 |
|
| FriendFeed is the easiest way to share online. Learn more » |
Andrew Clegg › Comments
Lombok feature overview - http://projectlombok.org/feature...
Annotations to provide things like getters, setters, toString etc. automatically.
- Andrew Clegg
guava-libraries - Project Hosting on Google Code - http://code.google.com/p...
A load of utility classes to take the long-windedness out of Java. Soon to be merged with Google Collections.
- Andrew Clegg
That’s Not a Memory Leak, It’s Bloat | Engine Yard Blog - http://www.engineyard.com/blog...
Rails memory usage tips.
- Andrew Clegg
Evolution and Language :: Mutations in the FOXP2 gene could help explain why humans can speak but chimps can't. - http://www.nature.com/news...
Mary Canady, Khader Shameer and Alexey liked this
"Two tiny changes in the sequence of one gene could have helped install the mechanisms of speech and language in humans. Experiments have now revealed that the human version of FOXP2, which has two different amino acids compared with the version carried by chimps, has differing effects on genes in the brains of the two species. These differences could affect how the brain develops, and so explain why only humans are capable of language. The study also lends weight to the idea that language didn't evolve from scratch. It "depended on the retuning of genetic pathways present in non-verbal ancestors, rather than the appearance of completely novel mechanisms", says Simon Fisher." \\ Konopka, G. et al. Nature 462, 213-217 (2009) http://www.nature.com/nature...
- Adriano
from Bookmarklet
There's an awful lot of utter bollocks written about FOXP2. It isn't a "gene for language" any more than any other "gene for X" hype-fests. Bit of history here: http://itre.cis.upenn.edu/~myl...
- Andrew Clegg
interesting counter-point: "No-one should imagine that the development of language relied exclusively on a single mutation in FOXP2. They are many other changes that enable speech. Not least of these are profound anatomical changes that make the human supralarygeal pathway entirely different from any other mammal. The larynx has descended so that it provides a resonant column for speech...
more...
- Adriano
Rackspace Cloud Computing & Hosting | NoSQL Ecosystem - http://www.rackspacecloud.com/blog...
Survey and comparison of scalable non-relational DBs
- Andrew Clegg
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
How to get a better indication of memory usage than ps or top will provide - http://groups.google.com/group...
ps and top can massively over-inflate memory usage reporting for multi-threaded apps -- here's a couple of better ways
- Andrew Clegg
Math Overflow - http://mathoverflow.net/ (via http://friendfeed.com/michael...)
Christopher Granade, Dan Freeman, imabonehead and Andrew Clegg liked this
Question and answer site for mathematics, with quite a bit of serious activity at a high level.
- Michael Nielsen
stackoverflow and serverfault are incredibly useful sites so it's nice seeing their codebase being used for something else
- Andrew Clegg
How FriendFeed uses MySQL to store schema-less data - Bret Taylor's blog - http://bret.appspot.com/entry...
Mahesh CR, Mike Chelen, Tom Walsh and 2 other people liked this
Heh. Perhaps MySQL was a better schema-less hash store than RDBMS, all along.
- Andrew Clegg
this always comes to mind when people say mysql doesn't scale, although it's rather different from normal usage :D
- Mike Chelen
NoSQL: If Only It Was That Easy « Marked As Pertinent - http://bjclark.me/2009...
Mike Chelen liked this
A comparison of non-relational large-scale datastores (Tokyo Cabinet etc.). Conclusion: most don't scale as well as they claim.
- Andrew Clegg
XPath Evaluator - http://b-cage.net/code...
Mike Chelen liked this
Put in some XML. Put in an XPath query. Click Eval! Handy.
- Andrew Clegg
Britain's Nobel winner condemns science funding reform - includes flat bicycle tyre and elaborate Swedish prank - http://www.guardian.co.uk/science...
