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Jay Bhatt › Likes
Chempedia: A Social Medium for Chemical Information - http://depth-first.com/article...
Jay Bhatt liked this
BioTorrents - a file sharing resource for scientists - http://betascience.blogspot.com/2009...
Jonathan Eisen, Itachi, Mike Chelen and 3 other people liked this
MarkUs: Protein Function Annotation Server - http://luna.bioc.columbia.edu/honigla...
Jay Bhatt, Peter Miller and Jean-Claude Bradley liked this
MarkUs is a web server to assist the assessment of the biochemical function for a given protein structure. MarkUs identifies related protein structures and sequences, detects protein cavities, and calculates the surface electrostatic potentials and amino acid conservation profile. The results can be browsed by an interactive web interface that allows to integrate Gene Ontology terms, UniProt features, and the Enzyme Classification.
- Deepak Singh
gave it a try with falcipain-2 - waiting for processing to complete
- Jean-Claude Bradley
Did you go into a queue at all? Or is it just processing time?
- Deepak Singh
it says pending http://luna.bioc.columbia.edu/honigla...
- Jean-Claude Bradley
Suggest there's a queue in place. Thanks
- Deepak Singh
It is done processing (though did not send an email when done). Something strange - it identified 4 chains but falcipain-2 does not have that and it does not find an overlap with the original file from the PDB http://www.rcsb.org/pdb...
- Jean-Claude Bradley
Web Developer Preview: Caffeine: Google’s New Search Index - http://www.resourceshelf.com/2009...
Jay Bhatt and Lisa Green liked this
The few brief queries I ran did return results in noticeably less time. It will be interesting to see where this leads in the context of the public beta release of Google Wave
- Jill O'Neill
The Wonderful World of Big Science - Neatorama - http://www.neatorama.com/2009...
Berci Mesko, MD, Jay Bhatt, Graham Steel and Neil Saunders liked this
IJCAI09 Open Notebook Science talk - http://www.slideshare.net/jcbradl...
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novoseek, Khalid Mirza, Mr. Gunn and 2 other people liked this
Jean-Claude Bradley presents on The Role of Openness in Scientific Automation: a case for Open Notebook Science at the IJCAI'09 Workshop on Abductive and Inductive Knowledge Development in Pasadena, CA on July 12, 2009.
- Jean-Claude Bradley
That's a whole lot of slides :)
- Andrew Lang
well the point was to find new collaborators from a quick overview of many projects in 45 mins
- Jean-Claude Bradley
in unique author identifiers - have we talked about Refworks-Cos' http://www.authorresolver.com/?
Jay Bhatt and suelibrarian liked this
First I've heard of it -- seems to run on top of another proprietary database: "Author Resolver profile information is drawn from Scholar Universe, an editorially controlled database of more than 2.1 million profiles of full-time faculty researchers in 2,210 universities and 75 countries."
- Bill Hooker
NFAIS Event: Google, The Web, and the Future of Publishers and Librarians
http://docs.google.com/View...
Jay Bhatt and Richard Akerman liked this
Science Blogging 08 => Science Online 09 #soloconf_09 - http://wwmm.ch.cam.ac.uk/blogs...
Jay Bhatt liked this
Test essay 3: Blogs, Wikis, Microblogging & benefits/threats to ... - http://scienceblogs.com/christi...
Jay Bhatt, Steve Koch and John Dupuis liked this
A nice summary by Christina Pikas that should be helpful to brief people trying to learn about new forms of scientific communication.
- Jean-Claude Bradley
More on chemistry and the data web - http://mndoci.com/blog...
NextBio, Jay Bhatt, John Dupuis and 5 other people liked this
I still view that the glass is very much half full - so much progress in the past year alone
- Jean-Claude Bradley
and so much from people around here
- Deepak Singh
so much in the last two months even!
- Cameron Neylon
and, if we can not do it, nobody will do it ;-)
- joergkurtwegner
What do you mean by reference architectures? Reference for what? Also, it's not clear how the fierce competition plays a role in this. Why would less competition be beneficial?
- Rajarshi Guha
For example, you could develop a platform for doing something. The actual architecture and standards used can be published, your own implementation can be proprietary. Think MapReduce and BigTable. Google published enough to allow Hadoop, HBase, etc to exist, but their own implementation is proprietary. Think of a data management system you develop for the FDA. That can be one implementation of a reference architecture for data management, where different people can implement in their way (contd_
- Deepak Singh
... around a common set of architectural guidelines and data standards
- Deepak Singh
Competition around a very finite and small user community = things will remain closed and licensing protected for a while. Not from the quality standpoint
- Deepak Singh
Hmm, regarding your FDA example, one could say that a reference is already in place - the FDA guidelines. Though it probably doesn't go as low as formats/data standards etc (?) Actually, I'm not sure that FDA is a great example for this since the cost of failure (security, compliance etc) is very high - it seems that'd be a barrier for multiple implementations
- Rajarshi Guha
I am definitely talking about formats and data standards. The reason I use the FDA example is that it was part of a project I was part of and very much a reality. The FDA would have an application built for them, but others could use internally developed applications that met a certain set of minimum standards (way more common that you think, since almost all clinical databases are custom DBs built to a spec).
