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Attila Csordas › Comments
Retrospective—The mythology of bioinformatics | Code for Life - http://sciblogs.co.nz/code-fo...
Ruchira S. Datta, Duncan Hull, Bosco Ho and 6 other people liked this
what do you think of this? "By contrast, early bioinformatics work was almost invariably founded on biological concepts from the onset. A biological issue was raised and then a technique to address that issue was presented. That is, theoretical biology was the foundation on which [early] bioinformatics was built. I fear this is being lost in the mass-data and technology-hype driven bioinformatics. It seems to me that unless companies and research groups are careful many will waste time and money “stamp collecting and cataloging”. Certainly the organized data is useful, but only if it is applied with biological principles."
- Attila Csordas
from Bookmarklet
I like that post a lot. I don't know that data organisation is a waste of time/money but I agree that it isn't biological science.
- Neil Saunders
I think one downside of the 'data deluge', is that it's easy to get divorced from (biological) reality and treat the data as numbers. But of course, this can be said of any field where there is large amount of data.
- Rajarshi Guha
It could also be considered a challenge. How do you get meaning from all that data
- Deepak Singh
But that's the point - just playing with the numbers doesn't necessarily get you to meaning (though it might). The biological context is vital - in absence of that, what is the value of any conclusions?
- Rajarshi Guha
Rajarshi, not disagreeing at all. But to be able to reach those conclusions you need to learn how to manage that data (in a meaning biological context), which in itself is a challenge
- Deepak Singh
from IM
and the response http://mndoci.com/2009... ... well not exactly a response
- Deepak Singh
Then there's the "Chris Anderson" school, which says that we just store the numbers, release the robots and science will emerge :-)
- Neil Saunders
I wonder if the robots know what they're looking at?
- Deepak Singh
So was Carl Linnaeus a stamp collector doing data-driven science or a "real" biologist?
- Duncan Hull
Duncan, both :), but you can think of his stamp collection as a way of managing his data. Those days you could wear both hats
- Deepak Singh
I would be happier if this post targeted a certain, perhaps quite large, class of bioinformaticians, rather than bioinformatics. My interest in becoming a computational biologist has always been driven by my fascination with theoretical biology. My leisure reading is dominated by popular expositions of biology. I read textbooks such as _Evolution_, _Ecology_, and _Brock Biology of...
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- Ruchira S. Datta
A number of comments in this thread do not reflect what was written in my article. I would encourage people to ask me at my blog site if you have concerns or are confused. I did not write "data organisation is a waste of time/money" and I *certainly* did not "tar all bioinformaticians". (I do not "tar" people; implying that I did offends me.) Ruchira: I would encourage you to re-read the article, you have it the wrong way around on several points. Best wishes to everyone!
- Grant Jacobs
Grant, I'm very sorry to have offended you.
- Ruchira S. Datta
got the advice from my wife that before sleep I should relax w/ other types of literature than programming/biology & w/o backlighted screens
Schadenfreude, Khader Shameer, Piaw Na and 5 other people liked this
Reading anything right before going to bed is bad. Give yourself at least 30 minutes to unwind: lie on the sofa, watch mindless TV - anything that requires no brain!
- Neil Saunders
I read Newspaper before sleeping and sometimes those editorials are good for sleep. :)
- ashish
sudoku...
- Andrew Su
thx guys, were staying up late in the last couple of days due to thinking on coding problems hard instead of sleeping and realized that the iPhones next to my bed are not helping me, probably will move them to another room.
- Attila Csordas
Watching TV is a bad way to go to sleep. Reading books is great.
- Piaw Na
My 'going to sleep' material is usually science fiction or fantasy.
- Michael R. Bernstein
For unwinding I find that if you include a glass or two of red wine, - all of the above works :-)
- Nils Reinton
s/red wine/vodka
- Bill Hooker
Reading books: history of Science, SF, art, comics
- Pierre Lindenbaum
Psychology books or... FriendFeed ;)
- Pawel Szczesny
a good novel is my favorite way to relax before sleep
- Mike Chelen
another problem: I'm getting a Kindle tomorrow, can I use it in the bed to read fiction, comics, art... all the light things that makes us easy more or less?
- Attila Csordas
Not comics. Fiction, absolutely
- Deepak Singh
No art or comics, just fiction and non fiction.
- Piaw Na
Can you read the H+ magazine on your kindle ? Is it color ? Let me know if you can because I need to find a good way to read this and other pdfs.
- Nils Reinton
I could give you a list of selected publications that make me fall asleep whenever I try to read them ;-)
- Lars Juhl Jensen
LOL @Lars!
- Bill Hooker
Amazon.com Help: Source Code Notice - http://www.amazon.com/gp...
