Bill Hooker
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8 hours ago - scienceblogs.com - Link
clearly we need some evolution away from the human-readable paper and the standalone database as containers for the things we know, or the things we believe. The information space is simply too big for any one brain to process any more, and Google simply isn't as efficient for science as it is for culture... Tagged by sennoma under oaos.quotes, - Bill Hooker
8 hours ago - ingallslab.wordpress.com - Link
Tagged by sennoma under oaos.examples, - Bill Hooker
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13 hours ago - nsaunders.wordpress.com - Link
Tagged by sennoma under openscience, PSB2009, - Bill Hooker
13 hours ago - scienceblogs.com - Link
Tagged by sennoma under lostart, - Bill Hooker
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16 hours ago - sciencemag.org.liboff.ohsu.edu - Link
J. A. Evans's Report "Electronic publication and the narrowing of science and scholarship" (18 July, p. 395) suggests that (i) the average age of citations to scientific papers dropped over the years as more electronic papers became accessible and (ii) the citations are concentrated on a smaller proportion of papers and journals. Such conclusions are not warranted by Evans's data. To measure the evolution of the average (or median) age of the references contained in papers, one has to look at all the references in all published papers and observe the evolution of their age over time. As we have shown using Thomson Reuters's Web of Science data for the period 1900 to 2004 (for a total of 500 million references in 25 million papers), the average (and median) age of all references began to decrease in 1945 but has increased steadily since the mid-1960s. This trend is visible in all sciences, including the social sciences and the humanities (1, 2). The median age of references in fields... - Bill Hooker
Behind a paywall for me, I'll get it later... but this looks very interesting. - Michael Nielsen
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15 hours ago - efoundations.typepad.com - Link
position papers for the W3C Workshop on the Future of Social Networking are now available. Tagged by sennoma under social.science, socialsoftware, social.networking, - Bill Hooker
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16 hours ago - blogs.nature.com - Link
Tagged by sennoma under peerreview, - Bill Hooker
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Sunday at 11:07 am - blog.openwetware.org - Link
Tagged by sennoma under openscience, - Bill Hooker
last sentence - bottom up approaches are certainly doing a lot for OS these days - Jean-Claude Bradley
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Friday at 10:56 pm - littlebirdhouse.wordpress.com - Link
Tagged by sennoma under lostart, - Bill Hooker
that was a weird experience - I thought you had written this until the last paragraph :) - Jean-Claude Bradley
Ha! I wondered about that when I saw it appear here -- I think I need to build a Simpy feed that will (e.g.) ignore everything not tagged 'ff" so that I only share useful things here. Like MrGunn (http://friendfeed.com/e/adf0f5...), I think FF will work best if we all try to keep the signal up and the noise down. - Bill Hooker
Viz., FF's signal:noise ratio is currently the best of any social site I've ever used, and I don't plan to be the one dragging that down! :-) - Bill Hooker
But the damage is done - my hippocampus has already encoded the information. I automatically think that you like knitting when your name comes up - even though I know better :) - Jean-Claude Bradley
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Sunday at 2:47 am - thenecks.com - Link
Tagged by sennoma under music, want, stuff, - Bill Hooker
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“Oh man. Shimmering on the wall behind my monitor is what looks like heat haze -- I thought the monitor or external hard drive that sits behind it was frying! Turns out that the sun is setting behind me, and in between is the hospital steam room, sending up clouds of steam...”
Saturday at 4:45 pm - Link
you are working too hard man... - Cameron Neylon
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Saturday at 10:38 am - spheredev.org - Link
Tagged by sennoma under work, organising, collaboration, - Bill Hooker
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“How hard is it search a (protein) database with, not a sequence, but an artificial construct (matrix) that gives each residue a probability of appearing at each position?”