- Deepak Singh
Aah, interesting
- Rajarshi Guha
ETech Preview: Science Commons Wants Data to Be Free - http://radar.oreilly.com/2009...
Jean-Claude Bradley and Jay Bhatt liked this
Open Access News:- "Interview with Science Commons' John Wilbanks James Turner, ETech Preview: Science Commons Wants Data to Be Free, O'Reilly Radar, February 19, 2009. A podcast interview with John Wilbanks, with transcript.".
- Graham Steel
On Open Access:- JL One area that is clearly under attack is the traditional model of the expensive scientific journal, through mechanisms like the Public Library of Science. How successful is that movement being? JW Well, I mean I would say that it's become an adolescent? Which means it's trying to steal dad's car, and it's acting up. It's made it out of early childhood, that's for...
more...
- Graham Steel
Python course in Bioinformatics - http://news.ycombinator.com/item...
Chris Lasher, Jay Bhatt, Kevin Johnson and Thomas Brox Røst liked this
"Bioinformatics only caught on around 1999/2000. When I got into the industry there were very few people who knew their way around, especially from the programming side. I've done a lot of nano over the years (before I ever did bio), and there is a lot out there, but nano in the nanomachine sense is still a pipedream and will be for a long time (IMHO). On the funding side, the funds are there for sequences, Genome Wide Association Studies, etc. Bioinformatics is part of that effort, and critical, but not directly what the funds are for"
- Deepak Singh
So how relevant is a computational biology from 1999/2000? Haven't a lot of the tools been superceded?
- Zaki Manian
Not BLAST :D
- Deepak Singh
I think I was doing Blast as a ROCHE internship in 1999. It was miserable. Work doesn't generally involve to much genomic data. But I am really enjoying the Stanford Machine Learning lectures on Academic Earth. Plowed through a couple "episodes" on SF -Singapore flight
- Zaki Manian
Deepak, what is this Backtype entry? What is the original article, page, or conversation that it's supposed to be a comment on?
- Chris Lasher
Click on "parent" (not too obvious is it) http://news.ycombinator.com/item...
- Deepak Singh
Now that you point it out, I can see it. That's a crazy site. So minimal.
- Chris Lasher
Top 15 Twitter Acronyms | Pistachio - http://pistachioconsulting.com/top-15-...
Jay Bhatt liked this
Twitter / ScholarlyComm - http://twitter.com/Scholar...
Richard Akerman, John Dupuis and Jay Bhatt liked this
Twitter record of the Feb 19, 2009 Columbia panel on Open Science
- Jean-Claude Bradley
Chemistry, Clouds, Collaboration (Part 1) at So much to do, so ... - http://blog.rguha.net/?p=120
John Dupuis and Jay Bhatt liked this
Check out this Science 2.0 Webicon freshly made this morning: http://obamiconme.pastemagazine.com/entries... Make your own here http://obamiconme.pastemagazine.com/
John Dupuis and Jay Bhatt liked this
Where Are All the High School Computer Science Students? - http://blog.acm.org/archive...
Jay Bhatt liked this
"I recently had a discussion with a professor from Virginia Tech on why can't we recruit more students for Computer Science majors at the university level, why can't we get women or minority students, and what can be done to turn this around? There is obviously a great deal of interest in recruiting students to our discipline, so why are we unsuccessful?"
- John Dupuis
The Thomson Scientific Journal Selection Process - http://thomsonreuters.com/busines...
Jay Bhatt and Garret McMahon liked this
Essay on the criteria for the journal selection process in use at Thomson Reuters Scientific
- Jill O'Neill
Open Notebook Science/Open Drug Discovery at GDCh nation meeting - http://www.steinbeck-molecular.de/steinbl...
Jay Bhatt and Egon Willighagen liked this
Very final countdown to Science Online 09 - http://blog.openwetware.org/science...
Jay Bhatt, Deepak Singh and Carmen Drahl liked this
Co-Researching spaces for Freelance Scientists? - http://scienceblogs.com/clock...
Jay Bhatt, Nir London, Helen Sventitsky and 7 other people liked this
In a way the student participants in our ONSchallenge are free-lancing. They just need access to a lab and a local supervisor open to the idea. Our last student to join, David, didn't seem to have a problem getting access: http://onschallenge.wikispaces.com/student...
- Jean-Claude Bradley
Thanks Jean-Claude - I forgot about that (was not thinking about the students when I wrote this).
- Bora Zivkovic
Thanks a lot Bora. After reading your post I finally understood that I shouldn't resist the idea of physical coworking space. :)
- Pawel Szczesny
For all but the most extreme loners, a physical space with people is important for any work. The point is having freedom in that space - a non-hierarchical place where you can bring your own ideas and your own work, not being told from up above what to do (and clock in and out every day).