Deepak Singh, Jan Aerts, Tom Walsh and 4 other people liked this
"When the head of the academy came on the phone, I said, 'I don't know who you are, but you certainly have a good Swedish accent.' - LOL
- Cesar Sanchez
from Bookmarklet
I like the new spelling: "rhibosomes". From article: "The three scientists were awarded the prize for making detailed atomic maps of "rhibosomes", the complicated biological machines lurking inside cells that translate genetic code into complex life, from bacteria to humans."
- Cesar Sanchez
An editor who got them mixed up with "rhizomes" probably.
- Heather
They've fixed that already
- Andrew Clegg
though "ribosomes" still has quotes around it which I'm not sure is entirely correct...
- Cameron Neylon
Rethinking the Design of Presentation Slides: the Assertion-Evidence Structure - http://www.writing.engr.psu.edu/slides...
Mike Chelen liked this
I'm not very good at designing slides -- this looks like a useful way to think about them
- Andrew Clegg
I am looking for a simple option to retrieve the mesh terms and publication date for a given PubMed ID. I was looking at Eutils tools like esearch and efetch. But not able to find the exact details or URL format to query PubMed using key workd and print only publication date and mesh fields - any suggestions ?
Paul Bacchus, Mike Chelen, Abhishek Tiwari and 2 other people liked this
If you're looking for a given ID, try this -- http://eutils.ncbi.nlm.nih.gov/entrez... -- then use grep to extract all lines which start with MH to get the MeSH keywords
- Andrew Clegg
Obviously you need something like curl or wget which can run from a script and download from a URL. If you need to search by something other than PMID (e.g. a text query), use esearch to run the query and get back the IDs, then efetch to download the docs corresponding with those IDs. Does that make sense?
- Andrew Clegg
e.g. to get all MeSH terms and the pub date for PMID 19614587, try this (from a Mac or Linux command line anyway): curl -s 'http://eutils.ncbi.nlm.nih.gov/entrez... '^(MH |DP )' -- ARGH, FriendFeed being 'helpful' has mangled the command and I don't know how to override that. If you give me an email I can send better instructions :-)
- Andrew Clegg
Download you data as XML ( http://eutils.ncbi.nlm.nih.gov/entrez... ) and then extract the MESH terms using XSLT. Do you need help for this ? For example, see the http://code.google.com/p... in my repository.
- Pierre Lindenbaum
Pierre, mere mortals can't write XSLT. ;) At least I failed miserable the last time I tried to do something simple
- Michael Kuhn
tutututu, XSLT is simple for simple things (http://www.w3schools.com/xsl... ) . and XSLT is complicated for difficult things ( http://docbook.sourceforge.net/release... ). I mean , it takes less than one hour to make a simple task with XSLT.
- Pierre Lindenbaum
and the more people wil use XML+XSLT or RDF, and the more you will work with structured data instead of parsing/grepping/sorting meaningless tab-delimited files.
- Pierre Lindenbaum
Yes, it's only starts to become fun when you are pulling XML from more than one document :)
- Egon Willighagen
personally, I would use an xpath library to parse the xml and output in plain text. my understanding is that xslt (which uses xpath) is great for parsing xml but pretty much is designed to output XML or HTML only.
- Andrew Su
@andrew : can you use Xpath without programming ? which of tool is it ? Anybody can use XSLT as most browser embed an internal XSLT engine. You just have to add the URL of your stylesheet at the top of your XML document ( http://www.w3schools.com/xsl... )
- Pierre Lindenbaum
Seriously guys -- XPath/XSLT is overkill for this kind of thing. It's a one-liner. I've written is up here so it doesn't get mangled this time: http://biotext.org.uk/how-to-...
- Andrew Clegg
working code wins! ;) (But I will say that learning to use the perl XPATH library was surprisingly simple, even for someone whose skills are decaying as fast as mine...)
