Jekyll2026-06-15T12:00:19+00:00https://chem-bla-ics.linkedchemistry.info/feed/by_tag/defense.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenThe CDK/Metabolomics/Chemometrics Unconference results2008-04-07T00:10:00+00:002008-04-07T00:10:00+00:00https://chem-bla-ics.linkedchemistry.info/2008/04/07/cdkmetabolomicschemometricsAs announced earlier , Miguel, Velitchka, Christoph and I held a small CDK/Metabolomics/Chemometrics unconference. We started late, and did not have an evening program, resulting in not overly much results. However, we did do molecular chemometrics.

We used the R statistics software together with Rajarshi’s rcdk package (an R wrapper around the CDK library) and Ron’s (my PhD supervisor) PLS package (see this paper), to predict retention indices for a number of metabolites.

We ended up with this R script:

library("rJava")
library("rcdk")
library("pls")
mols = load.molecules("data_cdk.sdf")
selection = get.desc.names()
selection = selection[-which(selection=="org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor")]
x = eval.desc(mols, selection, verbose=TRUE)
x2 = x[,apply(x, 2, function(a) {all(!is.na(a))})]
y = read.table("data_cdk_RI")
input = data.frame(x2, y)
pls.model = plsr(V1 ~ ., 50, data=input, validation="CV")
summary(pls.model)
plot(RMSEP(pls.model))
plot(pls.model, ncomp=20)
abline(0,1, col="red")
plot(pls.model, "loadings", comps=1:2)
savehistory("finalHistory.R")

The AminoAcidCountDescriptor threw us a NullPointerException and there were a few NAs in the resulting matrix. The CV results were not so good as Velitchka’s best models, but still a good start:

No variable selection; 200 objects, 190 variables.

Questions:

  • Can we do this in Bioclipse2 too?
  • Can we improve the default CDK descriptor parameters to maximize the column count?
  • Rajarshi, what would be involved to write some wrapper code for atomic descriptors for rcdk?
]]>Egon WillighagenT plus 51 hours: a short photo impression2008-04-04T00:00:00+00:002008-04-04T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2008/04/04/t-plus-51-hours-short-photo-impressionI normally do not do these kinds of blog items, but, in reply to Christoph’s blog, here’s an overview of the ceremony (see also T-26 and T+18 ):

This is the doctorate certificate Christoph mentioned, with also Karin and our kids:

And, here (map) was the dinner in the evening:

]]>Egon WillighagenT plus 18 hours: dr and preparing for the afterparty, umm ^w^w^w, CDK/Metabolomics/Chemometrics unconference2008-04-03T00:00:00+00:002008-04-03T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2008/04/03/t-plus-18-hours-dr-and-preparing-forI am doctor now; I shall now be addressed as weledelzeergeleerde Egon; translating to something like quite-noble-very-knowledgeable, hahahaha. I’ll put up a few photo’s of the ceremony, which is actually quite formal at the Radboud University, later.

With this blog item, I would to thank everyone who left a message, sent email, etc with good luck messages. Very much appreciated! I’d also like to thank my supervisors, promotores Lutgarde Buydens and Peter Murray-Rust (he mentions the event here), and Ron Wehrens for their confidence in me and their guidance on the path towards the post-doc life. I also thank all those who attended my defense; I had a brilliant day, and actually enjoyed talking to those who took place in my promotion committee and who asked me the not-really-nasty-questions about my work.

CDK-Chemometrics in Metabolomics Unconference

For today, I organized a small, informal unconference, oriented around the CDK, chemometrics and metabolomics. I’m certain we will be online much of the day, as we typically do. The meeting will start around 10:00 CEST, but we’ll attend a seminar by Marjana Novič at 11:00 CEST. If you happen to be in Nijmegen, just drop in on the Analytical Chemistry department. Otherwise, join the #cdk chat channel in the irc.freenode.net network.

What we’ll do?? Hey, it’s an unconference; we have no idea yet :)

]]>Egon Willighagen