in PBS job script. 

$ nano -w netaging.pbs

Then change username in the following line

 cd /oasis/scratch/hongqin/temp_project/Slim-network-aging-bio386-fall-2015

Then exit and save. 

Then submit the job request

$ qsub netaging.pbs

If this runs, you are one of the first Spelman students to use a Federally funded super-computer. 

To check the status of your computing jobs

$ qstat -u username

bio386 20151105Thu

X student research project,

X data into R.

Gordon pbs job run.

Unix/Linux exercises

http://www.doc.ic.ac.uk/~wjk/UnixIntro/Exercise1.html

http://www.doc.ic.ac.uk/~wjk/UnixIntro/index.html

bio386 20151027Tue

Research topic update.

Gordon login, and Unix shell practice.
Problems:
1. There is a delay for Gordon to update user profiles. Some students cannot log into Gordon after I add them to Gordon.
2. My login attempt to "login.xsdede.org" led to "access denied".

bio386, 20151020Tue, go over exam 1, key

Screen cast of exam 1 key codes.
Use some of student video.

bio386, exam 1, due, Q&A sessions.

Ask students to work on their research project due.
Pick a primary research paper for presentation.

Many students submitted screencast on their exam problems. I realized that I can use student video as tutorials.

bio386 20151001Thu midterm exam released

Released midterm exam. Found the keys were somehow released as well, luckily I correct the error before most students downloaded the files.

I then let students worked on practical problems.

bio386, 20150924Thu

linear regression, abline plot

go over previous exam1

bio386, Tue, salary example

Go over salary example. Ask students to follow along. Some students were able to modify my code and apply it to different variables.
The EdX R course also prepared the students for R syntax.

Correlationhttps://class.coursera.org/rprog-032/forum/thread?thread_id=265

Announcement: Skip "program 2 assignment" on Coursera's R course.

youtube:
https://youtu.be/wrM2uA0NGNs

bio386 20150917Thu, coursera coding assignment part1

Problem: Almost all students did not watch the coursera videos. they seem to expect to finish the assignment without going over the lecture videos.

bio386 20150917Thu, coursera coding assignment part1

bio386, week 1, programming assignment

Problem: One student try to read in a file in a directory. "directory/file_name"

The first programming assignment of the Coursera is very challenging. Students started to have trouble to complete the programming assignment.

Pubmed in R

https://gist.github.com/freshbiostats/2de46d0c7a59cbf54ad0

bio386, 20150910Thu

30 min: Review of aging questions

UTK meeting announcement again, abstract submission

Spent the rest of class on Coursera week 1 assignment.


Open but independent exam

bio386, 20150903Thu, questions on cellular aging

Let students work through R programming problems on EdX course.

==========
Self-intro video review
R/Rstudio review

Q: weibull versus gompertz

Q: constant mortality rate?

Q: definition of essential genes in yeast

Q: definiton of replicative and chronological aging

Q: virus aging

Q: CR restriction pathways

Q: ROS theory of aging

Q: mitochondrial role in aging

Self-screen cast on Rstudio coding and demo, simple.R demo

bio386 student project

http://www.r-bloggers.com/getting-started-with-twitter-in-r/

http://www.r-bloggers.com/building-wordclouds-in-r/

Insilico DB

48 states network clustering project

bio386 20150827Thu

1pm, 7 students on time. snack reward.

Check "Progress" of EdX R course.  Some finished 3-4 labs and problem sets.  Some barely did anything.

1:15-1:35, variable assignment problem. 
as.character(var1)
var1_chr = var1

var1_chr = as.character(var1)


Spend the rest of class on introduction to aging.

Mentioned Linux and XSEDE HPC at the end of the class.

Note: K Parker helped me with the projector screen (1 bonus point promised).

bio386, 20150825 Tue, overview of R, reading assignment

X UTK meeting announcement

X many students were not present on the first day of the class.
Ask a student K Parker to demo live-recording on youtube.

by 1:44pm, all student installed  R and Rstudio are installed. Students all can run simple.R .
I associated .R with Rstudio on mac.

1:49 Ask students to register for EdX and Intro to R by microsoft DAT204x.

announced homework on EdX, module 1 and 2 for week1.

Reading assignment on cellular aging, Qin 2013 proposal.

yeast mitochondria genome

http://www.biomedcentral.com/1471-2164/16/451

Strope 2015 Genome Research, 100 S. cerevisiae genomes, McCusker lab

http://genome.cshlp.org.proxy.library.emory.edu/content/25/5/762/suppl/DC1

Strope PK,  McCusker group at Duke
Genome Res. 2015 May;25(5):762-74. doi: 10.1101/gr.185538.114. Epub 2015 Apr 3.

Strope15GR used its own strain nominations, even though the strains are obtained from others. This is quite annoying. 

I recognize M22, M1-2, YPS163

Strains are explained in Table S1, accession numbers are explained in table_S19.