- Andrew Su
@Andrew C.. yes of course , I agree :-)
- Pierre Lindenbaum
BTW XMLStarlet is great for doing XPath/XSLT/etc. from the command line -- http://xmlstar.sourceforge.net/ or you may already have it as /usr/bin/xml -- but try it the easy way first ;-)
- Andrew Clegg
Andrew C, where I think your one-liner gets a bit more complicated is when you request multiple documents (e.g., http://eutils.ncbi.nlm.nih.gov/entrez...) and then want to parse out multiple fields from each article on a single line. That I think is where the balance shifts a bit toward xpath...
- Andrew Su
@Andrew Yeah, it very much depends on what you want to do *next*...
- Andrew Clegg
from email
recently, @tpoi asked for a tool returning the number of paper per year ( http://twitter.com/tpoi... ). I wrote this stylesheet http://code.google.com/p... . He was then able to compute the result without knowing any command-line tool, but using his browser.
- Pierre Lindenbaum
(sorry to everyone else for hijacking this thread, but...) Pierre, very cool. How do you invoke your xsl? you need to reference it in an XML doc, right?
- Andrew Su
1) you can invoke a XSLT engine e.g. http://xmlsoft.org/XSLT... "xsltproc style.xsl doc.xml" 2) you can add a stylesheet url at the top of your XML document and open this document in firefox . See "Link the XSL Style Sheet to the XML Document" in http://www.w3schools.com/xsl...
- Pierre Lindenbaum
@All : Thanks a lot for the awesome responses. Let me go through them and try them. I was working on to contribute to GeneWiki3 (Thanks to Andrew Su, he assigned a small module for me to contribute to GeneWiki3) This is a true Science 2.0 learning experience. Thank you all !!
- Khader Shameer
WORLD UNIVERSITY RANKINGS 2009 - http://www.timeshighereducation.co.uk/WorldUn...
Sydney equal with Melbourne on 36. I both do and do not know what this means.
- Matthew Todd
"But 50 per cent of the final score is made up from qualitative data from surveys of informed people - university academics and graduate employers." So they compile citation counts etc very carefully, OK fine, but then they just ask people what they think and give this a 50% weighting? Fail.
- Dave Lunt
We (UCL) are 4th overall but nowhere near 4th in any of the 'areas of expertise'. No idea how that works. Not complaining though ;-)
- Andrew Clegg
Science Commons Salon October 15th in Mountain View - John Wilbanks, Reid Hoffman and Joi Ito will be talking about Innovation in Open Systems. There will also be some Pech Kucha style talks given at the beginning of the evening (still settling the details on that). If you will be in the bay area on October 15th please join us! Lisa
Richard Akerman, Davide Bennato, Heather and 6 other people liked this
Oops, forgot the registration link http://sciencecommons2.eventbrite.com/
- Lisa Green
Man, why couldn't you put it off till the next weekend when I'll be there for the Google Summer of Code summit...
- Donnie Berkholz
Donnie It would have been great timing to have it right before the Summer of Code summit - but it was so hard to find a day that John, Reid and Joi were all three available to be in the bay area that we couldn't be picky.
- Lisa Green
Totally OT, but how do you know when you've gotten comments on your posts? Do you just check back here all the time? Comments don't show in my RSS feed...
- Donnie Berkholz
Donnie, IM is great for that
- Deepak Singh
Gimme a FriendFeed-IRC gateway and I'd be good to go. =)
- Donnie Berkholz
Donnie, you can enable email notifications in FriendFeed settings
- Andrew Clegg
Roundtrip PDX-SJC, $250; overnight stay $100; taxi etc $50; seriously considering it.
- Bill Hooker
Thanks, Andrew!
- Donnie Berkholz
Bill I would pick you up at the airport :-) Lisa
- Lisa Green
If everything goes according to schedule, my daughter will be 1 week old then. Maybe next time?
- Mr. Gunn
@Lisa: I have some time off available, but whether I can take it will depend on external factors -- I should know by the end of the week. Do you happen to know a decent hotel/motel somewhere between the airport and the LinkedIn campus?
