The Life Scientists

Nice going, Pawel and Neil! - Iddo Friedberg via Bookmarklet

I'd say the greatest need for Open Science is actually good scientific practise... if we can show that reproducibility is a great scientific good, Open Science is the only logical solution... - Egon Willighagen

+1 Egon. - Bill Hooker

Guess who - Abhishek Tiwari

for "Defrosting the digital library: bibliographic tools for the next generation web" - Abhishek Tiwari

I agree, but innovation does not alway = commercial success. IN biotech, the FDA is more a barrier to entry than the Patent system, IMHO. - Jim Hardy via Bookmarklet

It's an interesting study, and I'm a big fan of encouraging an intellectual commons, but it's very simplistic about the type of patents being discussed. Unsubstantiated hypothesis (that could run counter to this study): in a world without IP, there are more "ideas/inventions", but fewer R&D/capital-intensive ideas/inventions. - Benjamin Tseng

That has a private feed, Ruchira :) - Allyson Lister

I was just requested to hide the feed, so it's now private again and will remain private. - Ruchira S. Datta

"http://www.youtube.com/watch..." - Jim Hardy via Bookmarklet

Hilarious, via Paulo Nuin - Jim Hardy

source listing comes from http://www.sciencebase.com/science... and contains over 500 twitter users - Mike Chelen

html can be scraped using xpath "//div[@class='scientwist']/a[contains(@href,'twitter.com')]/@href" for example in google docs http://spreadsheets.google.com/ccc... - Mike Chelen

the twinfluence api http://twinfluence.com/about_a... returns xml files which can be concatenated together - Mike Chelen

"Via web application software, data citation standards, and statistical methods, the Dataverse Network project increases scholarly recognition and distributed control for authors, journals, archives, teachers, and others who produce or organize data; facilitates data access and analysis for researchers and students; and ensures long-term preservation whether or not the data are in the public domain." - Bill Hooker via Bookmarklet

Okay. I'll try to give a bit more info about the JRA thing once I have it. Incidentally, on association studies (QTLs too?) I ought to mention one of the projects we have registered at MIBBI for reporting QTLs and association studies: http://mibbi.org/index... - Chris via twhirl

Science seems a pretty catty place too. Just try and talk about tectonic plates before people are ready to hear it. - Todd Hoff

I was unaware that science, collectively, had defined any "best practices". And what's reblogging? Plagiarism/copying, or discussion of other posts? Anyway, we don't apply stuff from science to blogs because, well, one is science and the other is blogs :-) - Neil Saunders

Someone needs to upgrade from dial-up...... And get off their ridiculously high horse. - Wladimir Labeikovsky via Bookmarklet

And indeed given some effort they might actually rise to the standard of several of today's web-only journals, one can at least hope... - Cameron Neylon

Just got an email from them to be on the SAB for the Biology journal. Do they typically ask people without Ph.D.s (yet)? I like the concept but have concerns about legitimacy, etc... - Shirley Wu

Yeah, I agree, Chris. It'd be much better w/o need for formal paper and "rigorous peer review" as they state now. Editorial or peer review should just make sure that necessary info has been included. Wonder if SAB members can change any of these decisions before they go "live?" - Steve Koch

So, everyone now knows what bioinformatics is and they've stopped searching for it :-) - Neil Saunders

"chemoinformatician" - ca. 350 :) It looks like chemists _really_ hate computers. - Pawel Szczesny

Duh! It's obtainable via KEGG XML files - Rajarshi Guha

There's a package, KEGGgraph in Bioconductor: http://www.bioconductor.org/package... - Neil Saunders

Sarah P. Otto has a good review of the literature on "why sex": http://www.journals.uchicago.edu/doi... - Benjamin Tseng

Cover your eyes! it's porn! - Benjamin Tseng

""To a student it could appear that this is a field to be in forever," Schlaeger says, "but you could be behind the curve if you're thinking of what's great now." Stem-cell researchers will need to be as flexible as the cells they study. Asked what expertise Pfizer will be seeking for positions in its new regenerative medicine unit, Ruth McKernan, the unit's chief scientific officer, says she wants candidates whose scientific curiosity extends beyond the narrow area of their training. Intellectual agility will be more important than any particular technique, she says. "We don't know what we'll have them doing a year from hire."" - Attila Csordas via Bookmarklet

