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Todd Harris › Likes
Article-Level Metrics and the Evolution of Scientific Impact - http://www.citeulike.org/user...
Bill Anderson, Bill Hooker, Anders Norgaard and 37 other people liked this
Article on ALMs by myself and Shirley Wu
- Cameron Neylon
Terrific. Are we still maintaining that list of "outputs resulting from FriendFeed"?
- Neil Saunders
I was planning on doing a demo of annotation at PLoS before the end of the year - perhaps this article would be a good candidate. As always, anyone willing to join is welcome.
- Daniel Mietchen
@ Neil: It's at http://spreadsheets.google.com/ccc... , and I have added the article as #25 (details missing).
- Daniel Mietchen
i added a note once, but now it won't let me add any other notes :( I don't see a rule about one note per person. I should have held off for a good one.
- Christina Pikas
I also just noticed that my "annotation" - provided the link to StackOverflow - shows up in the general discussion, where the title "Link" certainly is not helpful, and there is no way I can edit it.
- Daniel Mietchen
maybe something is broken, my note appears in general comments but also in that portion of the text as a comment. maybe that's why I couldn't add other notes?
- Christina Pikas
Not sure why you can't add more notes. Certainly been able to in the past. I see both notes where they are supposed to be I think. But they will also appear in the general comments as well I think.
- Cameron Neylon
Great article! I really need to add some comments or notes, just to prove the authors' point :-)
- Björn Brembs
BTW, when does PLoS finally get karma? I've been asking for proper 'show off' userprofiles for like ever :-)
- Björn Brembs
As in PLoS Overflow?
- Cameron Neylon
Cameron, et al. - What's the most useful thing I could do to nurture and support this renewed interest in article level metrics? (not from a competing data product point of view, but a let's get some good technologies out there with good visibility)
- Mr. Gunn
@Cameron: Exactly! I even think having a profile where you can post a pic and see how many papers and comments were published, papers edited, etc.was the very first thing I asked for when I signed up :-)
- Björn Brembs
But it needs to be federated across publishers... :-)
- Cameron Neylon
if authors put in their 'customer' weight, this will go faster, so why not go syndicate :-)
- Claudia Koltzenburg
I think I'll use this paper in my spring thesis class -- this is the main one where I discuss publishing models -- and maybe I'll demo Diigo with this as a class project next to an article that discusses IF.
- Mickey Schafer
While we're on the subject of functionality wish lists, I would also like an embed functionality for PLoS papers. Collecting my publications together but don't want to duplicate copies and reduce googlejuice for the journal - at least not for the OA papers anyway...
- Cameron Neylon
Whilst not a darts-player http://www.flickr.com/photos... , I think Cameron has hit the "triple-twenty" there :)
- Graham Steel
BTW, why isn't there a way to register this thread with the article? Why are we posting here and not on the article? There's got to be a lesson to be learned from this :-)
- Björn Brembs
from iPhone
http://bullseyevaluation.com/yahoo_s...
- Graham Steel
Done. See comment #4.
- Graham Steel
Search results: http://topsy.com/s... from Topsy http://labs.topsy.com/about/
- Jim Till
I've included a link to this thread in a blog post: Article-level metrics getting attention http://ff.im/bGuNY
- Jim Till
+1 Bjoern :-) another question along these lines would be: why does Cameron's intial FF message link to CiteULike and not to http://www.plosbiology.org/article..., or plainly doi:10.1371/journal.pbio.1000242 ?
- Claudia Koltzenburg
Because that was the way I brought the link in. I think that that pointer is appropriate. It is a pointer to the fact that I bookmarked it. Other people linked to the paper directly. Perhaps the issue is that we accidentally aggregated around the "wrong" item to talk about the paper. I'm not sure this is a problem as long as the referral works - its a UI irritation not a problem with...
more...
- Cameron Neylon
well, not directly, maybe in this ff-thread we're just providing some material for what you say in your paragraph "Technical Solutions to Social Problems", namely: "approaches that gather information from processes that are already part of the typical research workflow are also much more likely to succeed." - even though ff may not be part of 'the typical research workflow' (yet?) - and...
more...
- Claudia Koltzenburg
That's true, and certainly conversation sparked by the paper. But how to capture that in a way that is useful further down the line might be tough...
- Cameron Neylon
I am still wondering if we would not need at least one metric for each 'scientist type' as described in http://dx.doi.org/10...
- joergkurtwegner
joergkurtwegner -I'm interested to see what tenurometer comes up with re: h-index correction factors for disciplines.
