chem-bla-ics: 2007

Christmas presents...

Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, discussing and comparing different offerings like Pipeline Pilot, Taverna, and KNIME.

Userscripts

The paper on userscripts describes how Greasemonkey scripts can be used to combine different information sources (DOI:10.1186/1471-2105-8-487). A trailer:Background

The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information.

Dec

The molecular QSAR descriptors in the CDK

Pending the release of Bioclipse 1.2.0, Ola asked me to do some additional feature implementation for the QSAR feature, such as having the filenames as labels in the descriptor matrix.

Dec

Test results for the CDK 1.0.x branch

The Chemistry Development Kit has never really been without any bugs, which is reflected in the number of failing JUnit tests. For trunk/ this is today 106 failing tests (live stats). The stable cdk-1.0.x/ branch, however, the number of failing tests is not much lower: 64 failing tests today (live stats).

Overall, only a low percentage of the tests fails (<2% for cdk-1.0.x/ and <3% for trunk/), and, more importantly, it is particular algorithms that are typically broken.

Dec

Open Data getting more recognition

The OD part of ODOSOS is getting more and more attention, and it seems that Peter's Open Data battle is paying off (see his original OpenData article in Wikipedia): an open data specific license has reached the beta stage (see this announcement).

The idea behind this licenses seems to come down to:Facts are free. The Rightsholder takes the position that factual information is not covered by Copyright.

Dec

I don't blame Individuals in Commercial Chemoinformatics

The comment I left in the ChemSpider blog, was probably a bit blunt. ChemSpider announced having licensed software from OpenEye. I have seen such announcements more often, but am intrigued about the nature of such announcements. Is it bad that ChemSpider is using OpenEye software? Certainly not.

Dec

Tagging, thesauri or ontologies?

Controlled vocabularies, hierarchies, microformats, RDF. Nico Adams pointed me to this excellent video:

It's a really nifty piece of work, which goes into the differences between thesauri, controlled vocabularies, and, as such, ontologies, and social tagging systems. Both have their virtues; it is fuzzy logic versus ODEs all over again. Whether one is better than the other only depends on the problem at hand.

Dec

Open Source, Open Data at the European Bioinformatics Institute

I was pleased to hear that Christoph will move to the EBI early next year. Christoph has been working on Open Source and Open Data chemoinformatics since at least 1997. I first got in contact with Christoph when I wrote code for JChemPaint (which Christoph developed) to be able to read Chemical Markup Languages (CML). This also got me into contact with Dan Gezelter who is the original author of Jmol, to which I also added CML support.

Dec

My Open Laboratory 2007 submissions

As promised, here is my list of submission for the Open Laboratory 2007:Open Data is critical for Reproducible ResearchIf you ever made something fluoresce after you did a reaction with a transition metal…One For the BraveFun with singlet oxygenSMILES and Aromaticity: Broken?Resveratrol-Based Natural ProductsMaking Anti-Malarials: Feb 2007 Update

BTW, even though the judges have started their way through the submissions, you can still submit entries.

Dec

Web2O, Open Chemistry, and Chemblaics

Chemistry World December issue features a nice item on the future of data in chemistry: Surfing Web2O; Peter gave an excerpt, and Peter commented on it.

The article discusses many of the things that have been happening in the field of chemical data. It touches Jean-Claude's work on Open Notebook Science, and then moves to Peter's Open Data, mentions a number of other blogs and the Chemical blogspace.

Nov

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.