- Bora Zivkovic
Which is why it is better to work at a coworking place than in your company's HQ where the CEO also has an office.
- Bora Zivkovic
Interesting - something like a Science Hostel in Germany: http://www.dagstuhl.de/en...
- Bora Zivkovic
or The Institute for Advanced Study in Berlin: http://www.wiko-berlin.de/
- Bora Zivkovic
Just gave the Vice President of Academic Affairs a tour of what we've been doing with library instruction. He was very impressed and wants to make library instruction a required component of the Gen Ed curriculum. Woo hoo!
suelibrarian, jambina, Jay Bhatt and 4 other people liked this
This Is Awesome: Google In Quotes Lets You Find What Either Candidate Has Said About a Given Keyword - http://hotnessinacan.tumblr.com/post...
Jay Bhatt and Deepak Singh liked this
Lab note-books online..? - http://www.openmicroscopy.org/omero-b...
Jay Bhatt and Cameron Neylon liked this
I've been experimenting with using a wiki as a lab book after seeing your talks at Manchester and SciBlog08.
- Michael Barton
Michael it was really nice to meet you in person in Manchester! Having discussions on FriendFeed is convenient but nothing can replace a conversation in a pub and over dinner... I look forward to hearing about your wiki experiments
- Jean-Claude Bradley
It's time for Conference 2.0 - http://network.nature.com/blogs...
Jay Bhatt, Massimo Pinto, John Dupuis and 2 other people liked this
some good points in there - getting used to a lot of these features in smaller free online friendly conferences makes it harder when attending old school conferences like ACS
- Jean-Claude Bradley
The easiest part to change in a traditional science conference is probably the blogging part. Some of the conferences I attend have policies that make me avoid liveblogging or blogging in too much detail.
- Martin Fenner
a big problem with ACS is no wireless access, which tends to discourage liveblogging :)
- Jean-Claude Bradley
To be entirely fair, its not the fault of the meeting organizers. The largest convention centers are not built to accommodate wireless easily. The administrators of those facilities farm it out to third party providers who are charging exorbitant prices.(Unions also drive up costs here) Even a small conference such as the one my organization runs (250 people) could be charged thousands of dollars to provide the wireless to attendees. The economics are just this side of prohibitive.
- Jill O'Neill
some great ideas, including clarity about what is and is not bloggable. Also, the comment about speed dating is a good one - I went to a "speed dating" type activity at ASIS&T last year & met someone whom I now consider a trusted friend -- and co-presenter at a recent conference.
- Stephanie_Thankful
"Scientific conferences are essential both for the exchange of ideas and for networking. But they don’t have to be organized the same way as 10-20 years ago." Web 2.0 tools are now allowing us to share, communicate and develop new ideas in ways that makes learning, collaborating and researching so much fun! Use of 'Open Conference System' http://pkp.sfu.ca/?q=ocs is an excellent thought. Just wondering if there have any conferences conducted using this system.
- Jay Bhatt
A list of conferences using "Open Conference Systems": http://pkp.sfu.ca/ocs-con.... Speed geeking is apparently related to speed dating: a rapid succession of 5 min presentations.
- Martin Fenner
Scratchpads: a social networking tool to build, share and publish information on the diversity of life. - http://scratchpads.eu/
Jay Bhatt liked this
LiveScience: Era of Scientific Secrecy Near End - http://www.livescience.com/culture...
Shirley Wu, Sutee Dee, Björn Brembs and 9 other people liked this
An article on open science for a general audience.
- Michael Nielsen
Cameron Neylon, Jean-Claude Bradley and Sabine Hossenfelder all get extensively quoted. Nice to see!
- Michael Nielsen
indeed - thanks for bookmarking Michael
- Jean-Claude Bradley
The exciting news to me is that the "public" is interested in this. The article is being, clipped, dug, etc.
- michael sean wright
Most excellent -- one quibble, I'd like to see "no insider information" credited to Jean-Claude.
- Bill Hooker
well thanks Bill - the author removed it after some reformatting of the original paragraph :) I didn't ask for it to be removed - I have no problem with that paragraph
- Jean-Claude Bradley
so you think that private company will always permits to their scientist to share data with the rest of the world?
- Piero Giacomelli
@Piero: some will, some won't. The hypothesis is that the sharing model will prove more efficient, so early adopters will realize an advantage and eventually the mainstream will adopt their methods. There are no guarantees but I think it's worth testing the hypothesis.
- Bill Hooker
Depends on the information. Pharma companies are already sharing pre-competitive information. Stuff that they would need to repeat in the absence of any data availability. With things like GWAS, it might be impossible to do for a company, so they will collaborate with universities and make the raw data public (e.g. Novartis)
- Deepak Singh
Expression data (eQTL) too. See Rosetta/Merck.
- Chris Cotsapas
@Chris, oops. Should have included that one esp cause I have used that in talks :) (I was at Rosetta Biosoftware)
- Deepak Singh
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