"Amazon is pleased to make available to you for download an archive file of the machine readable source code ("Source Code") corresponding to modified software packages used in the Kindle device. By downloading the Source Code, you agree to the following:"
- Attila Csordas
from Bookmarklet
A Twitter Founder Turns to Electronic Payments - Bits Blog - NYTimes.com - http://bits.blogs.nytimes.com/2009...
"Square could be useful for people who run small businesses, like food carts or booths at art festivals and farmers’ markets, who would not otherwise be able to accept credit cards. Theoretically, it could even be a way for individuals to pay one another without exchanging cash or checks."
- Attila Csordas
from Bookmarklet
App Store Is a Game Changer for Apple and Cellphone Industry - NYTimes.com - http://www.nytimes.com/2009...
"“It’s still the Wild West, but the stakes are higher,” Mr. Decrem says. Tapulous has begun working with record labels and musicians to introduce paid special editions of Tap Tap Revenge featuring big-name artists. “Simply selling applications is ultimately not a scalable model,” he says."
- Attila Csordas
from Bookmarklet
Ten years of 22 - Wellcome Trust Sanger Institute - http://www.sanger.ac.uk/about...
Khader Shameer liked this
"First sequence of a human chromosome reaches ten years old"
- Attila Csordas
from Bookmarklet
I've lost a lot of telomeres since then -sigh-
- Mark A Jensen
Square Credit Payment System Could be the End of Cash - PC World Business Center - http://www.pcworld.com/busines...
Jorko Jorkov and Rajarshi Guha liked this
"he credit card data read from the magnetic stripe is not stored on the iPhone at any point. The magnetic data is converted to audio and input through the headphone jack, where it is encrypted and transmitted to Square for processing"
- Attila Csordas
from Bookmarklet
Except for the minor point that most places in the first world don't use the magnetic strip any more because it's inherently unsecure :-) That said I heard that phones would be shipping with RFID readers in 2010 recently which solves the same problem potentially.
- Cameron Neylon
great
- Jorko Jorkov
Google Closure: A New Way of Developing in JavaScript - InsideRIA - http://www.insideria.com/2009...
"The compiler is the Closure's ace in the hole and, as Google says, converts JavaScript into better JavaScript (much better!) and it's available in three flavors: an online gui application, a Java command line tool (the best choice in my opinion) and a web API service."
- Attila Csordas
from Bookmarklet
Precompetitive preclinical ADME/Tox data: set it free on the web to facilitate ..... (DOI: 10.1039/b917760b) - http://www.rsc.org/deliver...
Jean-Claude Bradley and Egon Willighagen liked this
"Web-based technologies coupled with a drive for improved communication between scientists have resulted in the proliferation of scientific opinion, data and knowledge at an ever-increasing rate. The increasing array of chemistry-related computer-based resources now available provides chemists with a direct path to the discovery of information, once previously accessed via library services and limited to commercial and costly resources. We propose that preclinical absorption, distribution, metabolism, excretion and toxicity data as well as pharmacokinetic properties from studies published in the literature (which use animal or human tissues in vitro or from in vivo studies) are precompetitive in nature and should be freely available on the web. This could be made possible by curating the literature and patents, data donations from pharmaceutical companies and by expanding the currently freely available ChemSpider database of over 21 million molecules with physicochemical properties"
- Attila Csordas
from Bookmarklet
I'm reading Coders @ Work by @peterseibel on the iPhone for a while now&can wholeheartedly recommend to rookie coders to learn from it
how are you reading it? Did you purchase an e-book?
- Frank
sure, you can purchase it
- Attila Csordas
Your Next Body Is Growing In a Lab Right Now - Dr. Anthony Atala - Gizmodo - http://gizmodo.com/5402485...
Ruchira S. Datta and Bill Hooker liked this
"We are currently working to engineer 22 different tissues and organs in the laboratory, including blood vessels, heart valves, bone, muscle, kidneys livers."
- Attila Csordas
from Bookmarklet
Recommendation against Python? - Unladen Swallow | Google Groups - http://groups.google.com/group...
"Thomas, Jeffrey, or Collin, I'm told that Google employees are being discouraged from using Python for new projects, which seems silly given how much Python code and Python support comes out of Google. I've hunted for more information but haven't found any. Do you know any details, or is this just a rumor? Thanks -- K"
- Attila Csordas
from Bookmarklet
PLoS Computational Biology: Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans - http://www.ploscompbiol.org/article...
"We have generated and made publicly available two very large networks of molecular interactions: 49,493 mouse-specific and 52,518 human-specific interactions. These networks were generated through automated analysis of 368,331 full-text research articles and 8,039,972 article abstracts from the PubMed database, using the GeneWays system."
