MSM guest lecture on R

Github: https://github.com/hongqin/MSM-guest-lecture

1.What is R? 

Wikipedia entry on R

Why R by Courtney Brown at Emory. 

Why R and beyond.

R blogger that provides recent and often interesting development about R.  

What is R video.

2. Install R to your own computers.

Instructions to download R. 

Install R studio.  RStudio provides a nice GUI to R.

Install packages to R: Video for Windows Version.

3. Introduction to R.

• TryR@code school
  
  
  R data camp
  
  
• Stephen J. Eglen's short intro slides. 
 
•  
 
•  
 
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Hong Qin's slides: Overview of R;   Basic programming in R; Input & Output in R;

Lydon Walker, getting started with R, an accelerated primer

Coursera course

 4. Simple exercises in R.

Qin's simple.R excises.  Please select 'Raw' and 'save-as' in text format. Unfortunately, web browser seem to automatically add 'txt' to the file name, and Rstudio does not run 'txt' format.  To solve this problem, we can 'create' a new R script, and copy-paste from code from the text file.

(The workshop audience mostly reached this step).

Youtube tutorial converting Excel data to CSV and load into R. 
    The sunflow seed Excel file is here.  

5. Make solution exercise.

Write an R function to calculate how much NaCl needed for X ml of Y mM NaCl solution. 

6. Simple statistical analysis in R.

Simple regression exercise.

7. Advanced training materials.

Multiple regression demo

Hierarchical clustering using cities. Code, Video.

Laddy Gaga and clustering analysis. Code. Video.

Bioconductor workshop materials.

8. Useful R materials.

• Hong Qin's R and computational biology GitHub site

• Stephen J. Eglen's PLOS article. A quick guide to teaching R programming to computational biology students. 

• 
  

http://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf

http://www.rseek.org. 

http://addictedtor.free.fr/graphiques/. 


Newly launched interactive cloud-based R for teaching: http://www.datamind.org/


Google-developers R programming videos


Avril Coghlan's little book of R for bioinformatics.


Github's collection of free R books

R by examples

9.   For preparation for the workshop

Wireless connection, laptops, power-outlets are recommended. 

Install packages and data on flash-drives in case internet connection is slow. (This can be a problem when all participants are download at the same time.)

A flow-chart on easel can be used for clarity.

Common problem is to set R working directory. 
 

backup webtools

Clustal
http://simgene.com/ShowClustalWResults

NEBCutter

bayesian in R

rejection sampling

http://www.r-bloggers.com/a-simple-explanation-of-rejection-sampling-in-r/

why computing in medicine

smart band aid
http://www.livescience.com/50559-smart-bandages-use-artificial-intelligence.html

personalized medicine

bio125, flow data analysis, April 21, 2015 tue

Section 1:
On Yosetmite, many students have problems to run flowSet code. On windows, many students cannot install flowViz to the R directory. 
I gave the plots to students instead.

Section 2:
A student installed Windows binary of FlowClust and FlowViz to R 3.2.0. but flowClust still give run-time error. This seems to be a bug then. Students use R 3.1 and R3.2.  I was using R3.0.

bio125, exercises, cancer, April 16, 2015

Section 1,

UCSC genome browser.
Problem: Some students changed the setting of the display control and was confused by the display.

Section 2,

Go through many questions.

Problem in math percentage calculation. 500ml 0.5%, how much do we need? I wrote on the board
500x0.5% = 2.5 which confused many students. They think I skipped some steps.  Another student
explained it as  0.5% = 0.5mL / 100mL = x / 500mL, and find out x. This made the students said that now they got it.

R causal inference and machine learning

R  causal inference
http://blog.revolutionanalytics.com/2015/03/targeted-learning-r-packages-for-causal-inference-and-machine-learning.html

HMM in R
https://www.inovancetech.com/hmm-tutorial-1.html

bio125, April 14, 2015. Regrowth of HU treated cells. site-directed mutagenesis

Spring 2015 final exam schedule
http://www.spelman.edu/docs/registrar/final-exam-schedule-spring-2015_v2.pdf?sfvrsn=2

Section 1: Final exam May 7, 2015  8-10am,
8:20am, asking student to spin down cells, add 500ul YPD. (many students did not resuspend the cells)

8:30am, incubation in YPD started.

8:40-9am. Went over pre-class assignments and in western blot assignment.

9am:  Started site directed mutagensis primer design, cognat sites in multiple sequence alignment.
  by 9:26am, finished three tutorial videos. Most students did not pay attention to the video. I then started the inclass assignment on G548C exercise.

 10am, take tube from shaker, take 5ul from both HU+ and - on a single slide. (HU treated sample show some budding, maybe 50% from sample to sample).

 10:12am, spin down, add 70% drop by drop to suspend the cells.

  Cells often form clumps in 70% ethanol. So, Dr. Kioko votexed the tube and add 70% drop by drop.

I used a empty pipette tip box to store the cell and put them in the shaker. (This has no air, so it should be

Course evaluations were done at the end of section 1.

