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Oops!

posted by cyrus in Science

I guess this isn't too surprising, but it's a bit troubling.

Nice smackdown by Richard Gibbs: "I don't know of any good scientific work that has been compromised by cross-species contamination..."

Oops!

Speaking of information technology...

posted by cyrus in Science

The aforementioned articles about computational biology in Science make some reasonable points. But I find it ironic that I'm reading article in PDF form where there are no links to the references. Here we are discussing the future of science and the scientific publishing community still doesn't have links to references contained in the paper in the PDF! The HTML version of the paper is a little better, as some of the references have links to Medline (and CrossRef and Web of Science, whatever those are) but, in general, the references aren't hyperlinks, as one would hope in any modern publication. I agree that mathematical training is important for the future of the field, but it's also important that we bring scientific publishing into the '90s.

Speaking of information technology...

Interesting article by John Timmer

posted by cyrus in Science

In this article, John Timmer makes some interesting commentaries on the recent Science articles by Pevzner and Shamir and Robeva and Laubenbacher. Worth a read.

Interesting article by John Timmer

Chemistry

posted by cyrus in Science

So now that I have more than a passing interest in chemistry (and therefore cheminformatics/chemi-informatics/chemoinformatics/whatever-you-call-it), I'd like to see what the state of the art is for representing chemical information and if there are any decent libraries for working with these representations. At first glance, I'm in luck. There's CML, the Chemical Markup Language, there's the Blue Obelisk set of projects for open source/open data/open standards in chemsitry, and there's the CDK, the Chemistry Development Kit. This all sounds promising. Let's dive in.

Working in reverse order, let's start with CDK. Google CDK and it shows up as the first hit -- even before the Cyclin Dependent Kinases. This is good. Now let's follow the link. Uh oh. It's a link to sourceforge. That's alright, we'll click through and hope for the best. Ah, not only is it on sf.net, but it's a wiki site: http://apps.sourceforge.net/mediawiki/cdk/index.php?title=Main_Page.

Ugh. Alright, I'll try to overcome my biases and keep plugging away. It's not that all wikis are bad, but rather that, IMO, they are a poor substitute for a properly designed web site for a project. They certainly have a place, but the idea that all web content gets wiki-ized can lead to some rather difficult-to-follow web pages, again, IMO. The wikipedia example is a good counterexample to my claim, but, most other wiki sites don't have the complete, polished feel of wikipedia. In any event, let's keep plugging ahead with CDK.

Ah, here we go. Two publications in the peer-reviewed literature. This should help give us an overview of what CDK has and where it is going. One is in the Journal of Chemcal Information and Modeling (although it seems that when the article was published it was called the Journal of Chemcal Information and Computer Sciences. Alright, sounds promising. Click through the DOI link, which takes us to a page of American Chemical Society, the world's largest scientific society. Surely, this being a paper about on open-source toolkit and ACS being a society for the betterment of society, this is going to be an open-access journal, right? Or at least an open-access publication in a mixed-access journal, right? Click on the link to get the PDF... Get PDF -- WRONG! $30 for 48 hours of access. Damn. Ok, well, let's get the other paper, there were two on the CDK wiki. The next one is in something called Current Pharmaceutical Design. Uh oh. This doesn't sound promising. And, sure enough: "The full text electronic article is available for purchase. You will be able to download the full text electronic article after payment. $55.10 plus tax." This isn't getting us anywhere. At least CDK is open source. Let's go get the source. Well, first let's browse the documentation anyway.

Click over to the documentation look on sourceforge: http://apps.sourceforge.net/mediawiki/cdk/index.php?title=Documentation. How is the documentation different than what I was looking at before, or what's the difference between the documentation and the main page? Who knows. In any case, this looks promising: "A great source of CDK documentation or introductory reading is the CDK News, the quarterly newsletter of the CDK team." Click through. Ok, there's a picture of the (presumably) most recent issue, which is a link to the table of contents and a note about getting the PDF: "The full issue can be downloaded as PDF from http://sf.net/projects/cdk/". Hmm... Ok, click through that... And we're back on sf.net. Oh wait, that's not a link. Just some text. Cut the URL and paste into the nav bar in the browser... Hmm. Now we're at another sf.net page. So far we've got the "main" page, the "documentation" page and now the, presumably, "project" page. But now that we're there, we see that there is no mention of CDK News on this page. Damn. Alright, let's start clicking and see what we find. Ok, under the "Download -- Browse All Packages" link we get to a page that has CDK News on it. Maybe now we're getting somewhere. Click through that and we have a nice list of the various "Releases" of CDK News (this seems like an abuse of the Release mechanism, if you ask me -- these aren't different versions of the same thing, rather distinct issues, all of which shoud live on, but, OK, I think I see what they did there). Let's start at the beginning. Click on 1/1. Hmm... That just expands the HTML a bit to show another link for cdknews1.1.pdf. Ok, click that. Ah yes, no I remember why I hate sf.net. Do I get the PDF in my browser? NO! I get a window with a whole bunch of orange reminding me the name of the web site I know hate so much, some links to "share" the project (whatever the hell that means!), for related stuff and for forums (yet another set of pages to not get the info I want?) some google ads and some guy who looks like he hasn't slept in a week carrying stacks of cash, presumably, in an ad for nortel. Oh, and I link telling me who's providing this oh-so-handy mirror. Oh, and I almost forgot, some nice sponsor links! As opposed to the ads, I suppose. Where's my damn PDF? Who knows. Ah, this is helpful. Please use this "direct link": http://voxel.dl.sourceforge.net/sourceforge/cdk/cdknews1.1.pdf. Why the hell didn't they just give me that link the first place??? Ok, finally got CDK News 1.1. I suppose a (direct) link off of the CDK home page (or at least one of them) would have been to helpful for irritating newbies like myself. Ok, time to go read the first CDK News, since I can't get the peer reviewed articles about the project. More later.

Chemistry

The bees

posted by cyrus in Science

Joe DeRisi is on the case of the missing bees .

The bees