Monday, August 31, 2015

Twitter R interface



https://cran.r-project.org/web/packages/twitteR/index.html

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



cross-cutting



cross-division program

cross-directorate
 BIG data, critial tenchinique and techlogy for advancing big data science & engineering


cyberbridge 2015

NSF prioritizes  multi-PI team project

Kurose, "Nothing ever works unless it comes up bottom up." It has to be organic. 

Crosscutting and 



Software Institute

EAGER grants



cyberbridge discussion #5, #6

#5 cyber infrastructure in classroom.
#6 computer literacy
=> Sustainability of continuously changing curriculum
=> Balance of subject contents and learning programming skills



Mechnical Engineering
CS
Biology

challenge in classroom.

outdate technology in classroom.
technology change too fast.  limited teaching support (few money),
When technology is in classroom, it is outdated already.

=> Sustainability of continuously changing curriculum
Mobile technology device are discouraged in purchasing.
Emulated environment?

Intro to Programming for Engineering students

For undergraduate education,
C syntax overhead
Python, popular.

=> Balance of subject contents and learning programming skills

Computer literacy as Core requirement is too simple for Science major

 MATLAB has penetrated the undergraduate like a plague.

computing mechanical engineering. no time on computing language
MATLAB, coding in class

Requirement in CS courses

Level of complexity in engineering.
Subject content is already too heavy. Programming language not enough time.
Subject problem is too complex.

Research program versus 'polished programs'

MATLAB does not provide a good understanding of  "Computational concepts"


#4 interdisciplinary research
money and publications
Tenure and promotion focus on individual effort.






#3 data visulaziation literacy and IVMOOC discusion

data visualization literacy
=> understanding of data visualization
=> be able to present data through visualization
=> understanding caveats in visualization
=>IVMooc: art basic for technology-oriented people

---detailed notes --------
What is data visualization
compute security: privacy persvaing visualizaiton,
computational fluid dynamics: what parameters, what quantitiy to visulzie, different criteria? flow field, velocity field, vortex (different way to visualize the data)

=> understanding of data visualization
GIS: time series and spatial data

=> be able to present data through visualization
heat map, pick approriate parameters (key information)

=> understanding caveats in visualization
network science: for incomplete information, uncertainy, dynimc data, scalable visualion.

mecha eng:
biology:
Automatic control, optimization,
big data visualization
visualtion using parallel method, real-time data
info graphcis for scientific computing for public attention,
projection: 3d data to 2d map
multi demesion data to 2d map.
visualization of text labels

=> IVMOOC: art education and technology education
Basics: specialized visualization, connect to scientific topis


Cyberbridges, Arlington, Aug 31-Sep 1, 2015


http://www.rit.edu/gccis/cyberbridges/

Thursday, August 27, 2015

git push many files

I need to add 737 files from blacklight simulation. Using GitHub the process is too slow and exhausted the RAM.  I was forced to try command line version.

on mactower:

$ git add .
$ git commit -m "diggin.ms02.from blacklight"
$ git push origin master

This works. 

greenfield job run (successful)

[hqin2@greenfield ~]$ cat foo.pbs 
#!/bin/bash
#PBS -l nodes=1:ppn=15
#PBS -l walltime=5:00
#PBS -o test1.out
#PBS -j oe
set echo
echo hostname
module load R/3.2.1-mkl
R --vanilla --slave CMD BATCH ./myR.R



[hqin2@greenfield ms02GINPPI]$ cat ms02.pbs
#!/bin/bash
# Request 15 cores
#PBS -l nodes=1:ppn=15
#  Request 30 minutes of cpu time
#PBS -l walltime=30:00

module load R/3.2.1-mkl

echo hostname

pwd
cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI
pwd


R --vanilla --slave -f ms02-2015June24.R --args 1000 1001




I also updated the path in ms02-2015Aug27.R
Some input files were removed during the transfer and I put them back.












sbio233, chapter 2, cell structure and function

Preparation: 
Plastic sheets, pencils, dark markers, => contrast
Microscope
Play dough =>  morphology
A tray of water, a small bottle of oil, a micro pipetman and tips => thin lipid layer. 

2:30pm. Ask student to draw with colored markers. I draw a cell with a pencil.

3pm. Have trouble with video play in powerpoint. I played manually using the html file.

