chem-bla-ics: November 2007

Be in my Advisory Board #1: being a good Open Science citizen

I recently saw that blogger.com blogs gained a poll feature. From now on, I will try to be a bit more Open Science, in addition to Open Source. From now on, you can be in my Advisory Board. To do so, vote on my next chemblaics (aka Open Source Chemoinformatics) project. The poll can be found on the left side of this blog. Associated which each poll, which I may run more or less frequently depending on the time of year, will be one blog post where I introduce the options. Options not mentioned, or completely different things, you would like to suggest me to do, can be left as comments to these items.

Nov

Metabolomics workflows in Taverna

My current jobs description is to speed up metabolomics data analysis, and finally got around to making a first relevant workflow for Taverna, using the webservices just posted over at ChemSpider:

I uploaded the source to MyExperiment, so anyway can play with it. There is much to improve, such as using CDK-Taverna for further analysis of the results.

Nov

MetWare: metabolomics database project started on SourceForge

The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.

The databases design will be based on and ideally compatible with proposed standards like ArMet (DOI:10.1038/nbt1041) and those recently written up by the Metabolomics Standards Initiative (see the issue around DOI:10.1007/s11306-007-0070-6).

Nov

When standards fail...

Jim shows that some people do not think webservices standards are complex enough in itself:Toby provided a tonic: How do you know when you’re solving the wrong problem? When your solution involves a 133 page standard with a section entitled “Human Task Behavior and State Transitions”, just to allow a system to give tasks to people.

Nov

An R-based genetic algorithm

During my PhD I wrote a simple but effective genetic algorithm package for R. Because there was a bug recently found, and there is interest in extending the functionality, I have set up a SourceForge project called genalg.

The package provides GA support for binary and real-value chromosomes (and integer chromosomes is something that will be added soon), and allows to use custom evaluation functions.

Nov

Molecules in Wikipedia without InChIs #3

Third in the series of blogs about molecules in Wikipedia without an InChI (see also #1 and #2).

Nov

Last Call for Open Laboratory 2007

Pedro reminded me of the last call for Open Laboratory 2007, which prints the best blog items of 2007 in book form. The list of chemistry contributions is not so large yet, so go ahead and nominate some of cool chemical blog items of the last year.

I will post my shortlist later this week.

Nov

Scintilla and Postgenomic.com on Linux 2.6.17+

That's why blogging works! I reported last Friday on using my Wii for reading Scintilla and Postgenomic.com. Alf replied:It is the Linux kernel, yes: TCP window scaling was switched on by default in kernels since about a year ago (and in Vista too, I think), and one of our routers or firewalls doesn't like it. We're trying to get them upgraded, but it takes a while...

Ah, the trick word: TCP windows scaling. A quick google turned up a workaround in John's Tidbits blog:There are 2 quick fixes.

Nov

Using the Nintendo Wii for serious science...

On my desktop, the Scintilla and Postgenomic.com websites do not work. It is not a browser problem, but has something to do with TCP/IP packages not reaching its destination: the browser. Euan told me they are aware of the problem, but apparently have not found a solution yet.

However, my Wii does not have the problem, which makes me wonder if it is a disagreement between the Nature server and my Linux kernel...

Nov

Cytoscape in Amsterdam

Right at this moment I am listening to Andrew Hopkins from Dundee on chemical opportunities in system biology, at the Cytoscape conference in Amsterdam.