- Bill Hooker
Bill I will look into hotels for you. It would be great if you could come! Also, we are planning a Science Commons event in Seattle for February and I'd like to talk with you about that.
- Lisa Green
Bill how about a sleeper sofa at my apartment in San Francisco?
- Lisa Green
Another imovie 08 thread - The Digital Video Information Network - http://www.dvinfo.net/forum...
How to fool iMovie into seeing a disk image as a camera so it can import DV MPEGs
- Andrew Clegg
London BioGeeks tech meet + pub night tomorrow night (29-Sep-09). Topics: Search tech, gene expression, cloud computing, object-oriented Perl. All welcome. http://biogeeks.wordpress.com/2009...
Cass Johnston liked this
interesting, cant make this one but maybe in the future....
- Frank
If anyone's interested, the slides etc. from this meet are now here: http://biogeeks.wordpress.com/2009...
- Andrew Clegg
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
Its time for me to prepare a CV for my post-doc applications, any suggestions ? What are the must haves in a bioinfo post doc CV ?
Daniel Jurczak, Lucas Brouwers, Mike Chelen and 5 other people liked this
Focus on the position requirements, and do not add in minor stuff not required, unless where it serves as topic for the interview.
- Egon Willighagen
Keep it short. Use a template. Spelling/grammar errors look bad. Focus on the cover letter, not the CV. Say why you want the position and what you will bring to it - generic applications look very bad. Rather than listing skills, give examples of problems that you've faced and how your skill set solved them. Publications, presentations posters etc. can be a separate section in a smaller font, after the other stuff.
- Neil Saunders
Agree with both the above. You can tailor the CV itself to the job you're applying for -- don't have a one-size-fits-all. Emphasize different skills and experiences depending on where you're applying -- some could be left out for brevity in some job applications, but left in for others if they're more relevant. Plus it doesn't hurt to ask a slightly more senior friend or colleague if you could see theirs, to have something to work from.
- Andrew Clegg
Thanks Egon, Neil, Andrew for the different, yet important points.
- Khader Shameer
Agree with above about the cover letter. On the CV, one URL pointing to your publications (via citeUlike, zotero etc), another pointing to your LinkedIn profile.One URL for your blog. Restate your relevant skills, as appropriate for the job and thats about it.
- Frank
Pawel built nice tag cloud for his resume: http://www.flickr.com/photos...
- Pierre Lindenbaum
Frank: Do you think listing your pubs on your CV is out of date these days? Personally I think a link to a comprehensive online list would be better, but I'd worry about old-fashioned employers thinking that "wasn't the done thing". Also that puts the onus on the reader to actually fire up a browser and put the link in (esp. if it's a printed CV)
- Andrew Clegg
If it's a PDF CV, include links to the pubs?
- Rajarshi Guha
Frank : I am not yet an active blogger - is that an absolute requirement for a compbio postdoc or job :| ?
- Khader Shameer
I am planning to put a link to my publications in PubMed as suggested by Rajarshi, but some of them are conference abstracts / non-pubmed publications, so I need to use a combination of both.
- Khader Shameer
Don't forget to mention about you computational and programming skills in a detail, I guess most of Post-doc potions need programming skills well advance so just open up
- Abhishek Tiwari
Thanks Abhishek, will have a section dedicated to tech skills. But at the same time I don't want to enumerate n number of technologies / bioinfo tools am familiar with. That would easily fill 2 pages of my CV.
- Khader Shameer
Compliment @all. Nice crowd sourcing. Found via search for zotero. Trackback: http://identi.ca/notice...