- Mr. Gunn
Access denied? : Article : Nature - http://www.nature.com/nature...
Peter Miller, mariana, Duncan Hull and 8 other people liked this
"Every weekday, thousands of researchers around the world access the Arabidopsis Information Resource (TAIR), which contains the most reliable and up-to-date genomic information available on the most widely used model organism in the plant kingdom. But now, to those users' horror, TAIR faces collapse: the US National Science Foundation (NSF) is phasing out funding after 10 years as the data resource's sole supporter (see page 258). TAIR's plight is emblematic of a broader crisis facing many of the world's biological databases and repositories. Research funding agencies recognize that such infrastructures are crucial to the ongoing conduct of science, yet few are willing to finance them indefinitely. Such agencies tend to support these resources during the development phase, but then expect them to find sustainable funding elsewhere."
- Michael Nielsen
Redis, Memcached, Tokyo Tyrant and MySQL comparision | ruturaj.net - http://www.ruturaj.net/redis-m...
Todd Harris liked this
Playing around in #Balsamiq. Impressive while friendly at the same time. TIme to wireframe some #googlewave tools methinks
Todd Harris and Dan Hagon liked this
Great tool. And it's constantly evolving with weekly updates.
- Todd Harris
Apparently some issues with linux version so I think I'll play with the free web version (irritating popup every five minutes) until I get my Mac back and make a decision about purchasing...
- Cameron Neylon
Some of you have asked how I made the transition from science to marketing--check out my post and feel free to comment/ask questions. It's also a shout out for open source and dedicated to Warren DeLano. Communicating Science, or How Did I Get Here from There? | Biotechnology and Life Science Marketing Consulting: Comprendia - http://comprendia.com/2009...
Todd Harris, Nils Reinton, Ami Iida and 7 other people liked this
Cool post. I'm starting a new tag on delicious called "journeys" just for stories such as this. Students really like/need these stories.
- Mickey Schafer
We all like/need these stories :-)
- Nils Reinton
Models for financial sustainability of biological databases and resources - http://www.citeulike.org/user...
Peter Miller, Daniel Mietchen, Claudia Koltzenburg and 4 other people liked this
An introduction to scripting in Ruby for biologists. - http://www.citeulike.org/user...
Todd Harris liked this
I like this as much as a Perl scripter can. ;)
- Todd Harris
Funnily that's exactly how I feel !
- Ian Simpson
from twhirl
All three manuscripts submitted for the 2010 NAR database issue have now been accepted. Happy days :-)
Hari, Mike Chelen, Peter Miller and 4 other people liked this
Oh bother - talking to NAR about writing something on data licensing was on my list of things to do from last year. Guess I missed the boat again :-(
- Cameron Neylon
Cameron: don't worry, data licensing will not stop being in need of explanation any time soon ;D
- Mike Chelen
Why thankyou Mike, you really know how to brighten my day up...
- Cameron Neylon
Using BitTorrent to Retrieve Objects Stored in Amazon S3 - http://docs.amazonwebservices.com/AmazonS...
Todd Harris and Slade Publishing liked this
"Any object in Amazon S3 that can be read anonymously can also be downloaded via BitTorrent. Simply add a "?torrent" query string parameter at the end of the REST GET request for the object."
- Mike Chelen
Is that a security risk or a feature? :)
- Owen Greaves
Since the files are already public, it should be expected that people would download them. S3 bandwidth isn't free, so letting others help with distribution seems in the interest of the content author :)
- Mike Chelen
with a little more info about how the .torrent information is generated, could make a fantastic basis for file distribution
- Mike Chelen
This is a great feature of S3. Perl gurus might also want to see: http://search.cpan.org/~qantin... or http://code.google.com/p...
- Todd Harris
Byte Size Biology » A bioinformatician’s peeves (some of them) - http://bytesizebio.net/index...
Andrew Perry, Mickey Kosloff, Khader Shameer and 9 other people liked this
Could you have picked a more fitting picture with which to conclude that post? I laughed so hard. What's the source of that?
- Chris Lasher
Nice post, also applies to wet science- must contact all those collaborators and tell them what happened to th samples they sent...
- Richard Badge
from Nambu
@Chris it's one of those meme-ish pics that are everywhere. Don't know the source.
- Iddo Friedberg
from Android
Hilarious - perfect for hitting the trenches on a Monday morning. I'm always trying to instill in wet lab scientists that bioinformatics approaches are experiments just like any other and should be documented as such. Actually, I think bioinformaticists are often just as cavalier rarely taking good notes of their workflow.
