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New Genetic Information Web Portal
Wonko42 writes "A new portal, DoubleTwist.com, has been opened which allows scientists and researchers free access to tons of genetic information and data. Just type in a gene sequence, and it'll spew data back at you. It'll even notify you by email when there's new information about the stuff you're studying. Very cool. "
Ewan Birney, bio.perl.org hacker extrordinaire is heading up a new effort called ensEMBL which is intended to provide a free and open "baseline" annotation of the human genome. You can find more info at http://ensembl.ebi.ac.uk.
The idea of making a portal out of it is interesting but BLAST has been around for some time...
True. There's A LOT of sites dealing with various facets of genetic information. Starting from databases containing 'raw' DNA sequences coming off various genome sequencing projects (no, it's not only human; genomes of twenty or so organisms have been or are being sequenced at the moment) all the way to servers trying to interpret the data. Just check Pedro's list or one of the mirrors in Germany or Switzerland. And note that this is not so current (in fact nearly 3 years old) but already pretty long list...
is a genbank type interface which allows you to submit requests and have the agents email you sequences as they're entered in the databases. It should also let you select only complete sequences, specify a maximum number of sequences to retrieve from one species, and automatically search not just genbank but all the databases. This of course requires realtime access to all the databases.
If you want to get hits to your website you'd best get the word "Portal" tagged to it. This world works on key words. "E-commerce" and "Portal" are the two new words we learned in 1999. Everytime I mention any new technology to people, especially suits, their eyes glaze over but say one of the established key words and they instantly snap to attention.
For an average researcher, having a complete set of clusers usually is irrelevant. (Of course, it may not always be; once cluster information is available, people will probably figure out ways to use it well.) All they want to know is how similar their gene(s) of interest is/are to other known genes. And there are plenty of tools that do that already, most notably the set at NCBI. DoubleTwist offers little of use there.
The interesting concept is that of "agents" who go out and look for your data for you. Agents aren't new, but they have not been used much in biological research thus far. Most of the relevant data is at a very small number of sites, so setting up an agent might not be much easier than going around yourself, but if agents become prevalent it will allow biological information to sprawl all over the place to a much greater extent. I wonder if this is a good thing? It is nice to have all your data found for you automatically, but if that's the only way to find anything it may get burdensome.
One point of concern: some of these agents will poll existing sites daily for new sequences. What happens if a hundred thousand researchers all ask for daily polling on ten or twenty genes? Suddenly NCBI will be getting a million extra hits a day and will be slowed to a crawl. I would feel a lot more comfortable if DoubleTwist did the searches on its own machines and only downloaded the new data once a day--but from the description, it sounds as though they plan on searching the public databases repeatedly. (And since it costs them nothing, if 50 people all request information on the same gene, they may not have an incentive to avoid making 50 separate search requests.)
I share the skepticism that anything *really* novel or useful will be greeted with a cheerful reminder that this is an "advanced" feature that requires payment. Further, I'd bet that Celera Genomics is paying close attention here...they are currently racing the NIH to sequence the human genome, and claim that their commercially-funded sequencing will be available for free. However, the advanced tools to search and understand the sequence will not. If Pangaea's attempt here goes badly, watch for Perkin-Elmer (the underwriters of Celera Genomics, who build DNA sequencers among other things) to make Celera back off on their openness statements and start getting really aggressive with patenting....
According to the data I retrieved from doubletwist.com, Rob Malda is my daddy!
Come to think of it, the game starts when someone hooks up a nucleotide sequencer to that site.
Isn't that what Nymphoseek is for? (j/k)
/offtopic/ How come every time I see a topic that I REALLY can add to on Slashdot, I catch it 4 hours too late?
aims to bring the Internet back to its roots -- back to the days when the Net was primarily used by scientists and researchers sharing ideas and data.
Okay, not a bad idea. My guess, (and NO, I didn't bother to research it at all) is that it's going to be a pay for play kinda site, but who determines power usage?
'I need info on Genetic String Xydl;XY89$ajffdasd...'
'Okay Doctor Dooright, that'll be $520, since this is something a power user would need'
I guess it would be set up as some kind of subscription type basis, but at what point are the "free" members limited from the "power" information? Maybe it's just me, but I don't recall the "roots" of the internet charging for scientists and researchers sharing ideas and data
Anyway, don't get me wrong, I'm fully in support of this idea... Especially being the casual nerd that I am. I don't need DNA comparisons between a duck and cat-tailed marmadillo very often (don't ask me what a cat-tailed marmadillo is either), so it's not gonna hurt me any. But I'm worried that there's going to be a paper due, or a project, in which I REALLY need some information, and they're gonna say "Sorry buddy, you've used up all the information you can handle this month... Fork over $250 and I'll see what I can do." (???)