3:10  playdough exercise on morphology.
 3 playdough balls. Roll two of them to cylinder. Roll one cylinder into spiral.

3:30pm, surface/volume ~ radius function. Which figure? Socrative poll.

3:35pm, membrane structure

Summary.
Ecoli negative. Bsu positive.
Resolution and wave length.
Contrast.
Three types: rod, cocci, spirilum.
surfae to volume ratio
membrane structure

Class stoppped at 2.8

Problems: The podium computer windows does not play the video in powerpoint. I had to play them with html files.

http://hongqinlab.blogspot.com/2014/08/bio233-chapter-2-microscopy-intro-to.html

Greenfield, sample pbs job scripts



This  is an example to run a serial job on Greenfield using PBS: 

#!/bin/csh
#  Request 15 cores 
#  Note that this means the job will be allocated 750GB of memory 
#PBS -l nodes=1:ppn=15
#  Request 5 minutes of cpu time
#PBS -l walltime=30:00
#  Combine standard output and error into one file
#PBS -j oe 
set echo
cd $PBS_O_WORKDIR
module load R/3.2.1-mkl
# run my executable
R --vanilla --slave CMD BATCH ./example.R


And here is an example of “packing” several runs in one job,
so that they all run simultaneously. The output files should be all named different:


#!/bin/csh
#  Request 15 cores 
#  Note that this means the job will be allocated 750GB of memory 
#PBS -l nodes=1:ppn=15
#  Request 5 minutes of cpu time
#PBS -l walltime=30:00
#  Combine standard output and error into one file
#PBS -j oe 
set echo
cd $PBS_O_WORKDIR
# Define where /tmp files will be written
 setenv TMPDIR $PBS_O_WORKDIR
module load R/3.2.1-mkl
# run my executable
numactl -C +0 R --vanilla --slave CMD BATCH ./example0.R &
numactl -C +1 R --vanilla --slave CMD BATCH ./example1.R &
numactl -C +2 R --vanilla --slave CMD BATCH ./example2.R &
numactl -C +3 R --vanilla --slave CMD BATCH ./example3.R &
numactl -C +4 R --vanilla --slave CMD BATCH ./example4.R &
numactl -C +5 R --vanilla --slave CMD BATCH ./example5.R &
numactl -C +6 R --vanilla --slave CMD BATCH ./example6.R &
numactl -C +7 R --vanilla --slave CMD BATCH ./example7.R &
numactl -C +8 R --vanilla --slave CMD BATCH ./example8.R &
numactl -C +9 R --vanilla --slave CMD BATCH ./example9.R &
numactl -C +10 R --vanilla --slave CMD BATCH ./example10.R &
numactl -C +11 R --vanilla --slave CMD BATCH ./example11.R &
numactl -C +12 R --vanilla --slave CMD BATCH ./example12.R &
numactl -C +13 R --vanilla --slave CMD BATCH ./example13.R &
numactl -C +14 R --vanilla --slave CMD BATCH ./example14.R &
wait

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).

Wednesday, August 26, 2015

turn on ssh login in osX


The Apple Mac OS X operating system has SSH installed by default but the SSH daemon is not enabled. This means you can’t login remotely or do remote copies until you enable it.
To enable it, go to ‘System Preferences’. Under ‘Internet & Networking’ there is a ‘Sharing’ icon. Run that. In the list that appears, check the ‘Remote Login’ option.
This starts the SSH daemon immediately and you can remotely login using your username. The ‘Sharing’ window shows at the bottom the name and IP address to use. You can also find this out using ‘whoami’ and ‘ifconfig’ from the Terminal application.

qsub debug

qsub -q debug?


F. Lyons, 20150826

FL is interested in gene network and clustering analysis, and XSEDE HPC.

HHMI fellowship requires biomedical research project.

We agreed on human gene expression analysis.

I asked her to learn R and Unix shell on EdX. FL is not clear why she has to learn R. So, I showed her the EdX course on RNA seq. I explained that she need to learn how to walk with R first.

Topic:
Analysis of biceps brachii muscles from men and women 19 to 28 or 65 to 76 years of age. Results provide insight into the influence of gender on age-related changes in the molecular properties of the skeletal muscle.
http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4858


Aging effect on bone marrow hematopoietic stem cells

vi usage



http://www.openvim.com/

greenfield job run (failed)



temporary storage place:  /crucible/mc48o9p/hqin2

emacs ms02.pbs













10:44am, $qsub ms02.pbs 

Error: 






Testing at $HOME, myR.R 
by 11:15am, I successfully submitted a job to greenfield. 