- Attila Csordas
from Bookmarklet
authors are not humble: "We described and made publicly available the largest existing set of text-mined statements; we also presented its application to an important biological problem"
- Attila Csordas
Networking in VIVO, Online networking, Cross-disciplinary collaboration, News, Naturejobs - http://www.nature.com/naturej...
Cameron Neylon and Mary Canady liked this
more details on where the big $12.2-million grant goes to:"The site's algorithm searches for scientific topics, and VIVO yields detailed 'hits' broken down into the most relevant subcategories — such as researchers, activities, events, organizations, publications or subtopics related to the term. "If you search for people, you'll just get people," says Conlon"
- Attila Csordas
from Bookmarklet
JustHost & support: email answers w/in an hour usually but now waiting > as I have more serious Rails questions, switch to vim, sqlite3 no
Are you trying to host rails apps?
- Deepak Singh
rails is enabled on their server and so I try using it
- Attila Csordas
... Attila ah. Cause if that's all you're doing there might be better options
- Deepak Singh
from IM
let me know those options, I'm just an E1 embryo concerning Rails, started to hack with it yesterday :)
- Attila Csordas
you should definitely take a look at Heroku, http://heroku.com. See Rich Apodaca's blog as well http://depth-first.com
- Deepak Singh
from IM
+1 To what Deepak said. It's free too.
- Michael Barton
Deepak, thx for the tips, 1st heard of heroku yesterday, well, I have other plans with my domain/host too than learning RoR
- Attila Csordas
by all means keep both, but for app deployment, Heroku should definitely be in the equation.
- Deepak Singh
from IM
NPG shut down Nature Reports Stem Cells and blog "the Niche". Not sustainable business-model for publisher? Analytical professional content can not be for free? So sad that the excellent idea died. http://blogs.nature.com/reports...
Mr. Gunn, Slavomira Vladimirova, Jim Till and Nakao M. liked this
Nature really gone bad! I'm pissed off. Instead of acquiring tons of small useless journals they should realize the real thing - online community and its impact. It was under-under-underestimated.
- Alexey
It would be very interesting to find out what criteria were used by the NPG to evaluate "Nature Reports Stem Cells" and "the Niche". Not enough visitors? If so, how many visitors would be enough?
- Jim Till
You can make a comment at The Niche blog if you have any questions for the editors. (Go to link above).
- Maxine
I did make a comment at "the Niche". The comment has been posted, but, so far, no response.
- Jim Till
Monya Baker and Natalie DeWitt commented, in their final post to "the Niche", that they "are sad". So, I suspect that the decision was a business one. Other blogs will need to fill the gap left by the closing down of this high-quality contribution to the stem cell field.
- Jim Till
Here is a link to another frindfeed thread about this (http://ff.im/ajDua). As I mentioned there I think this was an interesting experiment in online community building. It had the things I though were important to stimulate user participation but users were not really participating. I wish they had a bit more detailed explanation about this closing down. Particularly about the numbers of users reading/participating on the site over time.
- Pedro Beltrao
commenting section under the final Niche post is updated http://blogs.nature.com/reports... @Jim - I'm sure that decision was a business one. I suspect based on budget NPG decide to cut off something. Of course it was freely available online resource - it doesn't make money. @Pedro it was great experiment which actually reach the...
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- Alexey
for a sec I was thinking about the option that a community (like us) could continue&maintain NRSC & the Niche in a freely rebranded way...here's a post I made for the Niche back in 2007 http://blogs.nature.com/reports...
- Attila Csordas
It was great Attila! Other "members of community" also participated in making of Niche - http://blogs.nature.com/reports... or NRSC - http://www.nature.com/stemcel... Professors and freelancers wrote for NRSC, but not only NPG journalists. So it was made by community and for community finally.
- Alexey
I wrote the necrology - http://hematopoiesis.info/2009...
- Alexey
HI Everyone, It would be really amazing to see the community pick this up. You might be able to do this through Nature Network. I can make some introductions for you if there's interest. (Though I think you likely know the relevant players already). Thanks so much for your enthusiasm. Monya
- Monya Baker
If one searches, using the key words "stem cell", for all of the Forums currently using Nature Network, 13 Forums match these key words. None of these Forums appears to be very active. See: http://network.nature.com/forums... For example, the "cancer stem cells (CSC) forum" currently has 25 members (one of whom is Alexey), but 0 topics and 0 replies: http://network.nature.com/groups...
- Jim Till
Jim, I gave up discussions on NN about 2 years ago, because it was zero interest to the topic and all discussions were dead. I don't know maybe something changed now, but i'm doubt about it. I think NRSC+Niche was the best model for unite community and discuss online. Even so, Niche commenting was not as active as me and editors wanted.
