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Attila Csordas › Comments
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...
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...
Paul Bacchus, Danica Radovanovic, Rafael Sidi and 15 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?
Jeannette Høvring, Daniel Jurczak, Jason Winget and 20 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 or @gmail.com can't see any way to check :D
- Mike Chelen
is there any good way to import contacts? it seems to work through the google contacts system like gmail
- Mike Chelen
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...
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- 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
A conversation between author Cormac McCarthy and the Coen Brothers, about the new movie No Country for Old Men - TIME - http://www.time.com/time...
"J.C. But you know, there's something about it--there were echoes of it in No Country for Old Men that were quite interesting for us, because it was the idea of the physical work that somebody does that helps reveal who they are and is part of the fiber of the story. Because you only saw this person in this movie making things and doing things in order to survive and to make this journey, and the fact that you were thrown back on that, as opposed to any dialogue, was interesting to us."
- Attila Csordas
from Bookmarklet
Access : Origins and functional impact of copy number variation in the human genome : Nature - http://www.nature.com/nature...
Chris Miller, Greg Tyrelle and Jan Aerts liked this
look who's in Nature :) amongst others: "Donald F. Conrad1,7, Dalila Pinto2,7, Richard Redon1,3, Lars Feuk2,4, Omer Gokcumen5, Yujun Zhang1, Jan Aerts1, T. Daniel Andrews1, Chris Barnes1, Peter Campbell1, Tomas Fitzgerald1, Min Hu1, Chun Hwa Ihm5, Kati Kristiansson1, Daniel G. MacArthur1, Jeffrey R. MacDonald2, Ifejinelo Onyiah1, Andy Wing Chun Pang2, Sam Robson1, Kathy Stirrups1, Armand Valsesia1, Klaudia Walter1, John Wei2, The Wellcome Trust Case Control Consortium, Chris Tyler-Smith1, Nigel P. Carter1, Charles Lee5, Stephen W. Scherer2,6 & Matthew E. Hurles1"
- Attila Csordas
from Bookmarklet
FT.com / Management - Roche and Genentech saga - http://www.ft.com/cms...
Greg Tyrelle and imabonehead liked this
"Mr Schwan says Roche will maintain Genentech’s policy of hiring a large number of post-doctoral students to work alongside employees; time for staff to pursue personal research projects; and encouragement for them to publish findings in leading academic journals – once they are patented by the company. After all, Avastin, the “blockbuster” cancer treatment, was first identified and cloned during the “discretionary time” allocated to Napoleone Ferrara, one of Genentech’s scientists, in 1989."
- Attila Csordas
from Bookmarklet
FT.com / Management - Roche and Genentech saga - http://www.ft.com/cms...
"If Genentech’s scientists in California feared they would lose their freedom, investors in both companies were just as concerned that the disruption would destabilise a lucrative partnership. Also anxious was Severin Schwan, who had taken over as Roche’s chief executive in Switzerland less than four months before. “The biggest question both externally and internally in July 2008 was [whether there would] be an exodus of scientists,” says Mr Schwan in an interview in Roche’s headquarters in Basel. “I’m happy to tell you the result is beyond my expectations. We lost not a single scientist in research and early development.”"
- Attila Csordas
from Bookmarklet
R gurus: am unable to install the mva package in R on Mac OS X for cluster analysis, any clue?
What error messages are you getting?
- Michael Barton
for 1: I don't find it in the package repository, it's not available w/ available.packages(), can it be Windows only?
- Attila Csordas
I'd like use the hclust function
- Attila Csordas
hclust should be in the stats package which comes bundled with R
- Michael Barton
I can't find mva either. What functions are you looking for in particular? R has many multivariate functions included by default.
- Michael Barton
Try ade4 which is pretty good - http://cran.r-project.org/web...
- Michael Barton
Aslo there are R views for multivariate analysis (http://cran.r-project.org/web...) and clustering (http://cran.r-project.org/web...)
- Michael Barton
thx, Michael, good info, I tried to reproduce this: http://statwww.epfl.ch/davison... & it said: 'using the (hierarchical) hclust function (from the mva package)'
- Attila Csordas
Try this - http://gist.github.com/203019
- Michael Barton
hey, last 1 worked, thx :) I'm learning
- Attila Csordas
Enhancing navigation in biomedical databases by co...[BMC Bioinformatics. 2009] - PubMed Result - http://www.ncbi.nlm.nih.gov/pubmed...
Mike Chelen liked this
"In our experiments, we simulate community voting by adding various levels of noise to nearly perfectly labelled instances, and show that, under such conditions, classification can be improved significantly. CONCLUSIONS: Using PepBank as a model database, we show how to build a classification-aided retrieval system that gathers training data from the community, is completely controlled by the database, scales well with concurrent change events, and can be adapted to add text classification capability to other biomedical databases."
- Attila Csordas
from Bookmarklet
YouTube - thenobelprize's Channel Live Webcast on announcing the Medicine Nobel Prize, announcement within 5 minutes time - http://www.youtube.com/thenobe...
george, Pierre Lindenbaum, Greg Tyrelle and Egon Willighagen liked this
The winners (or a subset) visits Uppsala each year... this time I am gonna take the kids, and give them some proper education :)
- Egon Willighagen
Ummm.... 11:30 CET != 11:30 CEST... so... ummm...
- Egon Willighagen
Oh... and 11:30 CET != 9:30 GMT... :( why can't people get this right ...
- Egon Willighagen
(time from the YouTube channel...)
- Egon Willighagen
& the winner of the 2009 Nobel Prize in Medicine is The Life Scientists group on FriendFeed for...