$ cat foo.pbs
#PBS -l nodes=1:ppn=1
#PBS -l walltime=5:00
#PBS -o test.out
#PBS -j oe
set echo
source /bin/bash
echo hostname
module load R

R -f myR.R















































emacs

On greenfield, Ctrl-Z stop emacs.


http://www2.lib.uchicago.edu/keith/tcl-course/emacs-tutorial.html

Notation

In the rest of this document I use the standard Emacs notation to describe keystrokes:
C-x
For any x, the character Control-x.
M-x
For any x, the character Meta-x (see below for more details on Meta characters).
C-M-x
For any x, the character Control-Meta-x.
RET
The return key (C-m actually).
SPC
The space bar.
ESC
The escape key, or, equivalently, C-[

CDC data



http://www.cdc.gov/nchs/nis/data_files.htm

greenfield, file transfer


xx@login.xsede.org


gsissh greenfield.psc.xsede.org





















Need to use /crucible for file storage
"Your /crucible home directory is  /crucible/group-name/user-name  wheregroup-name is the 7 character name for the PSC group associated with your grant."



$ ls /crucible/mc48o9p/hqin2



This works!















Tuesday, August 25, 2015

bio233, chapter1, Madigan v14

Items needed:
  Plastic sheet, pencils, and color markers -> concepts of contrast

Short lecture slides

Go over problems: worst question, virus and ribosomal RNA 85% correct.


Activity:
Contrast demo using plastic sheets. Use color to demonstrate contrast.

Possible discussion questions from Pearson
Q: Why only anaerobic microbes exisit on Earth for the first 2 billion years?
Q: why is it incorrect to say that an object is partially sterile?

Summary of the class. Lessons learned.

Reference
http://hongqinlab.blogspot.com/2014/01/bio233-jan-21-2014-chapter-1-review-of.html
http://hongqinlab.blogspot.com/2014/08/bio233-lec1-intro-to-microbe-20140826.html

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.




Monday, August 24, 2015

bio233, lab, 20150824 Monday, sampling microbes on campus

bio233 20150824 Monday

Problem: Apple side of the dual boot computer cannot be logged in. 

=> reminder, many assignments due before class.
  Remind students that quizs are adaptive, and slides are provided. 

=> pre-class survey on computing
=> survey on metric proficiency

X => Go over lab safety
Lab safety signature

=> laptops
Youtube live-event recording with powerpoint


Lab prep:
x nutrient plates
steril cotton swipes (plenty of them in 245 cabinets in the back)
marker pens (need to order more)
parafilms
scissors

serial number of the plates, student last name, place, location
make a serial number of each plate date-group#-plate#
label the plates on the sides in the back,

Demos, sterile technique,

sample the same size of area,

take picture of locations

parafilm seal the plates, leave at room temperature

Reference
http://hongqinlab.blogspot.com/2014/08/bio233-lab-sampling-microbes-on-campus.html

Announcement:
next Monday, Tue, instructor will be away. No class meeting, but online assignments (scale of microbes) will be given.

JCorley, 20150824Mon

Emailed my proposals to JCorley.
Went through Google-Hangout with her.
Signed HHMI document
HHMI require her to present on research day in the spring.
HHMI program is only for 1 year
JC worked on "peach" laptop.


biolaptops

biolaptop##\biolaptop
spel\d4

biolaptops cannot be login somehow.


Saturday, August 22, 2015

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
 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. 

Thursday, August 20, 2015

bio233 day 1, 20150820

names tags
print student names
IRB signature
syllabus
previous student projects, exams,

3pm. Socrative. Download app to smartphone.

Problem: forgot to mention that assignments are due before class.

For lab:
pre-class survey
Youtube real-time self-recording
pick papers to read

bio386 day 1

syllabus

name tags
preclass survey
IRB signature

 assignment: youtube  video for introducing yourself.
install R and Rstudio
x googleTalk conference call

research projects
setup dropbox account and share with instructor

YouTube for screen-cast
EdX Microsoft intro to R course
Pick papers to read


Tuesday, August 18, 2015

Spelman Office 365 (todo)

All spelman computer/laptop can be updated with Office 2013 freely. This should include office 365.