I am not religious, but I recall in the Upanishads, Torah, Chinese (Lao Tzu makes mention of it) and Greek myth a time of a golden age when mankind had a physical perfection, and lived lives roughly 4 times the current maximium life spans with a degree of youth and vigor. This genetic research we have now has already revealed the secret of telemeres which control aging by cell division and we have already sustained human cells and quadrupled the natural life span of a roundworm. Which genetically speaking is not as far away from human beings as one might think.
I could easily conclude that we have no idea how this may change the nature of mankind. The medicines and even perhaps the introduction of genetic fashions and beauty, or intellect by entepreneurs for the coming generation of childen will alter our own perceptions of our mortality. Our culture is very much based on that knowledge of our mortality, how we love, perceive ourselves, our religions, and even our artistic acheivments. It's scary, but I see some very positive changes down the road that might make the negatives easier to deal with.
For one if this genetic knowledge creates longer youthful lives it will mean a political shift that will dramatic. The average man is still left with the "me generation" philosophy of short term thinking thanks to the brinkmanship of the cold war's potental of nuclear annhilation. All we are now, even our sexual revolution stemmed from the concept that we could all die tomorrow. Our politicians think in short term, though it is begining to change, politicians that urge policies that think in the long term are commiting politcal suicide. If we manage to increase lifespans of the citizenry to some 300 years that short-term nihilism behind policies will have to change. If people beleive they have a long future, they have to plan for it, it won't be their children's problem anymore it will be theirs.
I can envision everything from environmental policy to the forgoing of cheap architecture for ornate and enduring stuctures made to be beautiful. Consumerism may change. Even love and family relationships may change, for a mother that is 200 would proably look about 25 and seem to be by appearance a peer not only to her daughter but to her grandaughter as well. A dirty year old man like me, should I make it to 250, might date an innocent young 80 year year old tht looks like she could be an 18 year old japanese anime character.
So open those floodgates of information, bravo!!! Like all mankind before me I will believe in the religion that will promise me immortality, and if science is the religion that can deliver us into that golden age then I will most certainly be a convert.
The idea of making a portal out of it is interesting but BLAST has been around for some time and lets you find information about other sequences. NCBI's ENTREZ gives you the opportunity to research information about proteins and other things. I admit those are a little difficult to use, but I doubt everyone would need to know what such and such sequence represents.
The web has become very important to anyone doing research in those areas and is the main source of information since it is far simpler and everyone can have access to the information.
I haven't seen the portal (login reasons) but I'd be curious to see how they would make it understandable to someone who doesn't have a lot of genetic background and such. All of this can be very cool and interesting but a gene sequence is about as dry as a looking at machine language and the information about the sequences isn't always easy to understand, especially since a lot of the sequencing now isn't puclished like it was before so all you have is the name of the gene. Even when it is published, there isn't a lot of efforts made to make it easier to understand (unless it's in a Nature or something like that where you want the journalists to tell about it).
Anyway, if they can make it more available and more interesting, all the better. Genetic is surely one of the areas where people could use a little more background (no changing one gene won't make you live 300 years, nor will it make you immune to cancer) and also one of the more interesting fields around now (ok I'm biased because that's what I'm studying in, but it's still true).
In my mind, when I hear 'portal' I think 'link farm'(one domain with links to diverse resources of information of interest to people from many differant walks of life). This aproach has proven usefull in finding information, and has proven valuable to many companies bottom line.
Doubletwist.com appears to have focused one a finite area of interest, and has choosen to "do one thing very well". Does this aproach match your definition of 'Portal'? What does the term mean to you?
A quote from the site: DoubleTwist is the first internet portal to make on-line genetic research fast, easy and free for all life science researchers.
The gov't. doesn't want you to download crypto, but you can download diseases (from gov't servers, even). Note that it may be possible to use this information to create deadly plagues. If not now, then someday.
u ery?uid=4262346&form=6&db=n&Dopt=g
Here's Ebola, complete genome:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/q
Not to mention HIV, hepatitis, tuberculosis, foot-and-mouth disease, encephalitis, chlamydia, strepp, and 3600 others.
You get the idea. I can't download Netscape with 128-bit crypto (since I'm in Japan), but I can download some of the world's worst mass-murderers. Of course, synthesizing Ebola isn't easy. Probably.
P.S. I have 128-bit Netscape anyway.