Mote carlo simulation demo in R.

http://www.r-bloggers.com/quantitative-finance-applications-in-r-5-an-introduction-to-monte-carlo-simulation/

Brownian motion travel distance ~ sqrt(t), based on its wiki page,

todo: John Snow's cholera data, other math data from UAH

http://www.math.uah.edu/stat/data/Snow.html

http://www.math.uah.edu/stat/data/index.html

bio125, SDS PAGE gel running, cancer and cell cycle

0.5 hour on protocol, wester blot, probes
1 hour loading gels
1 hour, Cancer and cell cycle, virtual lab on cell cycle and cancer.
MSH2 expression and cell cycle

The SDSPAGE gels were run for 2 hours. Dr. Kioko transfer the gel after the class, and stained with primary antibody.

bio233, ch9, viruses, jeopardy

=> clicker poll on exam logistics
=> Viruses youtube video
=>Viruses Game show rule
=>  Viruses game show. Presentation style can show the next slide, and I can give clues to students.
  The prizes are travel mixer bars.
=>Exam 2 were given back to students.

=> student went through their practical exam on streaking plates. 

I forgot to mention the virus trade off paper discussion. I need to announce in news forum.
=>Virus trade-off paper to read, questions to answer

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

Yeast media

http://www.sunrisescience.com/pages/ystmedia_faq_home.html

Spring exam schedule, Spelman

Bio233, May 8.

Bio125, May 5, 10:30-12:30

http://www.spelman.edu/docs/registrar/finalexam2014_spring.pdf?sfvrsn=0

BIO125, research day poster on H658Y

FOA plate show that H658Y has as few colonies as potential wildtype MSH2 control. So, H658Y has nearly-normal MMR function. The mutation occurs in ATPase domain, so maybe human MSH2-H658Y just cannot repair as efficiently as the wildtype one, even though its actual repair machinery is normal.

It is also possible that protein expression level of H658Y is lowered.

In Gammie 2007, H658Y was shown to be '-' on MMR. So, our FOA results are not consistent with Gammie07. It is possible that H658Y cells were substantially lower than wildtype MSH2. 

Update Snow Leopard to Maverick

I backuped my Snow leopard laptop and then upgraded its osX to Maverick.

After the update, multiple 'mdworker' process heated up the laptop. I used a cold-pad to lower the temperature.  This went on for about 2 hours and 'mdworker' stopped.

Older version of ApE and VirtualBox stopped working, but Mathematica still works.

Console version R is lost. Reinstall R sovles the problem.

Github GUI can be installed now.

todo: convert chars to num in ms02

ms02_singlerun_v2() test

The code has trouble to deal with small network with many selfing or redundant pairs. 

Test on 48 states runs OK.

Kilometers versus miles: Does it really matter? 2014 report.

The link between metric systems, scientific literacy and attitude.

The daily life in the U.S.A. is based on customary units separated from the international systems of units (metric system) that are taught in sciences. Does this partition of daily life and scientific understanding hinder the scientific literacy for the American population and impose a negative connotation on science as a whole? These are the questions that we set to investigate. We designed a survey to gauge people’s scientific literacy and acceptance of scientific findings, while taking into account confounding factors such as educational background, gender, country, and age. The survey contains 3 sets of problems: one set on proficiency of the metric system, one set on scientific literacy, and one set on attitude and acceptance toward science. The survey is administrated online and through paper.

We previously reported our findings using 200 participants. The survey received 300 responses recently, and enabled us to analyze the link of proficiency of metric systems to scientific literacy and attitude toward science. 

First, we found the scientific literacy is significantly associated with proficiency of metric system (Figure 1), which is perhaps not a surprise because science is taught in the metric system. This correlation suggests that people that are familiar with scientific knowledge are also more proficient at metric usage.

Second, we found that attitude toward science is significantly associated with proficiency of metric usage (Figure 2). Attitude toward science is also directly associated with scientific literacy (data not sure), but this association disappears if the metric proficiency is controlled in regression (data not shown). This partial correlation suggests that metric proficiency is the causal factor for both scientific literacy and attitude (Figure 3). Updated on April 8, 2014. Attitude toward science correlated significantly with both metric proficiency and scientific literacy, even when age is controlled.


Third, we found that attitude toward science is significantly associated with age, suggesting that old people tend to have better attitude toward science, even when metric proficiency is controlled (Figure 3).  Because the current survey involved many faculty, it is not clear whether this association is due to our biased samples or not.  When educational degree is controlled, age is still significantly correlated with attitude toward science, and this correlation persists when people with Ph.D. are excluded from the analysis. This might mean another bias: People participated in the online survey tend to be more inclined toward science. On-campus survey were often done by papers, and target students that are not interested in science. This bias can only be mitigated by targeting a broader population.

Figure 1.  Scientific literacy correlates with metric proficiency.


 

Figure 2.  Science attitude correlates with metric proficiency and age. 

Figure 3. Science attitude correlates with age. 

Ages of Participants by gender

Figure.  Metric proficiency is significantly influenced by educations. 

We need a large data and more broad sampling scale to make this survey more meaningful.  Please help us persuade more people to take this on-line survey.

The current R code and survey data are deposit into Hong Qin's GibHub repository. 

References:

• Diverging Bases: The Case Against the Metric System, Lila Nordstrom 
• The Metric System, the United States of America, and Scientific Literacy, Adam Blankenbicke

Things to do: 

Some further analysis that I want to do. If people choose 'yes' for "My religious views are more important than scientific views", would answers to the rest of the attitude questions become predictably negative on science? 

Note on 2013 Nov 15, I may use interaction and auto-correlation to address the sampling bias.

bio233, microbial systematics, phylogeny, evolution

Student went through their practical exams: Plate images,

Phylogeny,

Exercises

Play-dough on trees, rooted and unrooted trees

The earth history calculation and play dough on tree seem to engage most students. The BLAST slides simply eluded most of them. Some of them probably worked for other courses in front of they computers.

On board exercise: If the earth history becomes 1 day, how long will the human history become?

Playdough exercise:

  How to root unrooted trees.

Video:

http://youtu.be/9ha2X_aIqBM

Upgrade mactower to Maverick

Upgraded mactower to Maverick. This take a few hours.

I backedup all data before the upgrade.

After the upgrade, it looks the all of data files are still there.   Good.
The network configuration also seems unchanged.

The shell link of "R" disappeared, even though the Rgui is still in /Applications/.  I re-installed R3.0.3 and 'which R' points to '/usr/bin/R'.

References
http://mactips.dwhoard.com/new-mac-checklist

pathogenic yeast, note, 2014 April 8

interesting ones
actin
pdr5

cis44??

non-informative ones
hsp104
hsc82
hsp82
pdr15

bio125, protein extraction

I spent 50 minutes to explain the protocol on board. Students were given spundown cells in eppendorf tubes, and begin with adding 160 lysis buffer.  The protein extraction took 1 hours and finished around 3:10pm. I used the rest of the time for course evaluation.

Video: http://youtu.be/piC1Koyu1No

yeast cell wall, membrane, nuclear envelope

Nuclear and cytosol

beta mecaptal ethanol

SDS PAGE gel


Protocol on board: 



After adding blue ESB to the protein pellet, the TCA will turn ESB into yellow. Use Tris to adjust the color back to blue.

Add DSB to pellet

Changed to yellow. 

Adjusted to blue. 

MSH2 expression, cell cycle, log-phase
hMSH2 has no putative NLS signal, but MSH6 have 3.
co-import is supported.

MSH2 deficient,