- Alexey
I too am sad the shut down The Niche. This just shows the downsides to letting business interests host the discussions. It would cost me absolutely nothing to host a blog and stem cell news discussion forum at my web host, and I could leave it running indefinitely because I don't need to answer to anyone in terms of return on investment. If the community were to run it, we'd be more free to innovate and try new things, getting away from Nature's static and (to me) somewhat unsightly look-and-feel.
- Mr. Gunn
@Mr Gunn sounds like a plan! ;) To be fair it does take a lot of work over and above the initial setup (and cheap webhosting) to get a contributing community going and somebody has to bear the time / money cost, right? There are lots of examples of sites started by people in their spare time and guiding it into something successful and sustainable - and an equal number where the tumbleweed has taken over.
- Euan
And just so that people don't think Euan is being a homer, I was about the write much the same.
- Deepak Singh
Google Should Make Apple Beg For Maps Navigation - http://www.techcrunch.com/2009...
"Navigation apps are a key category for mobile phones, and the iPhone is for once at a disadvantage here. Even the paid navigation apps in the iTunes store can’t compete because Google’s new navigation app is an extension (albeit a customized one) of its search engine. When a navigation app becomes an interface to Google’s massive search engine, it begins to deliver things that GPS app developers like Garmin and TomTom will never be able to build (search along a route, natural language search). Oh yeah, and did I mention it is free?"
- Attila Csordas
from Bookmarklet
A co-worker mentioned to me yesterday that a colleague of his is thinking about starting an online journal club type website for scientists. The idea seems to be discussions about papers, data sets, and other web-publishable materials, from any source, in a central location. It would also have discussions about scientific culture, which made me...
suelibrarian, Bruce Lewis, Holly Rae, FFer and 13 other people liked this
It would be a place where people (students, junior faculty, etc) could learn the ropes of academia and science without the pain and misery that traditionally is required. The differences I can see from existing services is the focus on journal club-style discussions and maybe a low barrier to entry
- Shirley Wu
from twhirl
But obviously, whatever he ends up pursuing should learn from the trials and tribulations of the many related services out there (including services like FF, which is also discussion-oriented)
- Shirley Wu
from twhirl
It's easy to immediately discount any proposal that sounds like yet another facebook for scientists, but there are still some interesting and potentially good ideas out there. Unfortunately, people who aren't as familiar with the existence of these tools always think of facebook as the ideal and as a brand new idea if applied to the scientist community. Hopefully I convinced my co-worker otherwise, while still encouraging the more innovative aspects of the concept. <end rant>
- Shirley Wu
from twhirl
Thanks for doing that.
- Mr. Gunn
AcaWiki is built around a very similar concept, and John Wilbanks makes an argument for bringing journal clubs online (cf. http://ff.im/airoV ).
- Daniel Mietchen
Shirley, Besides AcaWiki (great place to have these discussions, but I'm biased! http://acawiki.org/ ) your colleague also might be interested in GradTurkey, a journal-club discussion wiki originally aimed at grad students: http://gradturkey.fastcoder.net/
- Jodi Schneider
can discussion on AcaWiki be linkable and embeddable for public like you can do on FF? If not, so why don't do journal club on FF? Can't get it
- Alexey
I tried a site like this a few years ago. ResearchFire, or something like that? Never heard of it again.
- Neil Saunders
my comments on the topic in 08/07 http://pimm.wordpress.com/2007...
- Attila Csordas
Knol has many journal features built-in. Here is an example of a successful research journal on H1N1: http://knol.google.com/k...
- Bill Strathearn
John Wilbanks mentioned doing journal clubs online in his talk here recently: http://bit.ly/3jxnxr
- Walter Jessen
this topic came up during a discussion today with Mike Eisen of PLoS, re: why commenting hasn't really taken off - his thought is that people are more likely to comment if there's a central place to do it rather than individually at each journal website for each paper (how many of us access papers directly through journal websites except through PubMed anyway?). The whole time I was...
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- Shirley Wu
from twhirl
can somebody point to the platform for journal club online better then blog post? It's combine everything - presentation (ppt embedded from SlideShare or Gdocs, video embedded from YouTube/Vimeo...) presenter's opinion, discussion section under the post, embedded comments from FF, ranking of the presentation and number of views. Importantly you don't need to register or get account for commenting, it's public and linkable, moderatable . Whole world can participate. What can be better?
- Alexey
The final issue of Nature Reports Stem Cells http://www.nature.com/stemcel... they're shutting down,sadly
It was an interesting experiment. I though it had everything I would suggest to build a topic portal. It has editorial content that does not require user participation and then tools to let users participate if they want to. I guess this tells you that even if you always have fresh content and user participation tools that this is not enough to create a web community.
- Pedro Beltrao
I wonder if they got any lessons from it about how to do it better.