Friday at 11:26 pm - Link
Isn't that exactly what a statistical potential is, at least in structure space. And what a substitution matrix essentially does as well - Deepak
Assuming I understand your question correctly - Deepak
Here's what I'm after: nuclear export signals are fairly widely divergent; NESbase 1.0 (http://www.cbs.dtu.dk/database...) contains 75 verified NESs, and only about a third of those match the established consensus (see http://nar.oxfordjournals.org/...). So how would I go about turning the NESbase information into a 20x20 matrix with all the amino acids on one side, position in the NES on the other, and probabilities at each junction or whatever it's called? And having got that, how could I fool something like BLAST into treating it as a sequence? - Bill Hooker
I am not sure using BLAST per se is what you want to do here. What you need to do is take your sequence of interest, use a statistical function derived from the NES database and then search a sequence database using the statistical function to come up with Z-scores for various hits. At least that's how I'd approach the problem. I suspect others will have much brighter ideas :) - Deepak
or just use a threading algo :) - Deepak
Ah, never mind, I knew I couldn't have come up with this on my own. PSI-BLAST from NCBI does pretty much exactly what I describe, only you have to run an initial BLAST search rather than being able to slurp up a database. - Bill Hooker
can you transform your NESs into a prosite pattern ? ( http://www.expasy.ch/tools/sca... ) and then scan prosite ( http://www.expasy.ch/tools/sca... ) ? - Pierre
Ah, in other words you want to come up with a profile and use that to search. Duh!!! - Deepak
@Pierre, thanks, that looks do-able. - Bill Hooker
@Deepak: yup, you got it -- I just didn't know enough to even specify my question properly. Fortunately, I'm a trained scientist -- meaning, I'm quite used to having no idea what I'm doing! - Bill Hooker
I think I just proved that last part :D. It's actually a fun little problem - Deepak
If it were more readable, this sequence logo built from NESbase (http://nar.oxfordjournals.org/...) would make it reasonably quick to build a ProSite profile. Unfortunately I can't see any way to weight residues at each position in a profile -- I can have [ST] for "ser or thr" but I can't say "ser is 5 times as likely as thr at that position"... - Bill Hooker
There's a web app for generating sequence logos (http://weblogo.berkeley.edu/), so surely it can't be difficult to tweak that app to build a PSSM... ? - Bill Hooker
@Bill. OK, sorry :-) - Pierre
Google "PSSM logo" indicates that the logo app does in fact create a PSSM; now how to go about getting it out, and uploading it to PSI-BLAST? - Bill Hooker
@Pierre, I might still try it, even without weighting -- it's a good idea and might come up with some interesting things. I'll also email the weblogo folks and ask about the PSSM-->PSI-BLAST question. - Bill Hooker
Bill, I have used HMMER for similar purpose (short piece, some positions have strong residue signal). Here's a web-based version that lets you search across many databases http://toolkit.tuebingen.mpg.d... Anyway, for sequence logo or for HMMER you need an alignment first, although I haven't found one in the NESbase. - Pawel Szczesny
@Pawel: there isn't one, it's just a curated list of sequences. There are only 75, I can format and load them into Clustal easily enough. I've learned what a human-readable PSSM looks like, only to find that PSI-BLAST can't upload a human-readable version. Argh. I think the kind of thing I want to do here is routinely assigned to bioinfo students, it's sort of embarrassing to fumble around with it so badly... - Bill Hooker
Ah, the Tuebingen toolkit you linked also does PSI-BLAST from a Clustal input. I think I can do this now. - Bill Hooker
Oy, I give up for now. HMMER won't read the output from CLUSTALW, it keeps saying there are invalid chrs. I'll try turning a small Clustal output file into a FASTA file by hand and see if that works, then I gotta get some sleep. - Bill Hooker
Bill, if you need some help with the toolkit just let me know (we can skype or something like that). - Pawel Szczesny
BTW, Bill did you try to paste output from Clustal or use Clustal on the toolkit and then forward the results to FHMMER? The second approach should work. - Pawel Szczesny
Thanks Pawel, but it seems to be reading my handmade FASTA file OK. I'm not sure how much more I want to play with this -- I just wanted to see whether I could find an NES in my protein of interest. At this stage I'm just going to wait to see what my leptomycin B timecourse tells me when I work it up! :-) - Bill Hooker
Aw jeez, I never even thought to look for Clustal at the toolkit, I was using it via EBI. OK, let me try doing everything at Tuebingen... - Bill Hooker
Pawel, you rock. That works -- now I just need to process the NESbase info into a FASTA input for Clustal (no hits returned using only the first 25 of 75 NESs). It's 1:00am so I'm going to get some sleep first though. :-) - Bill Hooker
Do you mean this Tübinger toolkit? http://toolkit.tuebingen.mpg.d... ? BTW, CLCBio does also sequence logos, and I miss Tübingen ;-) - joergkurtwegner
@Joerg: yes, that's the one. - Bill Hooker
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December 30 at 12:13 pm - scholcomm.columbia.edu - Link
A panel discussion on the debate about the best way to rank the importance and influence of scholarly publications. Panelists: Marian Hollingsworth, director of Publisher Relations at Thomson Reuters and former assistant director of the National Federation of Abstracting and Information Services; Jevin West, an Achievement Awards for College Scientists Fellow at the University of Washington's Biology Department and head developer for Eigenfactor.org; and Johan Bollen, a staff researcher at Los Alamos National Laboratory and the principal investigator of the MESUR project. Columbia University Librarian Jim Neal introduces the talk. Tagged by sennoma under scientometrics, bibliometrics, impactfactor, - Bill Hooker
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Thursday at 9:52 pm - bioinformaticszen.com - Link
Michael Barton with another neat idea. - Bill Hooker
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Thursday at 1:09 pm - earlham.edu - Link