- Markus Merz
@Andrew. I think it depends on the job, if you are going for a research position, they generally want to see what you have been doing, a non research position a reference list is probably irrelevant. I would agree that producing a list of your publications actually on the CV is outdated and would probably extend the page limit, I did suggest adding a link rather than listing them :). They would have to navigate to Pubmed to "read" them anyway.. or at least check the dates
- Frank
@Khader, wether you blog or not is your decision, I doubt it would be a deciding factor. I probably would expect to see some online activity, opensource project, link to research code, etc. However, I do understand this largely depends on the work you have actually been doing and is not a given
- Frank
Regarding publications: how about a handful of key relevant papers on the CV itself, plus link to full bibliography on one's website (w/ links to PubMed).?
- 'Mummi' Thorisson
Mummi: Dunno what Khader's CV is like, but if it was me applying for my first postdoc, those two lists would have been the same :-)
- Andrew Clegg
Frank, Mummi, Andrew - Thanks for the points. My thesis related papers are in different stages of review, so I may not be able to provide a link to full list of publication as of now. I am planning to provide list of publications within the CV as of now, once I get my papers accepted, I can substitute it with a link to PubMed. I think Chris Millers CV is a good template for an online CV http://www.chrisamiller.com/cv... . Now need to find one good template for an offline version.
- Khader Shameer
Thanks guys. Prepared my CV and cover letter with your suggestions and send the application yesterday. Today, I just finished my first post-doc interview. It was a nice experience.
- Khader Shameer
Publication list is the most important thing on a CV. One gets so many applicants, all of whom write their cvs so well, that one inevitably distinguishes between candidates on their publication record.
- Matthew Todd
Good luck, hope the news is good
- Andrew Clegg
Andrew, thanks ! It went on well - now waiting for the next steps : reco, thesis submission, etc.
- Khader Shameer
Hi - I'm a freelance journalist and lecturer specialising in bioinformatics and allied topics - I'm now researching for an article about the use of cloud computing in life sciences (particularly industry). Please email c.sansom@mail.cryst.bbk.ac.uk if you have any involvement in this or know any useful contacts. Many thanks! Clare Sansom
Mike Chelen, Daniel Mietchen, Ruchira S. Datta and 2 other people liked this
Um. I think you would do better, Dr Clare E Sansom, to treat this community as people not source material.
- Bill Hooker
Oh dear - I'm very sorry if this question offended anyone; I was recommended to post here by a fellow member of the community and I haven't been a member myself long enough to understand the netiquette... I'm just casting my net wide, really. :(
- Dr Clare E Sansom
Clare, I don't think your post was particularly inappropriate... my two cents, FWIW.
- Andrew Su
neither do I. Among the persons who are playing with cloud computing , you can have a look at @mndoci and @jandot.
- Pierre Lindenbaum
http://fortinbras.us/bioperl... - bioperl-max is a public Amazon Web Services Amazon Machine Image (AMI), preloaded with the major BioPerl packages. I think this one is an ideal bioinformatics example. Hope you have already looked at this short article by Alex Bateman and Matt Wood that discuss potential of cloud computing in bioinfomatics http://bioinformatics.oxfordjournals.org/cgi...
- Khader Shameer
You should also contact Konstantinos Krampis (http://friendfeed.com/agbiotec) at JCVI.
- Chris Lasher
Matt Wood would be the resident authority on harnessing the cloud for "biological computing" with all the work he did while at Sanger. Or you can get it straight from the horses mouth a.k.a Deepak Singh who works for Amazon web services .
- Hari
+1 @mza
- Pierre Lindenbaum
The other folks in this thread are right and I was wrong. My apologies, Dr Sansom; now that I re-read it I can't even say why your post set me off like that. I ask the room questions myself, quite frequently. I'm very sorry for the snark -- I'm glad you had a better welcome to the room from everyone else!
- Bill Hooker
Hi Clare, Andy here, Adrian Shepherd's former student :-) There's a seminar evening at UCL in a couple of weeks that I'm helping to organise, that includes a talk about doing bioinformatics on the Amazon cloud. Come along if you can make it. See http://biogeeks.wordpress.com/2009...
- Andrew Clegg
What are the best and most useful science apps for iPhone? Both for getting science news, and for doing science (e.g., Citizen Science projects)?
