Displaying 7 results from an estimated 7 matches for "alanine".
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alain
2012 Feb 10
0
a) t-tests on loess splines; b) linear models, type II SS for unbalanced ANOVA
...the population density of
bacteria (represented by "od" (optical density)) and the concentrations of
several chemicals, such as glycerol, in their growth medium (environment).
The data looks like this:
> head(df.yx.t)
uid cid date g t od glycerol alanine
6 6 Ma,1 25 Ma 1 0.1428571 3025750049 7843841013
7 7 Ma,1 25 Ma 2 0.4542857 3026668036 7902016686
8 8 Ma,1 25 Ma 3 1.4542857 3086406597 8017589237
9 9 Ma,1 25 Ma 4 2.5866667 2821935918 6595302338
10 10 Ma,1 25 Ma 5 3.0933333 2674142017...
2009 Sep 16
3
How to extract a specific substring from a string (regular expressions) ? See details inside
Hi all,
I have thousands of strings like these ones:
"1159_1; YP_177963; PPE FAMILY PROTEIN"
"1100_13; SECRETED L-ALANINE DEHYDROGENASE ALD CAA15575"
"1141_24; gi;2894249;emb;CAA17111.1; PROBABLE ISOCITRATE DEHYDROGENASE"
and various others..
I'm interested to extract the code for the protein (in this example: YP_177963, CAA15575, CAA17111).
I found only one common criterion to identify th...
2010 Mar 31
2
Generative Topographic Map
...use R version of package
I noticed the original MatLab Pckage is much better documented.
I had a look at the R demo code "gtm_demo" and found that variable Y is used in advanced of being created:
I wrote my own few lines as follows:
inDir <- "C:/Documents and Settings/Monville/Alanine Dipeptide/DBP1/DHA"
setwd(inDir)
T <- read.table("DHA_TNH.txt")
L <- 3
X <- matrix(nrow=nrow(T),ncol=3,byrow=TRUE)
MU <- matrix(nrow=round(nrow(T)/5), ncol=L)
for(i in 1:ncol(X)) {
for(j in 1:nrow(X)) {
X[j,i] <- RANDU()
}
}
for(i in 1:ncol(MU)...
2013 Nov 01
1
Package(s) for making waffle plot-like figures?
...differs for positions with different
numbers of residues. I am suspecting that I didn't use coord_equal()
correctly.
So I wonder how I can make the plots like I described above in ggplot2 or
with some other packages. Also, is there a way to assign a color to
different residues, say, purple for alanine, blue for glycine, etc, and
incorporate that information in the for loop?
Many thanks for any suggestion you may give me!
Zhao
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2010 Mar 01
0
Is package "dr" appropriate for reducing the dimensionality of molecules conformational space ?
I anticipate lacking of prior experience with dimensionality reduction problems.
Some scientists concerned with drug discovery performed several steered Molecular Dynamics simulations of the
alanine-dipeptide molecule dragged by a radial force from an equilibrium conformation to another different equilibrium conformation.
They sampled at regular intervals 7 dihedral angles, 5 bending angles, and 4 atom pair distances all along the trajectory from
the initial to the final conformation. Likewi...
2010 Apr 12
0
WMTSA "wavCWTPeaks" : Error in if (time.start < times.range[1]) time.start <- times.range[1]
....
Only columns 1 and 3 have to be considered. It is the work trajectory of a molecule migrating between two equilibrium conformations.
The curve has 2 peaks, as shown in its plot. But I keep missing the 2nd one. Here is my short script:
library(wmtsa)
setwd("C:/Documents and Settings/Monville/Alanine Dipeptide/Work_curves-Dir")
work <- as.ts(read.table ("calc_work_332")[,c(1,3)])
plot(work[,1],work[,2])
work.wt <- wavCWT(work, n.scale=1000)
scales <- attr(work.wt, "scale")
work.tree <- wavCWTTree(work.wt,tolerance=0.5/sqrt(scales))
work.peak <- wavCWTPeak...
2008 Apr 22
2
cloud plot has white(transparent?) background
I am using the code example from the R graph gallery to look at a
cloud plot:
require(lattice)
data(iris)
print(cloud(Sepal.Length ~ Petal.Length * Petal.Width, data = iris,
groups = Species, screen = list(z = 20, x = -70),
perspective = FALSE,
key = list(title = "Iris Data", x = .15, y=.85, corner = c(0,1),
border = TRUE,