YPD plates

PCAT, MCAT exams

bio386, 2014Oct29. Practice presentation of robustness poster

Practice presentation of the poster on robustness.

BIO233, Tue 20141028, R and Rstudio, anonymous comments

I let students work on R and Rstudio to do data analysis.

At the end of the class, I ask student to write anonymous notes. The comments are generally positive. Several students ask for review of questions and topics in exam and assignments.

Some student did appreciate the Excel worksheet study on LOH. Maybe I should be more explicit on the LOH and aging.

My NCBI citation

Video tutorial
https://www.youtube.com/watch?v=JYODIOD_YYE

mathramp, 2014 Oct 28

Rstudio was not moved into "Application".

Went over R code for simulating aging in permuted networks.

Went over R code for generating histogram of CV

bio233 lab, R and Rstudio analyze of serial dilution data

We spent about 1 hour install R and Rstudio. I then told many students to work as a team.
Some students have various windows computers, and their interface were different.

Then many students waited for xlsx package to be installed through wireless. I have to abadon the xlsx approach, and switched to csv approach.

I then let students reviewed their streaked plates. Only 1 plate can be given A-. The rest of them are at B- . About 2/3 of the plates have to be redone (below C).

I let the students try to streak the plates again. Next day, I found out that almost all students failed. Most students seem to pick the old colonies for every streak, meaning that they did not get the idea at all. 


Some students tried to open R code in the ZIP archive directly. This is a common mistake. This problem become more annoying with the different version of operating systems offer different viewing and extraction options. 

R code for midterm grade report

#require(xlsx)
rm(list=ls())

list.files()
tb = read.csv("some grades.csv")
empty.columns= NULL
for (j in 8:length(tb[1,])){
  #for( i in 1:length(tb[,1])){
  #  if( tb[i,j]=='-') {tb[i,j]=NA } 
  #}
 tb[,j] = as.numeric( tb[,j])
 tb[is.na(tb[,j]),j] = 0
 if( max(tb[,j])==0 ) { empty.columns = c(empty.columns, j)}
}
str(tb) 
tb2 = tb[, - empty.columns]
#tb2 = tb2[, -"Course.total"]
#tb2 = tb2[, - grep('Spring', names(tb2))]
#tb2 = tb2[, - grep('spring', names(tb2))]
tb2 = tb2[, -grep("Quiz.Retake..Fall.2014.Exam.1..part.2..online.part", names(tb2))]
names(tb2)
exam1 = c("Quiz.Exam1.Part1..Fall.2014" ,                                    
          "Assignment.exam1..part2..calculation.questions..fall.2014",
          "Quiz.Fall.2014.Exam.1..part.2..online.part"                )        
exam2= c("Quiz.Exam.2..closed.book.section..Fall.2014..Thursday",             
        "Quiz.Exam2..open.book.section..Fall.2014..Tuesday")

report= tb2[,1:2]
report$Exam1 = apply( tb2[,exam1], 1, sum)
report$Exam2 = apply( tb2[,exam2], 1, sum)

practical = "Assignment.Practical.Exam..microscope.and.morphology..Sep.29..2014"
report$practical = tb2[,practical]/20

scale = c("Quiz.Lab.assignment..Scale.of.Microbes",                    
"Quiz.scale.of.microbes..lab.report")
report$scale= apply( tb2[, scale],1, max)

misc= c("Quiz.DePaepeTaddei.Reading.Assignment" ,                                           
        "Quiz.Lab.assignment..E.coli.genome.studies")

tb2[1:5, misc]
report$misc= apply( tb2[, misc],1, sum)
report$ch1 = tb2[, grep("Chapter.1",names(tb2))]
report$ch2 = tb2[, grep("chapter.2",names(tb2))]
report$ch3= apply( tb2[, grep("Chapter.3",names(tb2))],1, max)
report$ch4= apply( tb2[, grep("Chapter.4",names(tb2))],1, max)
report$ch5= apply( tb2[, grep("Chapter.5",names(tb2))],1, max)
report$ch5= apply( tb2[, grep("ch6",names(tb2))],1, max)
report$ch7= apply( tb2[, grep("ch7",names(tb2))],1, max)
report$ch8= apply( tb2[, grep("ch8",names(tb2))],1, max)
names(tb2)[grep("Quiz", names(tb2))]

assignAndLab =c("scale","misc","ch1","ch2","ch3","ch4","ch5","ch7","ch8")
report$assignAndLab = apply( report[,assignAndLab], 1, sum)
maxS = apply( report[, assignAndLab], 2, max)
report$assignAndLab = 15*report$assignAndLab / sum(maxS)

report$highExam = apply(report[,c("Exam1","Exam2")], 1, max)
head(report)

midterm= c("highExam","practical","assignAndLab")
report$midterm= apply(report[,midterm], 1, sum) *100/70
head(report[,midterm])
hist( report$midterm )

grade2letter = function(x){
  if(x>94){    ret='A'
  }else if (x >90) {    ret='A-'
  }else if (x >87 ){    ret = 'B+'
  }else if (x > 84){    ret = 'B'
  }else if (x >80){    ret = 'B-'
  }else if (x > 76){  ret = 'C+'  
  }else if (x > 70){ ret = 'C'  
  }else if (x > 67){ ret = 'C-'
  }else if (x > 64){ ret = 'D+'
  }else if (x > 60){ ret = 'D'
  }else {   ret = 'F'
  }
  return (ret)
}
grade2letter(70); grade2letter(88)
report$letter = lapply(report$midterm,  grade2letter)

bio386 20141022 Wed t-test, constructive learning

The students were guided to learn the meaning of p-value and t-test.