Paul Bacchus, Mike Chelen and Dimitrios Diamantaras liked this
lol @ Eric, but probably true
- Andrew Clegg
The Chemical Touch
- Dan Gezelter
There are at least three arXiv iphone apps, including one by http://friendfeed.com/dabacon
- Michael Nielsen
Also there are numerous HP-11C and 15C emulators.
- Dan Gezelter
Solutions, from mekentosj gets used regularly on my iTouch
- Wladimir Labeikovsky
Sarcasm from The Neurocritic: Deep brain stim for severe alcoholism? No, but it's being considered for psych disorders - http://neurocritic.blogspot.com/2009...
Ruchira S. Datta and Mickey Schafer liked this
We still have no idea whether this will actually work...
- Noah Gray
from Bookmarklet
it'll work
- Christopher Harris
Personally, I'd rather have a full bottle in front of me than a full frontal lobotomy...
- Andrew Clegg
Andrew, I think you are on to something....will have to do my own research...well, at least into the first part....
- Noah Gray
Early Risers Crash Faster Than People Who Stay Up Late: Scientific American - http://www.scientificamerican.com/article...
Brian Krueger - LabSpaces, Andreas Matern, Ruchira S. Datta and 14 other people liked this
"An hour and a half after waking, early birds and night owls were equally alert and showed no difference in attention-related brain activity. But after being awake for 10 and a half hours, night owls had grown more alert, performing better on a reaction-time task requiring sustained attention and showing increased activity in brain areas linked to attention. More important, these regions included the suprachiasmatic area, which is home to the body’s circadian clock. This area sends signals to boost alertness as the pressure to sleep mounts. Unlike night owls, early risers didn’t get this late-day lift."
- Donnie Berkholz
from Bookmarklet
I knew it!
- Fossil Huntress
I always secretly knew we night owls were better adapted than those crazy-up-before-dawn people!
- Fa La La La Lindsay
Posted at 11:15 pm local time ... and still going strong!
- Donnie Berkholz
is SA late to this - that paper came out a few months ago. There was some good coverage of it, e.g., http://sciencenow.sciencemag.org/cgi...
- Bora Zivkovic
Slow and steady wins the race :-)
- Neil Saunders
For the record, I'm liking this at 12:32 AM Eastern.
- Chris Lasher
This reminds me, it's 5:58am here... Off to bed.
- Ricardo Vidal
from iPod
darn, now i have even less motivation to switch to an early-bird schedule
- Wladimir Labeikovsky
Glad to see one positive about us night owls. Many are touting the harm of going against circadian cycle. Have been a day sleeper for ten plus years-no harm no foul.
- Celt MacGann
I know this feeling... Have had far too many days where my brain only really starts to wake up at 6pm, just in time to leave office because girlfriend/social life/other commitments are calling
- Andrew Clegg
This is the most visited post on all of my blogs at all times: Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask): http://scienceblogs.com/clock... Four years old but still pretty much up to date. Explains it all.
- Bora Zivkovic
BUT...us early birds get a whole day's work done in that first hour and a half...lol
- Mary Canady
@Bora spectacular post! Love the wealth of information and dearth of politics :) Feel less guilty and more hopeful already. Here's one of my favorite lines from Bora's post: 'Of course, all of the above are the strategies to shift your clock to a "socially accepted" phase. But you are not crazy or sick. It is the societal pressure to get up at a certain time that is making you sick. Try...
more...
- Steve Koch
@ Bora -- loved the post, too! I especially appreciated the discussion of light -- I spent a few months reading up on the impact of light, and a Science channel feature on biochronology a few months ago found that very bright light did a lot to help Alzheimer's patients and that planning around an individual's circadian rhythm could ease the side effects of chemo while increasing...
more...