Office 365 can also be installed on 5 personal computers.

Request a ticket to upgrade Office on computers.


pandoc, lyx

http://pandoc.org/installing.html

lyx


Sunday, August 16, 2015

flow cytometer training


http://www.thermofisher.com/us/en/home/support/tutorials.html?socid=social_20150816_50608416&adbid=1195673353783588&adbpl=fb&adbpr=183929358291331

bio125
bio233

Wednesday, August 12, 2015

R code: find student pins, placement results for advising

rm(list=ls())
require(xlsx)
setwd("~/Dropbox/courses.student.research.dp/FYE_and_advising/FYEFall2015/match_placement")
list.files()

tb = read.xlsx2( "FYE_advisee20150812.xlsx", 1 )
for(i in 1:6) {
  tb[,i] = as.character(tb[,i]) 
}

lang = read.xlsx2( "World Languages 2015 Placement.xlsx", 1, 
                   colClasses=c("character", "character", "character", "character", "character") )
for(i in 1:5) {
  lang[,i] = as.character(lang[,i]) 
}

tb$ID %in% lang$ID
tb$language = lang$language[match(tb$ID, lang$ID)]
tb$langLevel = lang$level[match(tb$ID, lang$ID)]


pins = read.xlsx("qin-registration-pins20150812.xlsx", 1)
for(i in 1:4) {
  pins[,i] = as.character(pins[,i]) 
}
tb$pin = pins$Alternate.PIN[match(tb$ID, pins$ID)]


math = read.xlsx2(  "math Advisor Placements Fall 2015.xlsx", 1)
for(i in 1:6) {
  math[,i] = as.character(math[,i]) 
}
tb$ID %in% math$Student.ID
tb$MathCode = math$CODE[match(tb$ID, math$Student.ID)]
tb$MathPlacement = math[match(tb$ID, math$Student.ID), 5]
tb$MathOther = math[match(tb$ID, math$Student.ID), 6]

str(tb)

write.xlsx(tb, "qin-FYE-placement_and_pins_20150812.xlsx")

From TestGen to Moodle assignments and quizzs

Procedure:
In TestGen, export the questions to Moodle format.





















In Moodle, first create an appropriate category. Then choose Question Bank, and then import from file, and move these questions into an appropirate category.
To create a quiz, select the questions from the category.
































Note: I have not figure out to convert an entire quiz/exam to Moodle.

Tuesday, August 11, 2015

FYE 2015 tentative schedule (not anymore)

Fall Semester 2015

August  20 Opening Convocation with President Campbell
 
Sept. 10 Introduction to Course/Spelman/Text  (Text is A Pocket Guide to College Success by Jamie Shushan)

Sept. 17 Stress and Time Management

Sept. 24 Reading Texts and Note Taking

Oct. 1   Reading Texts and Note Taking (continued) (First Paper Due)

Oct. 8 Strategies for Studying and Taking Tests

 Nov. 20th (Revision Due)

Spring Semester 2016

Jan. 28 Introduction and Discovering Your Major

Feb. 4, 11 Financial Literacy (sessions)

Feb. 18 SpEl.Folio and Community Service

Feb. 25 Leadership

April 1 Community Service Essay Due

April (TBA) Portfolio Due

Saturday, August 8, 2015

qbio day 4


=> Rhys Adams, ENC
Aleksandra M. Walczak
http://q-bio.org/w/images/d/d5/Qbio2015_136.pdf
yeast display library of antigen <--> antibody, sorted by flow cytometer, identify the antigen by sequencing.



=> Growth rate variations establish distributions of generation times and division sizes in E. coli
http://q-bio.org/w/images/8/87/Qbio2015_91.pdf
high variablity of growth rate in E coli cells.

growth rate is the length increasing rate,
division rate is the cell division rate.