Section 2: final exam May 4, 2015 10:30 a.m. - 12:30 p.m
Students trickled in from a chemistry exam, complaining about having to finish 47 questions in 1 hour.

1:30, incubation in YPD started.

2:10-3pm, site directed mutagenesis. Codon bias, quarters by state, software sales,  the more -> the better,
   Most students did not pay attention to youtube video, but then complained about not knowing what to do. Some students try to use ApE to analyze protein sequences. Most students in section 2 worked alone and did not discuss with others. In contrast, many students in section 1 worked in groups.

3pm. take cells from YPD incubation.  5ul on slides.  Some students have trouble to focus on the cells.

3:25pm. Ask students to do course evaluations.

Eppendorf tubes in a box at 30C shaker for incubation.

Ideas Lab, Sandpit

http://knowinnovation.com/in-the-sandpit/

https://www.asee.org/conferences-and-events/nsf-ideas-lab/overview

Preliminary Ideas Lab meeting activities are as follows:

Day 1: Data gathering introductions and initial knowledge mapping
Day 2: Framing the problme statement
Day 3: Generating ideas for actionable Research and Development
Day 4: Creating solution
Day 5: Planning for action

exercises for ucsc genome browswer

http://www.explorebiology.com/apbiology/labs/

https://cbse.soe.ucsc.edu/news/article/1915

https://courses.soe.ucsc.edu/courses/bme200/Fall12/01


http://blog.openhelix.eu/?p=17616

flow cytometer, sample probes tend be clogged by yeast cell clumps.

When yeast cells were too dense, the sample probes of Calibur tend to be clogged. Presumably because chained yeast cells clumps.

ucscDb in R

ucscDb = dbConnect(MySQL(), user="genome", host="genome-mysql.cse.ucsc.edu")
result = dbGetQuery(ucscDb, "show databases;")
dbDisconnect(ucscDb)
result

bio125, hydroxyurea induced G1 arrest

X Email ppt to students

Section 1
bio125, hydroxyurea induced G1 arrest

check FOA plate
take pictures

http://en.wikipedia.org/wiki/Hydroxycarbamide

precision medicine youtube channel
whitehouse precicion medicine
https://www.youtube.com/watch?v=RIzbg8REzGw

http://www.pha.jhu.edu/~ghzheng/old/webct/note7_3.files/F13-22b.gif

MSH2 DNA mismatch-repair mechanism

at 10am, check +HU and -HU cells under micro scrope. The key difference is the missing of S-phased budded cell in +HU treatment. Yes, HU is working.


Section 2;

Same drill, and the experiment went more smooth.

FOA results in section 2 are mostly consistent with our expectaction.


Problems: 
Some student closed off the diagpham for microscope, some did not pull the switch for the vertical adaptor. Some did not know how to focus.

strain growth

Kioko: 1:100 in 3 days
Mon 4pm, 1:30 dilution for 8am section.

WORD language and formating bugs

Somehow, WORD changed the language default seeting to Partogese, and auto-corrected many words. I noticed this problem when I the auto-complete gave weird words.  I merged my writing with another person's revision.  I should always trust the own format style in my own file. Other persons often did the revision in hasty ways, and introduce more problems than they fixed.  I wasted at two hours to fix the language and format problems.

REU budget

$2500 for 8-10 week housing,
food allowance can be offered, see Yale's example. http://www.sackler.yale.edu/summer.htm

Spelman College, National Center for Education Statistics

http://nces.ed.gov/ipeds/datacenter/institutionprofile.aspx?unitId=acafacabb1ab

page margin, font size, NIH proposal

Remember the Details! Below are tips to assist you in meeting the requirements on font, font size, margins and spacing. Be sure to follow the format in the instructions and label sections as requested.
 

• Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.)


• Type density, including characters and spaces, must be no more than 15 characters per inch. Type may be no more than six lines per inch. Use standard paper size (8 ½" x 11) . Use at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins

See

http://grants.nih.gov/grants/writing_application.htm

https://researchadmin.asu.edu/faculty-toolbox/nih-writing-requirements

http://viceprovost.tufts.edu/grantwriting/resources/formatting-guide/

advising for fall 2015

8pm - 11pm. spent 3 hours for about 31 students.

bio125, April 2,2015 FOA

yeast strain growth 
5pm, yesterday, 1:10 dilution from stationary culture
today, 8am, OD=0.6 after 15 hours.


Section 1

By 8:15am, 3 groups and 7 students were there. missing 3 groups.

Wait for students to trickle in. Play MSH2 project video. Ask them a question on alternative GT repeat design.

I used playdough beads to explain micro satellite repeats.

by 9am. Students received 5ml of culture.

*After spin down, many students was not clear how to add 1mL water, what to transfer from the 15ml falcon tubes to 1.5ml eppendorf tube. This is a recurring problem.

*Some students were not clear which tubes contains the 1X dilution.

*some students did not suspend cells well before transferring.

amino acid solubility

amino acid in acid form are hard to dissolve.
aminoc acid salt are much easy to discolve.