- Pedro Beltrao
It would be a very interesting post mortem
- Deepak Singh
it was a top-down effort and building a community is harder that way
- Attila Csordas
See also another FF thread at: http://ff.im/akFhF
- Jim Till
A New Web Tool to Take Control of Your Health - NYTimes.com - http://www.nytimes.com/glogin...
"Although success is far from certain, Keas has some big partners, including Google Health and Microsoft HealthVault. Health technology experts say Keas is at the forefront of the effort to combine advanced Web and database technologies so it can personalize health education. The promise, they say, is a big step forward for online health tools, and could help accelerate their adoption — much as the spreadsheet program helped kick-start the personal computer industry back in the early 1980s."
- Attila Csordas
from Bookmarklet
Fwd: Facebook for scientists gets millions in funding - http://www.sfgate.com/cgi-bin... (via http://friendfeed.com/habib...) Congratulations to Cornell/Florida/Vivo on their NCRR grant: "The University of Florida, Cornell University and a handful of other schools have been awarded $12.2...
Matthew Todd, Daniel Mietchen, Paul Bacchus and 17 other people liked this
Here's a link to UF's coverage of the event: http://news.ufl.edu/2009... -- I'm curious, though about this: "The new program will draw information about scientists from official, verifiable sources and make it available using a type of technology called the Semantic Web. For example, information about researchers’ positions will come from their employers and a listing of...
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- Mickey Schafer
How is this different from Biomed Experts, SciLink, etc? After seeing the failure of a dozen of these sites, I'm skeptical of the premise that there's real demand for them. You can build all the semantic infrastructure you want, but if people aren't going to use it, then it's a waste.
- Chris Miller
Kind of what I was thinking, too, Chris. But the UF blurb does not address these concerns, so hard to know at this point. Maybe I'll send a message to Sarah Gonzalez tomorrow (one of the UF ref librarians who jump-started the idea) and see if she'll fill me in.
- Mickey Schafer
It really hurts to see money be wasted like this on a platform that doesn't really address the issues plaguing these types of sites that already exist. I think someone needs to be given 12 million to figure out how to get scientists to actually use the technology! (Or code tools we'd like to use ;) )
- Brian Krueger - LabSpaces
Brian: what are the differences between this system under development and tools that might be considered ideal?
- Mike Chelen
Mickey: scientists may be more likely to get involved for those reasons if they result in an effective operation. it is exciting to hear import and export of standard formats being given a priority, yet it may be longer before anyone sees if the process is functional
- Mike Chelen
Chris: anytime someone mentions "facebook for ____ " it seems a little vague and hard to understand what might differentiate the service :D
- Mike Chelen
Reading the press release, it doesn't sound like this platform is going to be any different from biomedexperts. I'm not sure there is an "ideal" system. It's going to be hard to offer every discipline the proper tools and content that will drive users and spawn collaboration. Having worked on my own site for the last 3 years, I've heard many scientists say the last thing they want to do...
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- Brian Krueger - LabSpaces
The question that has to be answered is what is the compelling reason for scientists to trust the people they encounter on "facebook for scientists". Non science social networking is low risk...
- Richard Badge
from Nambu
"The goal of the program is national networking of all scientists," said Michael Conlon, interim director of biomedical informatics for the University of Florida, in a statement. "Scientists have problems finding each other. We often find that researchers have pretty good networks with students or with scientists at institutions where they received their degree or worked before. But...
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- Attila Csordas
Previous discussion here: http://friendfeed.com/cameron...
- Mr. Gunn
Oh, and here: http://synthesis.williamgunn.org/2009...
- Mr. Gunn
I have the same response to hearing this that I imagine many of you would reading a grant proposal that proposes to do an experiment that others have already done and which didn't work, and the results of which aren't cited in the new proposal. They need to address how they're going to work in the face of all these past failures. If their branding strategy is any indication, I'm not sure they're aware of the past failures.
- Mr. Gunn
Mr Gunn nailed it. Where is the strategy for succeeding where so many have failed?
- Bill Hooker
Mr Gunn +3 saving role against hype.
- Paul J. Davis
I would like to point out that the Facebook for Science line is journalists trying to market this to the public rather than the investigators trying to address this groups concerns. I think that phrasing needs to be taken with a grain of salt. That doesn't mean the other criticisms aren't legitimate. I just think it is important to evaluate the project on its own merits rather than public mass market branding of it.
- Michael Habib
One point on how it is different from some other projects. It is NIH funded. I am not aware of any other solutions with such a mandate from the NIH. Second, it is a huge amount of money.to devote to the problem. Neither of these differences directly addresses the concerns expressed, but they are both factors that give this project an edge in potentially addressing the issues.