Friday, August 7, 2015

qbio day3

=> Chakraborty mit HIV vaccine
http://q-bio.org/w/images/1/12/Qbio2015-invited-Chakraborty.pdf
http://web.mit.edu/akcgroup/AKCcv2014.pdf

=> Robin Lee, Univ of Pittsburgh, NFkB 

=> https://med.uth.edu/ibp/faculty/john-f-hancock/

=> synthetic oscillator
IPTG, AraC, GFP, LacI

=> xiling shen, 
incoherent forward loop
cancer stem cell turn on? asymmetric division

=> Martin howard, fission yeast size.
Pom1 and Cdr2
http://elifesciences.org/content/elife/3/e02040.full.pdf
Pom1 gradient was thought as a reason, but the two nature papers were wrong. Pom1 is on membrane. 
Medial accumulation of cdr2. 
cdr2 is an area sensor. 
rga4D fatter cell, rga2D thinner cell
Jun & Taheri-Araghi, Trends microbiology 2015,  http://jun.ucsd.edu/ 
http://jun.ucsd.edu/files/publications/TrendsMicrobiol.2014.pdf
Ecoli adder
Scerevisiae between adder and sizer.
=> https://sysbio.med.harvard.edu/facultys/jeremy-gunawardena-phd

=> Li, vision
picture -> feature map -> salience map
16:30-17:00 Li Zhaoping, UCL, A theory of the primary visual cortex, its zero-parameter quantitative prediction, and its experimental tests

=> Xiao Wang, ASU, biomedical engineering
quorum-sensing crosstalk network






Thursday, August 6, 2015

qbio day2


microfuidic chip: pulse and change mediam of cells. useful for my radicicol experiment.

kar.kent.ac.uk/47681/

geodesic curves

=> microbes under pressure, oskar hallatscheck, uc berkley
http://www.evo.ds.mpg.de/

hypothesis: crowded microbes change their behaviors

Single cell assay for fission yeast. Minc et al Current biology,

Trapped fission/budding yeast cells in microfluidic devices.

https://en.wikipedia.org/wiki/Turgor_pressure

natural isolates (haploids) are valtro like and can generate much larger tugor pressure and crack PDMS device and agar plate.
Q: invasive pathogenic and noninvasive strains?

=> IgE, cornell, molecular memory
http://q-bio.org/w/images/e/ec/Qbio2015_148.pdf
microfludic chamber for mast cells
pulse of signals

=>  http://q-bio.org/w/images/b/bd/Qbio2015_48.pdf

"Our findings strongly suggest that the low channel capacities previously observed at a single cell level does not reflect an inherent physical limit, but rather a natural trade off between information transfer at the single cell vs. population levels. This implies that the level of noise in individual signaling networks and cells can be regulated to produce reliable information at the level of individuals or populations, depending on the phenotypic requirements of the organism."


=>14:30-15:00 Alejandro Colman-LernerUniversity of Buenos AiresUse of information far from steady-state by signal transduction systems.
budding yeast pheromone mating pathway.

yeast with truncated Ste2, fluorescent alpha factor, --> dose reponse of ligand binding to receptor.

=> http://arxiv.org/abs/1503.00909

On the connection between computational and biochemical measurement



=> 15:20-15:40 Jeremy PurvisUNC-Chapel HillSingle-cell dynamics reflect underlying signaling mechanisms
https://www.med.unc.edu/genetics/faculty/jeremy-purvis/purvislab

single cell data shared by Nan Hao, Andrew Hans and Erin O'Shea


=> Arthur Lander's group, Abed AlnaifUC IrvinePattern formation and morphogen gradients: A causality dilemma

=>16:30-16:50 Vernita GordonUT-AustinThe bacterial population’s spatial structure non-monotonically impacts bacterial growth
planktonic and biofilm bateria
http://chaos.utexas.edu/people/faculty/vernita-gordon

=>16:50-17:10 Nicholas C. ButzinVirginia TechEntrainment of synthetic gene oscillators by a noisy stimulus

=> Jeff Gore, mit
http://gorelab.homestead.com/
ecological systems biology, cross-protection allows a mixed population to survive,

flow cytometer monitoring of two population, two kinds of antibiotics











Wednesday, August 5, 2015

qbio15 day 1

qbio 2015, August 5, 2015 Wednesday

=> rule based modeling http://bionetgen.org/index.php/Q-bio-14
bionetgen use matlab for parameter estimation. The .m files can be converted to .c file for faster computing needs. Some kind of simulated annealing approach seems to be used.

Currently, rule-based modeling has not been applied to spatial modeling. "Everything is coded to ODEs".