- Todd Harris
Seventh graders describe scientists before and after a visit to Fermilab. - http://ed.fnal.gov/project...
Matt Snoulten, Euan, Steve Koch and 17 other people liked this
This one is lovely: "Their jobs sound very interesting because they can do whatever they want and they still get paid for it." ;-))
- Yaroslav Nikolaev
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
- TRsdr
I'm on (thanks to Steve Koch!): tom.tullius@googlewave.com
- Tom Tullius
Plotzie, My Google Wave Robot - http://lee-phillips.org/wave...
Chris Miller, Claudia Koltzenburg, Peter Miller and 4 other people liked this
A google wave robot that takes lists of numbers and converts them to sparklines. Interesting because it does image insertion and other things but also because of the sparkline webservice it uses and the way it gets around appengine limitations
- Cameron Neylon
Good stuff. After looking at Cameron's ChemSpidey, Igor, and now this, I'm really getting excited about the potential for bots and in-line modification of the info-stream.
- Todd Harris
Alternative talk styles http://www.academicproductivity.com/2009... #AcaProd | presentation styles for academics | take a look!
Todd Harris liked this
PLAST: parallel local alignment search tool for database comparison - http://www.biomedcentral.com/1471-21...
Mike Chelen, Yann Abraham and Todd Harris liked this
Avoiding dangerous missense: thermophiles display especially low mutation rates. - http://www.ncbi.nlm.nih.gov/entrez...
Todd Harris liked this
GEARFUSE » Cupcakes for Zombies - http://www.gearfuse.com/cupcake...
gmarketer, Ryan Sholin, Aaron D'Souza and 32 other people liked this
"Made using red velvet raspberry cake, french vanilla cream cheese frosting and a chocolate brain, baking extraordinaire Pamela created these awesome Brain Cupcakes, perfect for zombies who’ve gone vegetarian. The extra little splatter gives it that “just scooped out of the skull” look."
- April Buchheit
from Bookmarklet
Those do look delicious.
- j1m
halloween party idea!!
- Susan Beebe
Brilliant! And sick! But brilliant!
- rowlikeagirl
Genomewide comparative displays - http://ensembl.blogspot.com/2009...
Ricardo Vidal, Todd Harris, Deepak Singh and Nakao M. liked this
Public Access to Genome-Wide Data: Five Views on Balancing Research with Privacy and Protection - http://www.plosgenetics.org/article...
Paul Bacchus, Greg Tyrelle, Khader Shameer and 3 other people liked this
"Just over twelve months ago, PLoS Genetics published a paper [1] demonstrating that, given genome-wide genotype data from an individual, it is, in principle, possible to ascertain whether that individual is a member of a larger group defined solely by aggregate genotype frequencies, such as a forensic sample or a cohort of participants in a genome-wide association study (GWAS). As a consequence, the National Institutes of Health (NIH) and Wellcome Trust agreed to shut down public access not just to individual genotype data but even to aggregate genotype frequency data from each study published using their funding. Reactions to this decision span the full breadth of opinion, from “too little, too late—the public trust has been breached” to “a heavy-handed bureaucratic response to a practically minimal risk that will unnecessarily inhibit scientific research.” Scientific concerns have also been raised over the conditions under which individual identity can truly be accurately...
more...
- 'Mummi' Thorisson
Yet another high-throughput sequencing start-up: http://www.halcyonmolecular.com/
Khader Shameer, Sung W. Lim, Jason Chin and 6 other people liked this
Examples of others?
- Hope Leman
@Hope - Pacific Biosciences and Helicos maybe? Not sure on 454 and Illumina's origins.
- Paul J. Davis
Complete Genomics
- Eric Jain
NABsys
- Eric Jain
Hi, guys--thanks for the info!
- Hope Leman
Illumina has been around for a while and acquired Solexa, which was a next gen startup. 454 also been around a while and now part of Roche Applied Science. Pac Bio, Complete, there's one with nano in the name that I can't remember. Does Helicos still qualify as a startup (they are a public company)
- Deepak Singh
@Deepak, perhaps you're thinking of Oxford Nanopore Technologies? http://en.wikipedia.org/wiki...
- Rob Syme
Rob, I think that's it. Thanks
- Deepak Singh
Well-organized and well-delivered talk by @mndoci. Bioinformatics, reprezent! #hadoopworld
Todd Harris, Nakao M., Rob Syme and Pierre Lindenbaum liked this
What does MapReduce and Hadoop have to do with genomes, sequencers, and compute farms? Tomorrow, we find out. #HadoopWorld
Todd Harris liked this
Managing and Analyzing Next-Generation Sequence Data - http://www.citeulike.org/user...