- Michael Habib
"The University of Florida, Cornell University and a handful of other schools" any people here from those schools funded or know the people funded and can invite them? Would love to hear their angle
- Attila Csordas
I'll be doing a post doc at UF. I think I'll contact the head there and see if they need any help :)
- Brian Krueger - LabSpaces
I am at UF. I have met Sarah G. (one of the initiating reference libs) while doing a guest lecture in her class. But I don't know the other people. We could just forward this discussion to one of the contacts usually listed.
- Mickey Schafer
Michael Habib, I agree with your observation that "facebook for scientists" is journalist-speak. And in terms of explaining things to the UF community, it is a good analogy as my students constantly and consistently categorize social networks as either twitter or facebook.
- Mickey Schafer
I forwarded it to to Mike Conlon at UF. He said he'd take a look at this discussion and also for more information said we should read the RFA http://grants.nih.gov/grants.... The RFA says that it wants the platform to be a federated network distributed by partner institutions, which is novel in the SNfS field. It'll be interesting to see what they come up with.
- Brian Krueger - LabSpaces
Thanks, Brian (or really, should I use some southern-ism, like "Thaaank you, sweetie" which is actually what happens here, especially at places like Waffle House?).
- Mickey Schafer
The research objectives section makes for a quick and interesting read -- love the "background" info! http://grants.nih.gov/grants...
- Mickey Schafer
I think that background just shows how little actual background research was done before proposing this RFA :P
- Brian Krueger - LabSpaces
I wonder if they'll talk to OWW, Epernicus, SciLink, Laboratree, and the dozen other SNfS services out there to import or otherwise leverage all the data that's already been contributed by scientists. I can see it being useful as an aggregator and motivating standardization and data exchange, but would hate to just see it reinvent the square wheel
- Shirley Wu
from twhirl
We have a few author profiles in Scopus as well :)
- Michael Habib
Technology Review: Massive Gene Database Planned in California - http://www.technologyreview.com/read_ar...
Khader Shameer, Mike Chelen, Brian Krueger - LabSpaces and 'Mummi' Thorisson liked this
"The effort will make use of existing saliva samples taken from California patients, whose average age is 65. Their DNA will be analyzed for 700,000 genetic variations called single-nucleotide polymorphisms, or SNPs, using array analysis technology from Affymetrix. Through the NIH, the resulting information will be available to other researchers, along with a trove of patient data including patients' Kaiser Permanente electronic health records, information about the air and water quality in their neighborhoods, and surveys about their lifestyles."
- Attila Csordas
from Bookmarklet
‘Known Software Bug’ Disrupts Brain-Tumor Zapping | Threat Level | Wired.com - http://www.wired.com/threatl...
"But the bug is another reminder that increasingly smart medical devices are susceptible to the same kind of programming errors that have long afflicted less critical applications."
- Attila Csordas
from Bookmarklet
Stitching science together : Article : Nature - http://www.nature.com/nature...
Khader Shameer, Kubke, Ricardo Almeida and 4 other people liked this
"Solving the current problems in science communication requires the intervention of strong companies such as Google." reading Cameron's piece on Wave in Nature & thinking while the science-focused Google Research Datasets was shut down the general purpose Wave might suffice for science
- Attila Csordas
from Bookmarklet
The article needs more specifics and less gushing praise of Google :-)
- Eric Jain
Agree actually. The lack of available space made it really hard to detail the caveats or go more into specifics. 900 words is a tough space to write for
- Cameron Neylon
from twhirl
I think it is a great piece for Nature's readers, most of whom are scientists who have not even dipped any toe into "social web" or "web 2.0" and who only have dimly heard of Google Wave (probably).
- Maxine
not sure about the timing of the piece: scientists hearing for the 1st time of Wave because of this would like to try it out at once and then realizing they can't (hard to get invites) & forget about it and momentum lost so by the time Wave is free for everybody (when?) and assuming it really works as a good tool for scientists a reminder is needed in Nature :)
- Attila Csordas
Wires Inserted Into Human Brain Reveal Speech Surprise - http://www.wired.com/wiredsc...
by @9brandon
- Attila Csordas
doing/interpreting Functional Annotation Clustering w/ the DAVID tool http://david.abcc.ncifcrf.gov
Claudia Koltzenburg liked this
How do you like DAVID?
- Ruchira S. Datta
quite well, haven't find yet the pathway visualizer
- Attila Csordas
Massively collaborative mathematics : Article : Nature - http://www.nature.com/nature...
"For the first time one can see on full display a complete account of how a serious mathematical result was discovered. It shows vividly how ideas grow, change, improve and are discarded, and how advances in understanding may come not in a single giant leap, but through the aggregation and refinement of many smaller insights."
- Attila Csordas
from Bookmarklet
Could we have a list of google wave names somewhere so that I can figure out what Life-Scientists are on there?