- Attila Csordas
Atilla++
- Egon Willighagen
telomeres/telomerase
- Attila Csordas
Mmm... the video is really slow... maybe I just turn on the TV...
- Egon Willighagen
curious: do we have people here working in the labs of Blackburn, Greider, Szostak? congrats to your PIs!
- Attila Csordas
@mndoci 100 slides, 30 minutes: ru serious? what's your usual rule of thumb?
What feels right
- Deepak Singh
from iPhone
I'm a teacher/A-level lecturer. I'd say that a slide every 3-5 minutes is fine. Depends on the content though. I'd rather have lots of slides with hardly any info on than few that are crammed full.
- Rich
My slides are sparse to say the least. Usually either a picture or one line of text
- Deepak Singh
from iPhone
that's how I figured: 1 slide is about 15-20 sec this way so you're ok w/ your 100 slides for 30 min
- Attila Csordas
Yep .... that's pretty much the drill. There are a few where I do slow down
- Deepak Singh
25 minutes is what it took. I was down to 92 slides by the end I think
- Deepak Singh
story: 1. X.Y. invites me to connect on LinkedIn 2.my reply: where did we meet? 3. his reply: we didn't but we share a common ancestor in the last few centuries - based on 23AndMe results on Chromosome 1 - and are both mtDNA T1a, which may be where the connection comes from. 4. I'm rethinking my LinkedIn connection policies :) (What would you do?)
Eric Heupel, Duncan Hull, Michael Habib and 7 other people liked this
He is not a professional contact. http://www.geni.com is a better choice :-)
- Pierre Lindenbaum
In the future, our social networks will be prepopulated for us at birth, saving us immense amounts of time. ;)
- Todd Harris
Yes, and there will be a chart titled 'probability-of-death=f(year)':-)
- Pierre Lindenbaum
I'd imagine that most of us share a common ancestor in the last few centuries?
- Neil Saunders
@Neil: reminded me of a paper I saw a few years ago, saying that the most recent common ancestor (MRCA) of ALL of us lived just a few thousand years ago. Along with this cool result: "Moreover, among all individuals living more than just a few thousand years earlier than the MRCA, each present-day human has exactly the same set of genealogical ancestors" http://www.ncbi.nlm.nih.gov/pubmed...
- Steve Koch
end of story, beginning another: I accepted the invitation because the person in question is a programmer w/ a strong interest in genetics & would like to go back to college to study bioinformatics & we started to build a connection around bioinformatics
- Attila Csordas
Systems Biology Graphical Notation: 'The result was 3 languages to describe molecular processes, relationships, and the flow of activity through a system. Besides being complementary, the languages are also efficient; combined, they use only about 50 symbols.' - http://ow.ly/rrRP#
Khader Shameer, Duncan Hull and Greg Tyrelle liked this
'The next step will be to get the scientific community to accept SBGN'
- Attila Csordas
from Bookmarklet
'If this really is to be the language of future biological research, maybe considering how compatible it is with fax machines isn’t so important.' I don't know what Fry expects, any kind of standardization - the simpler the better - for visualization of biological pathways is very welcome.
- Greg Tyrelle
I saw a talk about SBGN recently, it seemed really well-thought-out. And a good diagram is a lot easier to parse than a page of (probably badly written) descriptive text.
- Andrew Clegg
Byte Size Biology: will you have your own genome sequenced? - http://bytesizebio.net/index...
Andrew Perry, Alexey, laura and 5 other people liked this
Yes. I am not sure when and under what circumstances, but pretty sure I will
- Deepak Singh
Yes, as soon as possible. I doubt I'll get picked up for the PGP (no siblings etc) so it'll have to wait until I can afford it myself.
- Bill Hooker
No, as of right now.
- ashish
No. I do not trust that the information will not be used to deny me health care.
- D0r0th34
@Deepak @Bill RTFP http://is.gd/3JwSl There is a description of a hypothetical but not too far-fetched future where personal genomic sequencing is cheap and readily available. OTOH there are some other hitches....
- Iddo Friedberg
sure thing
- Attila Csordas
definitely, sooner or later.
- Endre Sebestyen
I certainly will at some stage in the not too distant future. Not quite sure when or how, but I'm pretty open to it. :)
- Ricardo Vidal
I've had a genetic error identified... does that count? I have an extra ccgg in there on some chromosome. Seems that knowing that would require sequencing.
- Nina Jansen
@Nina. We're talking whole genomes.
- Iddo Friedberg
a little twist can be introduced into the question by asking: will you sequence your own genome in the future by yourself? after all we're life scientists here & some of us are also bioDIY enthusiasts :)
- Attila Csordas
I imagine I would, once it becomes dirt-cheap and routine. I was toying with a 23andme account when their prices dropped, but then the "financial crisis" struck, taking the US/AU exchange rate with it.
- Neil Saunders
I have to say as soon as it comes within *my* budget, I will do it. If anyone lets me near a Solexa unsupervised for long enough though..
- Daniel Swan
Good post/poll combo. As for the question, I'm still on the fence on this - I guess it will depend on the details...
- Mickey Kosloff
At this point, absolutely not. Too much risk for too little benefit. If we succeed in closing all the insurance loopholes about "preexisting conditions", then yes. Certainly not until then.
- Chris Miller
sometimes I wonder what is the mean number of Googlers sitting at #googletechtalks & what is the standard deviation http://www.youtube.com/user...
Pierre Lindenbaum liked this
actually this talk was the trigger http://is.gd/3KyQk lot of ghost-Googlers perhaps but not real ones
- Attila Csordas
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