Run R code in command line

# R -f ms02_driver_20180523.R --args bg.phys.csv bg.3.csv 100 0.025 9 > log.3.txt

https://stackoverflow.com/questions/18306362/run-r-script-from-command-line

convert Rmd to R code, knitr

http://felixfan.github.io/extract-r-code/

library(knit)

purl("test.Rmd")

Qin Spring 2019 schedule

Monday lab
Tue Thu 10:50am-- 12:05pm, lectures

Biocarta

http://amp.pharm.mssm.edu/Harmonizome/about

data sets for MS02 manusciipt

Standard data sets for enrichment test by Li, Wei, Genes 2017, pathway enrichent analysis with networks (random walk)



NCBI GEO Potential data sets with GEO2R

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50864

Gong Y, Zack TI, Morris LG, Lin K et al. Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. Nat Genet 2014 Jun;46(6):588-94. PMID: 24793136

distributed graph processing, HPC graph algorithm, SC2018

https://sc18.supercomputing.org/presentation/?id=ws_ia121&sess=sess168

Many-Core Graph Workload Analysis
https://sc18.supercomputing.org/presentation/?id=pap335&sess=sess218


https://sc18.supercomputing.org/presentation/?id=bof142&sess=sess409

ShenTu: Processing Multi-Trillion Edge Graphs on Millions of Cores in Seconds

https://sc18.supercomputing.org/presentation/?id=gb106&sess=sess467

faimGraph: High Performance Management of Fully-Dynamic Graphs Under Tight Memory Constraints on the GPU
https://sc18.supercomputing.org/presentation/?id=pap167&sess=sess208


There Are Trillions of Little Forks in the Road: Choose Wisely! -- Estimating the Cost and Likelihood of Success of Constrained Walks to Optimize a Graph Pruning Pipeline
https://sc18.supercomputing.org/presentation/?id=ws_ia116&sess=sess168

graph 500

http://graph500.org/?page_id=12

mini autoclave

https://www.laboratory-equipment.com/laboratory-equipment/bioclave-autoclaves.php

biosafety hood

https://www.terrauniversal.com/product/1688-92A-48

Cat #	Description	Qty	$/Each	Total
1688-92A-48	Hood; 48"W x 30"D, ValuLine WhisperFlow, Vertical Laminar Flow, 120V	1	$2,187.00	$2,187.00
Total:				$2,187.00

This hood is 48" W x 30" D x 41" H

This should work with OT2 opentron, whose dimension is width 63cm, depth 57cm, height 66cm.

Consensus pathway database and Wilcoxon enrichment test

http://cpdb.molgen.mpg.de/

Respondus personality change

Respondus personablity refer to blackboards, canvas, moodle etc.

This can be changed in start settting.

NetBAS running time problem, yeast PIN, GOBP ~ GOBP 4.2 hours

The following codes run for 4.2 hours on applejack laptop using single core.  Need to use parallel method to speed this up. 

```{r}
pairsBuffer = data.frame(matrix(NA, nrow = 1, ncol=3))
names(pairsBuffer) = c("name1", "name2", "tag")
for ( i in 1:length(pairs[,1])){
  print(i)
  #els1 = sort( unlist( strsplit(  pairs$cat1[i], split=",") ))
  #els2 = sort( unlist( strsplit(  pairs$cat2[i], split=",") ))
  sub1 = cats[ cats$id == pairs$name1[i], ]
  sub2 = cats[ cats$id == pairs$name2[i], ]
   
  tagbuffer = allCombinationsOfTwoVectors ( sub1$GO, sub2$GO)  #all combinations
 
  # generate a dataframe buffer with ids
  currentBuffer = data.frame( cbind(rep(pairs$name1[i], length(tagbuffer)),
                        rep(pairs$name2[i], length(tagbuffer)),
                        tagbuffer                        ))
  names(currentBuffer) = c("name1", "name2", "tag")
 
  pairsBuffer = rbind( pairsBuffer, currentBuffer) #combine with dataframe buffer
}

F.obs = data.frame( table(pairsBuffer$tag))
names(F.obs) = c("tag", "freq")
F.obs

likelihood family tree based CNN image classification

the best image label always as maximum Prob, so penalty need to be given to change from image label to another image label.

inteactive R

https://www.displayr.com/interactive-globe-r/

yeast PIN ms02 Zscore map

An interesting curve was seen. Only 2 ms02 null were used in this plot.