Tom Tullius, Jeannette Høvring, Daniel Jurczak and 21 other people liked this
toddwharris@googlewave.com
- Todd Harris
just added you to Life Scientists wave
- Cameron Neylon
from twhirl
A Google Wave might be appropriate for tracking such a group.
- Shiran Pasternak
shiranpasternak at the same domain.
- Shiran Pasternak
search "with:public research" and you will find the "Research collaborations in Wave" wave endre.sebestyen@googlewave.com
- Endre Sebestyen
yann.abraham@googlewave.com
- Yann Abraham
Searching Google Wave with "tag:the-life-scientists" will get you to "Research collaborations in Wave", a good starting point for life scientists.
- Martin Fenner
b.brembs@googlewave.com
- Björn Brembs
mndoci
- Deepak Singh
I also missed out on the invites .. if anyone knows someone .. :)
- Pedro Beltrao
I'm firstname.lastname
- Ruchira S. Datta
firstname.lastname here too
- Andrew Clegg
I don't get how you search in public waves. I've tried searching for tag:the-life-scientists and it gets no hits -- I think it's just searching my own waves
- Andrew Clegg
there was a thread by Kol about wave usernames couldn't find the link
- ffcode
Aha -- with:public . They really should include a button for that
- Andrew Clegg
anna.k.croft
- Anna Croft
Lots here: http://ff.im/91NZC
- Kol Tregaskes
thanks Kol
- ffcode
attilacsordas
- Attila Csordas
I never got invited to the party :(
- Lars Juhl Jensen
AndrewJamesPerry
- Andrew Perry
avijitguharoy@googlewave.com
- A Roy
allyson.lurena@googlewave.com
- Allyson Lister
@Endre: You can link to waves, eg: https://wave.google.com/wave...
- Nick Lothian
mbembee@googlewave.com
- embee
000.cacarr@googlewave.com
- Christopher A Carr
cassjohnston
- Cass Johnston
plindenbaum
- Pierre Lindenbaum
firstname.lastname också
- Egon Willighagen
diegomorelli76@googlevave.com
- diego morelli
abhishek.twr@googlevave.com
- Abhishek Tiwari
Would like to be added to life scientists wave, please! david.rothman@googlewave.com
- David Rothman (☤)
@David: done
- Pierre Lindenbaum
Many thanks, Pierre. :)
- David Rothman (☤)
churchsg
- Sally Church
life scientists wave: me too, thx
- Attila Csordas
Count me in: matt.j.wood
- Matt Wood
jeanclaude.bradley at googlewave dot com
- Jean-Claude Bradley
chrisamiller@googlewave.com
- Chris Miller
inspiring2designllc@googlewave.com
- Justin H. Johnson
somebody please add me too attilacsordasat...
- Attila Csordas
Attila: can't seem to find attilacsordas@googlewave.com.
- Shiran Pasternak
it does exist I can tell ya :)
- Attila Csordas
@Attila: tried a different way... yer in.
- Shiran Pasternak
An undergraduate student in our lab, Caleb, just got his wave invite. I told him to look at this thread for possible people to connect with.
- Steve Koch
+1 skhadar@googlewave.com
- Khader Shameer
got it, thanks
- Attila Csordas
murvine - thanks!
- Christopher Murvine
Afternoon all. I've written my first robot, which hopefully will embed an interactive mass spectrum into a blip whenever a UniProt name is encountered in the text, and corresponding mass spec data is found for this protein. I say "hopefully", as I've not been able to test it for real, as, alas, I have no account. When are the next batches released? If it's not for ages, does anyone fancy testing it anyway?
- Neil Swainston
Am now Waving as ben.blackburne.
- Ben Blackburne
Now waving as lars.juhl.jensen
- Lars Juhl Jensen
waving too: sciphu@googlewave.com
- Nils Reinton
waving as fgibson
- Frank
aemonten@googlewave.com. How can I get started with the life scientists wave?
- Alejandro Montenegro
my wave ID: macmanes@googlewave.com
- Matthew MacManes
dan.swan@googlewave.com searching is sloooooow trying to find the life scientists wave right now!
- Daniel Swan
chris.lasher@googlewave.com
- Chris Lasher
sjcockell@googlewave.com
- Simon Cockell
jwhabig@googlewave.com - Jeff Habig
- Jeff Habig
comprendia[at]googlewave[dot]com Mary Canady
- Mary Canady
rebeldad@googlewave.com Brian Reid (PR guy for life science types ... I promise to behave)
- Brian Reid
bronxman
- Jack H. Pincus
I'm trying to get a Solexa/Illumina Sequencing Wave going. Search "with:public Illumina" or add me macmanes@googlewave.com
- Matthew MacManes
waving as georgkam
- george
For some reason, I'm stevekoch3 but glad to finally have a preview account!