Ricardo Vidal, Tom Walsh, Todd Harris and 4 other people liked this
PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000369. Brent Richter, David Sexton
- Yann Abraham
Scholarly Reputation Management Online*: The Challenges and Opportunities of Social Media - http://www.slideshare.net/habibmi...
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Todd Harris, Mr. Gunn, Berci Mesko, MD and 7 other people liked this
First publication based on a collaborative effort using FriendFeed/TLS: The Gene Wiki: community intelligence applied to human gene annotation -- Huss et al., Nucleic Acids Research - http://nar.oxfordjournals.org/cgi... (via http://friendfeed.com/yokofak...) - Congrats to all authors
Todd Harris, Pierre Lindenbaum, Neil Saunders and 3 other people liked this
This isn't the first publication of the Gene Wiki which was first described in PLoS Biol in 2008:
- Todd Harris
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics - http://www.biomedcentral.com/1471-21...
Todd Harris, Pierre Lindenbaum and Frank liked this
What features should future scholarly wikis (or their descendents) have? - http://en.wikiversity.org/wiki...
Todd Harris, Bora Zivkovic, Chris Leonard and 6 other people liked this
A tentative list is here at http://en.wikiversity.org/wiki... , coming out of http://friendfeed.com/danielm... . Please add your suggestions here.
- Daniel Mietchen
from Bookmarklet
Added: <li>Integration with mind maps (which structure knowledge) and databases (which harbour bits of knowledge that do not make much sense without a broader context).<br /></li>
- Daniel Mietchen
Thinking of unconventional ways to visualize exome resequencing results to search for causative SNPs using #processing http://www.nature.com/nature...
Sutee Dee, Paul Bacchus, Todd Harris and 3 other people liked this
Don't know yet if I can come up with one/some... But trying to keep an open mind.
- Jan Aerts
That's what I'm missing: a good idea for an unconventional way to visualize a *omic thing :-)
- Pierre Lindenbaum
I think a few of us are thinking along these lines. Processing brings visualisation to people who would normally find it too complex, which is great (especially that Ruby API). But to be honest, I'm disappointed with the examples I've seen. They are either trivial demos, or else examples that look very flashy and impressive, but do not (for me) convey information effectively. Thinking about large biological datasets in the processing framework is quite a challenge and a mental shift.
- Neil Saunders
This comes back to the discussion long time ago if modern big data research needs graphical designers/artists to help visualize the stuff. We might have the data, but not the skill to visualize (other than in histograms/piecharts/DAGs).
- Jan Aerts
I prefer it if a complex dataset can be distilled down to a simple bar or scatter plot. I find that too much data can distract from the main point. I bought and read the Visualizing Data book but I wasn't moved to try and start creating things in processing.
- Michael Barton
Having said that though I find the R syntax very frustrating. I would love a combination of R functionality with Ruby readability and metaprogramming.
- Michael Barton
I like simplification through statistics too. The opposite approach, in a way, is the data integration approach - display everything to the user, somehow. I feel there must be a way to do that without overwhelming, most likely via web apps (javascript) but perhaps via something like processing.
- Neil Saunders
That visualization of a set of SNPs was great & original http://benfry.com/isometr...
- Pierre Lindenbaum
Although I also like simple statistics, I feel that showing everything to the user can be really useful because it can give a better "sense" for what's going on. But it's difficult: the data must be presented in such a way that trends present themselves, rather the researcher having to define the trends and then drawing them. The data must draw the patterns to the screen; not you. (If you know what I mean....)
- Jan Aerts
This is how genetics works! - http://imgur.com/JaFUM
Jérôme Flipo, Ricardo Vidal, Vishy and 6 other people liked this
(via reddit)
- Michael Kuhn
from Bookmarklet
:-)
- Ruchira S. Datta
Now that's Awkward.
bnoise, Zulema ◕ ◡ ◕, beersage and 32 other people liked this
High larious
- Eric @ CSTechcast.com
from iPhone
hehehe!
- WorldofHiglet
Maybe she likes the fact that he'll be hanging around the house less all in a bad mood. Just a theory.
- Eric @ CSTechcast.com
from iPhone
Hahaha
- Rodfather
Maybe she wants grandkids. lol
- Joshua Schnell
hah, that is beyond silly.
- Nicholas Kreidberg
Thanks for the re-post. :)
- Ben Hanten
HAAAAAAAAHAHAHHAHAAAA!!!
- FFing Enigma (aka Tina)
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