nodalpoint.org - DNA mania - Comments

Yeah, need to update my

ejain — Tue, 22 Jan 2008 19:47:42 -0500

Yeah, need to update my blog...

700?

nuin — Tue, 22 Jan 2008 13:18:11 -0500

At 700 a pop for an Action Figure?

Dude, Where's My NAR?

Duncan — Tue, 22 Jan 2008 13:09:27 -0500

Hello Maximillian, I wasn't attacking NAR, was just wondering about what proportion of the data is dead. It is an interesting technical challenge to find this out. It would also be useful to measure the cost of gathering noisy, redundant and poorly understood data in terms of wasted resources (people, time, money, computers, false positives etc). Perhaps somebody has done something like this already? Especially with all the irresponsible sequencing just for sake of it that goes on...

As for the physicists, I mentioned them for comparison. Like you, I doubt they will use 100% of their data either, but will probably use much more of it. However, they keep delaying switching their big machine on, which means they are still waiting for the data. That is, unless when they finally flip the switch on the LHC, we all disappear into a black hole, tombs and all :)

It doesn't matter, they got published

lbbros — Tue, 22 Jan 2008 06:46:50 -0500

Does it matter that large quantities of this data will probably never be used?

Probably not, as their authors are already happy enough to have those published, and then they can ~~stop mantaining~~ move on to another ~~project~~ publication. It is indeed a sad state of affairs.

Swiss Prot Databases / Action Figures

Duncan — Mon, 21 Jan 2008 18:12:33 -0500

Hi Eric, yeah even more redundancy there. Talking of SWISS Prot people, I'm just wondering when your Amos Bairoch action figure will be available in shops?!?! What are you up to now that you've moved on from SWISS Prot to Seattle?

Why NAR

maximilianh — Sun, 20 Jan 2008 10:59:14 -0500

I add the usual defense of the NAR databases: At least they are indexed by pubmed, so as there are biologists that are not used to checking in google if there are websites about their subject, they will find them quicker via NAR. The data is not dead, websites can always be exported. (I've made the experience that for smaller databses it's usually quicker to scrape the data from an html page with something like HTTP::Recorder than writing to the person responsible for the data to send you an sql dump.) In addition, people get papers for their databases like this and other people can cite the database properly, so NAR makes the web citable and advances someone's career a little bit. It already eases the transition from a traditional paper-based science to a more web-orientated world. Databases are peer-reviewed, so they don't contain complete crap, a paper in NAR assures some minimal quality. And a write-only database is better than none at all, at least someone has collected something and you can scrape it from its tomb.

I would just love to see a minimal requirement for a publication in NAR: They should all offer some simple text-based export, e.g. tab-delimited flatfiles. That could save me a lot of time...

Of course, large quantities of these data are never used and never read. But, heck, this is research, right? 90% will not be used in the end. It's not too different from those 500 alignments algorithms, 200 genomic analyses, hundreds of papers that describe "new" cloning strategies, yet another new gene, etc. I don't believe that the physisists use 100% of their 1,5 GB / sec either.

Also, think of all the

ejain — Fri, 18 Jan 2008 20:12:16 -0500

Also, think of all the redundant effort that goes into setting up the basic technical infrastructure each database needs (data storage, user interfaces etc)...

-10 Ooops

Duncan — Fri, 10 Aug 2007 05:05:19 -0400

Ooops, my semantic web agent did the sums wrong (bad ontology) and made Jim aged 89 not 79....corrected it now!

+10 ?

radmap — Thu, 09 Aug 2007 23:30:12 -0400

Man, that sequence must have been pretty scary ... seeing his own genome sequence instantly aged Lucky Jim an extra 10 years! ;-)