- Steve Koch
And I found the research collaborations wave by the following search: "with:public tag:the-life-scientists"
- Steve Koch
mine is pedrobeltrao@googlewave.com (thanks to Mr Gunn)
- Pedro Beltrao
In case there is still someone with spare invitations: piotr.byzia at gmail.com
- Piotr Byzia
tom.sante@googlewave.com
- Tom
Im steelgraham7@googlewave.com
- Graham Steel
sametstalker@gmail.com
- Samet Güngören
michael.kuhn
- Michael Kuhn
Requesting for life scientists wave, abhishek.twr@googlevave.com thanks in advance
- Abhishek Tiwari
The usual, neilfws.
- Neil Saunders
now that I am finally on board: danjurczak@googlewave.com
- Daniel Jurczak
i'm mightyfib(at)gogglewave(dot)com Your most welcome to add me...:O)
- Jeannette Høvring
mine is dave.lunt
- Dave Lunt
michael.chelen@googlewave.com - seems to use the google contacts system like gmail
- Mike Chelen
pengwen.not.penguin@googlewave.com
- Parvez Halim
mstalnos@googlewave.com
- Tresterling
I'm on (thanks to Steve Koch!): tom.tullius@googlewave.com
- Tom Tullius
Welcome to the world, Charlotte Nola Gunn! 7#, 11 oz on Twitpic - http://twitpic.com/l0u3y
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Alexey, Khader Shameer, Abhishek Tiwari and 4 other people liked this
Live long and prosper.
- Bill Hooker
Nola as New Orleans, Louisiana? :)
- Attila Csordas
The 2009 Nobel Prize in Physiology or Medicine has been awarded for the discovery "how chromosomes are protected by telomeres and the enzyme telomerase" published in 1982. It was not mentioned that the theory of telomere shortening was published a decade before by Olovnikov http://www.youtube.com/watch...
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Olovnikov1973.pdf 632 KB
Ricardo Almeida, Nils Reinton and Alexey liked this
interesting & who is the person behind 'reflection'? Maybe that person knows Olovnikov himself. http://en.wikipedia.org/wiki...
- Attila Csordas
Is not it strange, that a person who is well-known as the author of the telomere theory is not even mentioned? He was nominated for the Nobel prize as well, so he could have been at least acknowledged. It means that doing theory is not rewarding?
- reflection
Agreed, this is strange. But it is typical of the Nobel process, which wants to make superstars and doesn't have much to do with actual science, and so it ignores the complex connections that actually drive discovery. Look at the Chemistry prize for "discovery of GFP" that went to three people OTHER than the actual discoverer.
- Bill Hooker
IMHO, Nobels should be granted for sustained and conclusive work in a field, so personally, I think they got it right... http://www.ncbi.nlm.nih.gov/sites...]
- Andrew Su
Interesting that the wikipedia article was started today. Unless that was one of you...
- Jason Winget
Bill, but I associate GFP with those other three people who really brought that to fruition. That's fine by me. In other words I agree with Andrew
- Deepak Singh
Actually I'm not even right about who *discovered* GFP... Shimomura found the protein, 20 years later Prasher cloned the gene. I still think Prasher got ripped off though, since it was only a couple of years after he made the clone available that it started to be widely used as a tag, whereas the protein was known for 20 years before that and no one could do anything with it. Not that...
more...
- Bill Hooker
I am thinking about the 1962 Nobel prize for the discovery of the molecular structure of DNA. The prize was awarded to the people who did theory. But that seems to be the only exception. Other than that, all prizes were awarded to the experimentalists.
- reflection
Also remember that it took till 1962 to award the prize because otherwise there would have been four. The issues over that were only resolved when Rosalind Franklin died because the prize is never given posthomously. In the case of DNA you might argue that Wilkins was the experimentalist of course
- Cameron Neylon
Interesting... from the book of Stephen S. Hall: "Cell paper confirmed the existence of telomerase and opened the door to one of the most productive areas of research in modern cell biology. It also confirmed Olovnikov's original hypotheses, but his train stil didn't arrive at the station, because Blackburn and Greider failed to mention his earlier theoretical work in their paper. "We...
more...
- reflection
"typical of the Nobel process, which wants to make superstars and doesn't have much to do with actual science".....hmmm......interesting perspective. Anyway, while discussing who was left out because of the three rule, S. Moncada is a recent one (NO).
- Maxine
Maxine, my take on this is, the people who got it usually deserved it, and we should begrudge them their efforts. What we need to make sure is that deserving folks don't get left out. The three rule is tough one especially when big science comes into play.
- Deepak Singh
Just as well science isn't literature or "peace" (aka politics!), where far more subjective elements come into play and the emotional reactions to the prizewinners seem to be far more extreme.
- Maxine
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