They spent about 1 hour on the t-test.R example, and figured out small p-value means 'null hypothesis is disproved'.

I then tried to see whether they can apply their newly learned knowledge in the metric-survey data set.  The students have trouble to state the null hypothesis for the metric_v2b.R

t.test(tb2$metric[tb2$gender=='Female'], tb2$metric[tb2$gender=='Male'])

At this time, we reach the end of class, so I left this as homework.

Fastlane submit a revised budget

Access the Proposal Revised Budget Screen
 

1.  On the FastLane Home Page screen, log in as a PI to Proposals, Awards, and Status (see PI/Co-PI Login).  The Principal Investigator (PI)/Co-Principal Investigator (Co-PI) Management screen displays (Figure 1).

 

Figure 1   Principal Investigator (PI)/Co-Principal Investigator (Co-PI) Management screen. The Proposal Functions link is circled.

2.  Click Proposal Functions (Figure 1). The Principal Investigator (PI)/Co-Principal Investigator (Co-PI) Management Proposal Functions screen displays (Figure 2).

 

Figure 2   Principal Investigator (PI)/Co-Principal Investigator (Co-PI) Management Proposal Functions screen. The Revise Submitted Proposal Budget link is circled.

3.  Click Revise Submitted Proposal Budget (Figure 2). The List of Proposals screen displays (Figure 3) with the list of your organization’s proposals.

 

Figure 3   List of Proposals screen. The View button is circled.

4.  Highlight the proposal whose budget you want to revise from the List of Proposals (Figure 3).
5.  Click the View button (Figure  3). The Proposal Revised Budget screen displays (Figure 4) with the following options:
•  View the budget
•  Edit the budget
•  Refresh to the last submitted budget
•  Assign a PIN to the Revised Proposal Budget
•  Forward a Revised Proposal Budget to the Sponsored Project Office (SPO)
•  Add/Delete Senior Personnel
    (Click on a link above for instructions for that action.)
 

Figure 4   Proposal Revised Budget screen.

 

Edit the Submitted Budget

1.  Access the Proposal Revised Budget screen (Figure 1) (see Access the Proposal Revised Budget Screen). 

Figure 1   Proposal Revised Budget screen. The radio button for Edit the Budget and the OK button are circled.

2.  Click the radio button for Edit the Budget (Figure 1).
3.  Click the OK button (Figure  1). The Project Budget screen displays (Figure 2). For instructions for editing any budget year, see Budgets (Including Justification) and Enter the Budget Data Online.

Figure 2   Project Budget screen.

Once you have calculated and saved the edited budget, it is listed as the Working Budget on the View/Print Revised Budget(s)screen (Figure 3).

Figure 3   View/Print Revised Budget(s) screen with the new Revised Proposal Budget now listed as the WorkingBudget (circled).

bio233 exam 2 open book online quiz

In the current Moodle system, when essay questions are not graded, the final grade is shown as "not yet graded".

"Mark" shown seem to give hints to students.

bio233, counting sectioned colonies for serial dilution lab

I took pictures of the MLA plates.

Students were given 3 marker pens with different colors and a tally to count colonies. Many students ask for more tallies. (I need to order more tallies next time).

Many students for some reasons did not input their data to GoogleDoc spread sheets. It seemed that some wrote in their notebook or just some piece of paper that were available to them. The counting and calculation took more than 2 hours.

I did not have time to merge the data and do regression analysis. I showed some students how to install R and Rstudio. The wireless connection took a long time for some student download R and Rstudio.

Install R and Rstudio on Windows and Mac computers

1. Install R (This is the main computing and programming engine). 
1.1 Go to:
http://mirrors.nics.utk.edu/cran/
1.2 Pick the right R version for your computer platform.
For Mac OS X users, you need to identify the version of your system and download the right one.


2. Install Rstudio (This is the user-friendly editor and environment to run R). 
http://www.rstudio.com/products/rstudio/download/
Note: Rstudio must be installed after installation of R.

Video: 
Install R and Rstudio on Windows computers
http://youtu.be/eD07NznguA4

Install R and Rstudio on Mac computers
http://youtu.be/Ywj6yNfc5nM

bio386 R learning, apply, margin, t-test, p-value

I let students first reviewed R code 1-100 lines.

Then, student worked through 100-165.

I asked student to study examples of 'apply' and "margin". I then used a table on a paper to explain this. (I could do a youtube demo on this).

When we reached t-test and p-value, students have mis-conceptions. One student thought "as close to the one" means p-value should be close to 1 from the wikipedia entry on p-value.

bio233 exam 2 review

I gave out previous questions and worked through them in class.

I also handout some MCAT prep questions on paper.

Time runs out pretty fast. I finished less than 10 questions in class.