- Mickey Schafer
That was my first true science post, from January 2005, the one that showed me there is interest in this and I could move from blogging politics to blogging science. I posted it on a brand new blog that nobody knew about, just set up, and the next day it was linked by BoingBoing, Andrew Sullivan and others. Even today, it is still my most visited post ever (and that counts ONLY the...
more...
- Bora Zivkovic
Dear lazyweb :-) Does anyone have any pretty-looking gene or protein network diagrams that they could let me use as window-dressing in a presentation? Try as I might, my poor Cytoscape skills (and lack of data) have hampered my attempts to make ones that look as striking as some I've seen. Thanks!
Mike Chelen liked this
Aha, thanks, the project in question relates to mitosis so that's doubly appropriate. Cheers, will attribute appropriately.
- Andrew Clegg
y'welcome
- Simon Cockell
A FLORA of Protein Structure to Protein Function - http://bytesizebio.net/index...
Andrew Clegg, Stylish Eve, Khader Shameer and 5 other people liked this
I presented this paper in my lab meet, but I was not able to find the expansion of FLORA in the paper.
- Khader Shameer
I work in the Orengo group -- but not on FLORA, this was all before I arrived. Thanks for the article, I've sent the link around the lab. PS see also comments on article
- Andrew Clegg
Placebos Are Getting More Effective. - http://www.wired.com/medtech... (via http://friendfeed.com/peterno...)
Konrad Förstner, Yann Abraham, Andrew Clegg and 3 other people liked this
"Potter discovered, however, that geographic location alone could determine whether a drug bested placebo or crossed the futility boundary."
- Michael Kuhn
"In one study, Benedetti found that Alzheimer's patients with impaired cognitive function get less pain relief from analgesic drugs than normal volunteers do. Using advanced methods of EEG analysis, he discovered that the connections between the patients' prefrontal lobes and their opioid systems had been damaged. Healthy volunteers feel the benefit of medication plus a placebo boost."
- Michael Kuhn
My comment on another thread: Think for a minute about what the placebo response is. It is partly a reflection of "things will get better anyway." The rest of it is "someone is ill whose body had all that was necessary to heal itself." So if placebo becomes more effective, either (a) the spontaneous recovery rate is going up -- which I don't think it is because diagnoses require...
more...
- Daniel Dulitz
Daniel, what's traditional medicine?
- Andrew Clegg
Andrew, it's practiced by people called anything from healers to shamans to "witch doctors." It's popular in the East (i.e. "Chinese traditional medicine"), it often uses herbs, touch, energy work, etc.
- Daniel Dulitz
How is all that stuff one tradition? And wasn't the concept of "traditional Chinese medicine" a political invention from Mao after WWII? (see e.g. http://bit.ly/SDdt0 )
- Andrew Clegg
Amira to Amira's feed, Culture & Society, Polytopia/collective intelligence, Languages, Science Online, The Life Scientists, Minds on FF
Logic and language are not the same thing | BPS Research digest - http://bps-research-digest.blogspot.com/2009...
Kol Tregaskes, Peter McLean, Sean O'Hanley and 7 other people liked this
"It's difficult for us to imagine what our mental lives would be like without language. Some theorists have even gone so far as to argue that language and logical thought are one and the same thing. A new brain imaging study challenges this notion by showing that logical inferences based on simple "not", "or", "if", "then" terms activate a separate, though overlapping, network of brain regions compared with logical inferences based on grammatical judgements. (...) Monti's team said their findings were hard to reconcile "with the claim that language and logic are a unitary phenomenon". Rather, they argued their results are consistent with language and logic being separate processes. The grammar-based statements appeared to be solvable using language networks of the brain, whilst purer logic was dealt with by a distinct neural network not dependent on language. (...) The new and old findings together show that "much of thought is not embedded in language", they said."
- Amira
from Bookmarklet
Of course language is logic. It's just not the same as simple predicate logic.
- Peter
@ Peter -- What sort of logic is language? And what definition of language are you using?