Glenn S. McGuigan and Robert D. Russell, The Business of Academic Publishing: A Strategic Analysis of the Academic Journal Publishing Industry and its Impact on the Future of Scholarly Publishing, Electronic Journal of Academic and Special Librarianship, Winter 2008. Tagged by sennoma under serialscrisis, readthis, - Bill Hooker
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December 31 at 3:01 pm - drmaciver.com - Link
Tagged by sennoma under oaos.examples, - Bill Hooker
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December 31 at 1:36 am - sharescienceideas.wikispaces.com - Link
This is the Wikispace companion to SCIEnCE - Share Collaborative Ideas, Enact Cooperative Efforts. Scientific ideas are collaboratively composed using Wiki functionality. The result will be research designs that are optimized before funding and embarking on a project. Once a core group of contributors and proposals are accumulated, SCIEnCE will seek funding to reward the best contributors and projects. Tagged by sennoma under openscience, - Bill Hooker
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The White Tiger: A Novel
December 30 at 12:29 pm - amazon.com - Link
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December 30 at 12:13 pm - mesur.org - Link
MESUR is now producing large-scale, longitudinal maps of the scholarly community and a survey of more than 60 different metrics of scholarly impact. Tagged by sennoma under scientometrics, bibliometrics, impactfactor, - Bill Hooker
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December 25 at 3:24 pm - molbiolcell.org - Link
If you like that I just printed out a whole folder full of fun for you. :-) - Bill Hooker
F'rinstance, Did You Know(TM)? Nocodazole doesn't really synchronize cells, and it blocks them at a weird point in the breakdown of the nuclear envelope at prometaphase -- so you can isolate nuclei, but they're probably leaky, and you've no simple way of knowing what proportion of your cells have already no nuclear/cyto separation... Meh. - Bill Hooker
Ignorance is not bliss, it's wasted bloody experiments, that's what it is! - Bill Hooker
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December 25 at 10:36 am - scienceblogs.com - Link
Tagged by sennoma under lostart, - Bill Hooker
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December 25 at 10:33 am - radian.org - Link
Tagged by sennoma under intellectualproperty, freeculture, - Bill Hooker
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December 22 at 11:49 pm - scienceblogs.com - Link
Tagged by sennoma under lostart, - Bill Hooker
I didn't realize authorship was a "winner take all" situation, Bill. - Mr. Gunn
In the comments, I argue that it isn't. I disagree strenuously with PP on this. - Bill Hooker
@Bjoern, check this shit out: here's PP describing his procedure for evaluating junior faculty applicants: "...Those that survive this initial triage get a closer look that takes a minute or so for each application. If the applicant has no first author pubs in a >10 impact factor journal, then it is highly likely they are not going any further. One exception might be an impressive number (like five or more) first-author pubs in 5-10 impact factor journals." Argh. - Bill Hooker
sorry, should have read more closely. That's messed up, man! - Mr. Gunn
That's why I'm glad I don't work in these guy's fields... - Cameron Neylon
@Mr. Gunn - don't feel too bad...who has the time to wade through 77 previous comments to find fancy-ass PP's worthless piece of shit comment #78? No offense, @Bill Hooker. - The Neurocritic
Still stunned that anyone can even write such garbage. Talk about a screwed up system. It just enhances everything that I find wrong with the system - Deepak
None taken, neurocritic. Thing about PP is, he's actually smart and thoughtful -- you just have to ignore the schtick and make allowances for the fact that he's a product of his (wealthy, privileged) environment. I give him props for being able to see as much of his own privilege as he does, notably in re: women in science. I disagree with him on most things, but find him a useful 'proving ground' for my ideas. - Bill Hooker
Which is why I do wade through those comment threads occasionally -- though I quite understand why most folks wouldn't. :-) - Bill Hooker
Blog
December 22 at 3:27 pm - sennoma.net - Link
poor kido! It's not even knee high! Go get a shovel and start working out those nice arms of yours. - Paulo Nuin
I would, Paulo, but there's nowhere to shovel to. All the buses are canceled, and I'm not shoveling the whole 5 miles from here to work! :-) - Bill Hooker
Make mountains!! - Paulo Nuin
Chilly here in Sydney too, apparently forecasting only 22 C Might have to put on a long sleeved shirt... - Cameron Neylon
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“Backyard, from kitchen window.”
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December 22 at 3:33 pm - Link
what is your elevation Bill? - Maureen
I dunno -- we're on Holgate, right around Woodstock. I guess we're at about 1/3 or 1/2 the elevation of Pill Hill. - Bill Hooker
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December 22 at 4:10 pm - ncbi.nlm.nih.gov - Link
how to search for total number of records in any PubMed database Tagged by sennoma under pubmed, - Bill Hooker
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December 22 at 9:59 am - blogs.nature.com - Link
Tagged by sennoma under opendata, - Bill Hooker
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December 20 at 5:35 pm - sennoma.net - Link
Interesting... again, I'm in the wrong business... :( - Egon Willighagen
As Richard Smith says, "Robert Maxwell got rich through publishing science, not newspapers." http://www.guardian.co.uk/comm... - Graham Steel
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December 20 at 10:49 pm - scienceblogs.com - Link
Tagged by sennoma under lostart, - Bill Hooker
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December 20 at 8:23 pm - libraryjournal.com - Link
Tagged by sennoma under oa.money, oa.numbers, serialscrisis, - Bill Hooker
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December 20 at 6:52 pm - elsevier.com - Link
Tagged by sennoma under oa.money, oa.numbers, publishing, publishing.models, - Bill Hooker
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