Nice one :-) - Andrew Clegg

congrats Iddo - Abhishek Tiwari

So far I've been playing with the PDB's web services, where I can basically run a blastp and get results back in html/xml. But I still need to parse each matching pair to find my residue of interest in the query sequence (based on the PDB residue number, which I need to map to the sequence), find its matching residue, figure out that residue number somehow, get the PDB file, do stuff with it, etc. Seems like there should be an easier way. - Donnie Berkholz

Thanks all for the help and suggestions. This is the first time I've used web services, so it's been a bit of a learning adventure. I think I'll be able to come up with a reasonable solution using a combination of a couple of web services and BioPython. - Donnie Berkholz

What sort of global similarities do you mean? - Michael Barton

@Ruchira please is it possible to share FLOCK? and some documentation? It sounds like something i would want to use as well for the current clustering work. thanks - george

I'm sure there are, but I don't know to what degree the Pro affects specificity. Phosphatase binding to substrate seems to be rather different to kinase binding. This looks like a nice review: http://www.ncbi.nlm.nih.gov/pubmed.... - Neil Saunders

A discussion with John Wilbanks addressing: " * In an age of digital content and communication, does the notion of the scientific ‘article’ remain relevant? Is the 300-year old approach to structuring findings – from abstract to references – still valid in the era of the multi-media research object? * How should new types of content such as video protocols and embedded datasets be peer-reviewed, and does it matter? * Will opening access to the outputs of scientific research really improve innovation? * Does more access to research data and information necessarily mean we are better informed? * When it comes to communicating research findings, what are the fundamental building blocks and what is the wallpaper?" - Hilary

See also http://ff.im/4A4qx on this. - Daniel Mietchen

"We polled the attendees before the event and found that they knew almost nothing about it, and had little interest in learning about it. We set up a friendfeed room for the group and frankly have not had much adoption." No point evangelising to the closed-minded, is there? - Neil Saunders

I think Noah's got a point. It's to some degree a generational thing. Online sharing and collaboration just makes sense to people who've grown up with the internet, and just kinda looks like a waste of time to people who are older and already established in the types of communication networks that were prevalent when they were coming up. - Mr. Gunn

From PLoS ONE; article concludes that "Medical research news should be clearly referenced and state the evidence level and limitations to inform the public of the maturity and quality of the source." Many (including myself) have been calling for this kind of disclosure for years...Astonishing that even after 3 yrs, almost 1/4 of the front page stories never passed muster in peer-review!!!!!!!!! - Noah Gray via Bookmarklet

Not surprising at all. A lot of the stories I've seen in MSM are "exclusive" access pieces. I guess that's the drawback of trying to get a story no one else has. - Brian Krueger - LabSpaces

"One thing is that knowledge is suffering over there." - Abhishek Tiwari via Bookmarklet

I think it's inaccurate to say that knowledge is "gone". More like, it's being misplaced. He's complaining about the implementation of the search interface. That can be improved; as he well knows, these systems are works in progress. With improved search tools, developed by the companies themselves or possibly by third parties, all that knowledge will be retrievable again. I'm quite... more... - Ruchira S. Datta

"The AAAS Science and Human Rights Program (SHRP) works with scientists to "advance science and serve society" through human rights. The Program carries out its mission by engaging individual scientists and scientific associations in human rights efforts; applying scientific tools and technologies to enhance human rights work; bringing human rights standards to the conduct of science; and promoting the human right to enjoy the benefits of scientific progress." - Mike Chelen via Bookmarklet

Upcoming event: July 23-24, 2009 AAAS Science and Human Rights Coalition Meeting https://secureapps.aaas.org/EventRS... - Open Science Information via IM

Not sure if this is good (will drive semantic web tech) or bad (who will get to use that tech?)... - Bill Hooker via Bookmarklet

BBN -- old skool. They pretty much invented the internet. But I don't remember them being major players in the comp. linguistics game... - Andrew Clegg

Even top federal cancer officials say the system needs to be changed. “We have a system that works over all pretty well, and is very good at ruling out bad things — we don’t fund bad research,” said Dr. Raynard S. Kington, acting director of the National Institutes of Health, which includes the cancer institute. “But given that, we also recognize that the system probably provides disincentives to funding really transformative research.” The private American Cancer Society follows a similarly cautious path. Last year, it awarded $124 million in new research grants, ... Dr. Otis W. Brawley, chief medical officer at the cancer society, said the whole cancer research effort remained too cautious. “The problem in science is that the way you get ahead is by staying within narrow parameters and doing what other people are doing,” Dr. Brawley said. “No one wants to fund wild new ideas.” - Maureen via Bookmarklet