- Mickey Schafer
Linguists have known for years that human language is not logic. One person can say "there's nothing wrong with that" or another "ain't nothing wrong with that" -- both people mean exactly the same. A single phrase like "the ambassador was entertaining last night" can mean two different things -- he was behaving in an amusing manner, or he threw a party. One word like "sanction" can actually mean two opposite things -- allow to happen, or block from happening. You don't need brain scans to tell you this...
- Andrew Clegg
Are there any other workflow composition tools out there, like Taverna, that also speak SOAP? Bioclipse can too, presumably?
Mike Chelen, Pierre Lindenbaum, azalea and 5 other people liked this
Yes, Bioclipse can. There is KNIME, Cyrille2 too
- Egon Willighagen
Thanks!
- Andrew Clegg
Sure about Cyrille2? The paper only talks about Moby, and the wiki doesn't have much apart from a dependency on SOAPpy
- Andrew Clegg
Pipeline PIlot http://accelrys.com/product...
- Duncan Hull
The Cyrille2 author is now in NZ but very friendly...
- Egon Willighagen
Duncan -- can you add an arbitrary third-party web service to PP? All the material I've read talks about dedicated components and component collections
- Andrew Clegg
@Andrew I'm told by Paul Dobson http://dobsonlab.wordpress.com/ that you can though I've not done it myself. PIpeline pilot isn't free or open source.... but the user interface is more appealing to many
- Duncan Hull
Ta -- I'm preparing a talk for industry people so non-free isn't necessarily a problem
- Andrew Clegg
This paper may also be of help: http://www.sciencedirect.com/science...
- Egon Willighagen
PP is free for students
- Abhishek Tiwari
Andrew ... Pipeline Pilot can add arbitrary services. The entire idea is to be able to develop and deploy code within an organization, so the full version is actually targeted at developers. The component collections are just a distribution mechanism for "things that go together". And although it's been a few years since I used it and things might have changed, it's a breeze to use and I believe the web services aspects have improved quite a bit.
- Deepak Singh
Non-free can be a problem for some businesses, especially when the license fees for software are expensive. I think even GSK grumbles about the cost of PP, which gives an idea of how expensive it can sometimes be...
- Duncan Hull
You have to wonder about people selling their software at a price where even some of their biggest potential clients think it's too expensive. But that's another thread
- Andrew Clegg
That is another thread. Get me a gin and tonic and I can talk about ACCL pricing for hours (never liked it). Having said that PP growth suggests that it has not been a blocker
- Deepak Singh
another thread another plug: http://code.google.com/p/papy/ (to avoid consfusion: the workflow-node functions can use SOAP e.g. via SOAPpy but no "SOAP component collections" exist, it might be a useful feature if you are interested please make a ticket).
- marcin
Job offer: The University of Edinburgh - http://www.jobs.ed.ac.uk/vacanci...
"Most biological search interfaces start with a text based query interface and in many instances this works adequately. The complexity of the brain limits this approach to basic queries. We want to focus the query on the brain structure itself and project a highly graphical, interactive method for exploring the brain querying and visualising data associated with brain structure and function. For example, rather than search based on the name of a brain regions, users should grab a 3D model, rotate and zoom through to the structure of interest."
- Björn Brembs
from Bookmarklet
Douglas is my co-supervisor (although I don't work on this project) and this is a great project to get involved with. You will also be housed in the Universities new Informatics forum which is a superb place to do research.
- Ian Simpson
Did we meet when I was visiting Douglas? Did you comment on my blog? I suck at remembering names...
- Björn Brembs
I hate to say it, but I cannot remember either !
- Ian Simpson
It sounds like you guys need some intuitive, interactive method for browsing and querying your brains. Err, wait...
- Andrew Clegg
lol :-) I gave a talk about habit formation in fruit flies. I think it was in June or so?
- Björn Brembs
Yes pretty sure it wasn't me ! which is at least a relief to my enfeebled mind.
- Ian Simpson
Other ways to read this feed:
