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Yann Abraham › Comments
STITCH 2: an interaction network database for small molecules and proteins - http://www.citeulike.org/user...
Nucl. Acids Res. (6 November 2009), gkp937. Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/. 10.1093/nar/gkp937 Michael Kuhn, Damian Szklarczyk, Andrea Franceschini,...
- Yann Abraham
Predicting new molecular targets for known drugs - http://www.citeulike.org/user...
Nature, Vol. advance online publication (01 November 2009) Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. Because many drug–target combinations exist, it would be useful to explore possible interactions computationally. Here we compared 3,665 US Food and Drug Administration (FDA)-approved and investigational drugs against hundreds of targets, defining each target by its ligands. Chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations. Thirty were tested experimentally, including the antagonism of the 1 receptor by the transporter inhibitor Prozac, the inhibition of the 5-hydroxytryptamine (5-HT) transporter by the ion channel drug Vadilex, and antagonism of the histamine H4 receptor by the enzyme inhibitor Rescriptor. Overall, 23 new drug–target associations were confirmed, five of which were potent (<100 nM). The physiological relevance of one, the...
- Yann Abraham
Question of the day: How do you calculate standard deviation for fold change values?
Is your fold change normally distributed? what do you need the sd for?
- Yann Abraham
The question is whether you can calculate standard deviation for fold change values if the groups you compare are not matched.
- Berci Mesko, MD
So you are considering the ratio of values derived from 2 unmatched populations, like testing 2 populations with different treatments? In that case I would use an ANOVA rather than working with the ratio... or did I miss something?
- Yann Abraham
One group of controls and one group of diseased patients.
- Berci Mesko, MD
Ten Simple Rules for Searching and Organizing the Scientific Literature - http://www.citeulike.org/user...
Nature Precedings, No. 713. (16 October 2009) The exponentially increasing number of published papers (1.4 million per year by one estimate) makes it more and more difficult for us to manage the flood of scientific information. Each of us has acquired some protocol to find and organize journal articles and other references over the course of our careers. Most of those protocols are likely to have been formed by old routines or idleness rather than a structured approach to save time and frustration over the long run. Furthermore, with the Web 2.0 revolution, new ways of handling information are emerging (O’Reilly 2005). For example, traditional standalone tools for reference management like EndNote are being supplemented by centralized resources like RefWorks and social bookmarking sites as described subsequently. This fusion of personal and public information offers the promise of efficiency through better organization, which in turn leads to better science.How can seasoned scientists...
- Yann Abraham
Drug Discovery and Natural Products: End of an Era or an Endless Frontier? - http://www.citeulike.org/user...
Science, Vol. 325, No. 5937. (10 July 2009), pp. 161-165. Historically, the majority of new drugs have been generated from natural products (secondary metabolites) and from compounds derived from natural products. During the past 15 years, pharmaceutical industry research into natural products has declined, in part because of an emphasis on high-throughput screening of synthetic libraries. Currently there is substantial decline in new drug approvals and impending loss of patent protection for important medicines. However, untapped biological resources, "smart screening" methods, robotic separation with structural analysis, metabolic engineering, and synthetic biology offer exciting technologies for new natural product drug discovery. Advances in rapid genetic sequencing, coupled with manipulation of biosynthetic pathways, may provide a vast resource for the future discovery of pharmaceutical agents. 10.1126/science.1168243 Jesse Li, John Vederas
- Yann Abraham
Introducing Webel - A cheminformatics toolkit built solely on webservices - http://baoilleach.blogspot.com/2009...
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Cameron Neylon, Yann Abraham and Rajarshi Guha liked this
Nice!
- Yann Abraham
Y'a des Goldorak de 40 cm *avec la soucoupe* au rayon jouet chez carrouf' . Ils ne m'auront pas ! Ils ne m'auront pas ... peut-être... :-P
Yann Abraham liked this
avec la soucoupe?!? Voila pourquoi ma femme ne voulait pas me laisser aller faire les courses!
- Yann Abraham
Increasingly unconvinced that wave is "what email would look like if invented today". Suspect that would be more like a feed reader.
D0r0th34, Yann Abraham, Michael Kuhn and Jan Aerts liked this
guess email will stay what it is for professionals while people will turn to facebook status updates instead
- Yann Abraham
or twitter, for that matter ;-)
- Yann Abraham
The whole niche of twitter, and I've heard this from many people, is to avoid the clutter and privacy invasion of Facebook
- Mr. Gunn
Design, synthesis and selection of DNA-encoded small-molecule libraries - http://www.citeulike.org/user...
Nature Chemical Biology, Vol. 5, No. 9. (02 August 2009), pp. 647-654. Biochemical combinatorial techniques such as phage display, RNA display and oligonucleotide aptamers have proven to be reliable methods for generation of ligands to protein targets. Adapting these techniques to small synthetic molecules has been a long-sought goal. We report the synthesis and interrogation of an 800-million-member DNA-encoded library in which small molecules are covalently attached to an encoding oligonucleotide. The library was assembled by a combination of chemical and enzymatic synthesis, and interrogated by affinity selection. We describe methods for the selection and deconvolution of the chemical display library, and the discovery of inhibitors for two enzymes: Aurora A kinase and p38 MAP kinase. Matthew Clark, Raksha Acharya, Christopher Arico-Muendel, Svetlana Belyanskaya, Dennis Benjamin, Neil Carlson, Paolo Centrella, Cynthia Chiu, Steffen Creaser, John Cuozzo, Christopher Davie, Yun Ding,...
- Yann Abraham
A Quick Guide to Organizing Computational Biology Projects - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 5, No. 7. (31 July 2009), e1000424. William Noble
- Yann Abraham
*despairs* ...especially on reading the para 'The trouble w/ a 'scientific' argument...' http://www.dailymail.co.uk/debate... h/t @bengoldacre #NuttSack
Peter Ansell, Pierre Lindenbaum and Neil Saunders liked this
Terrific. The Mail has gone way beyond self-parody on this one. UK commentators are so going to enjoy dismembering them.
- Neil Saunders
Ouch, my head hurts, although I stopped reading after godwin point was reached
- Yann Abraham
Userscripts for the Life Sciences - http://www.citeulike.org/user...
Maxamad (Amazigh), Egon Willighagen, Mike Chelen and 4 other people liked this
BMC Bioinformatics, Vol. 8, No. 1. (2007) BACKGROUND:The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This pens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources.RESULTS:Several userscripts are presented that enrich biology...
- Yann Abraham
Yeah - I'd love to see a community building greasemonkey scripts for life-science sites - pubmed, citeulike, etc. Hell, maybe I'll start working on some...
- Chris Miller
@Chris what about Ubiquity?
- Yann Abraham
Chris: these look like a great place to start, the main project page is: http://sourceforge.net/project...
- Mike Chelen
With a Git repository with just the userscript stuff at: http://github.com/egonw...
- Egon Willighagen
nice, there may be so many scripts that it is easiest to work with as its own project
- Mike Chelen
Sweet.
- Maxamad (Amazigh)
Mike, that was sort of the set up in SVN too, which is why there still is userscript/trunk (though we never made tags of branches, which is why there is no matching userscript/branches or userscript/tags ...
- Egon Willighagen
How does the music-identifying app Shazam work its magic? - By Farhad Manjoo - Slate Magazine - http://img.slate.com/id...
Shazam doesn't only help an audience find music. Sometimes it helps music find an audience.
- Yann Abraham
Revolutions: REvolution Computing gets major funding, new CEO - http://blog.revolution-computing.com/2009...
Now isn't it... weird?
- Yann Abraham
Neil Saunders, Brian Krueger - LabSpaces, John Dupuis and 9 other people liked this
Awwwwwwwww.
- Bill Hooker
Congratulations Dr father Gunn
- Nils Reinton
Congratulations!
- Chris Lasher
Congratulations!
- Yann Abraham
Congrats William!
- Walter Jessen
So cute!
- Stephen Francoeur
Seriously, what's with the 30+ºC temperatures for the last weeks? It's almost November... Give Autumn a chance...
not much better here actually with tempartures around 0C #giveautumnachance #heidelberg
- Yann Abraham
My rough statistics show that Portuguese university professors check email every 1.5 weeks. In some cases, more seldom. :P #fail
Pierre Lindenbaum liked this
Are they printing them to read them too?
- Yann Abraham
Could we have a list of google wave names somewhere so that I can figure out what Life-Scientists are on there?
Jeannette Høvring, Daniel Jurczak, Jason Winget and 20 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 or @gmail.com can't see any way to check :D
- Mike Chelen
is there any good way to import contacts? it seems to work through the google contacts system like gmail
- Mike Chelen
pengwen.not.penguin@googlewave.com
- Parvez Halim
Google Wave Add-on for Firefox at That Smith - http://thatsmith.com/2009...
Google probably isn’t going to be happy about this, but I present to you the first ever Google Wave Notifier… for Firefox.
- Yann Abraham
i don't have time for google wave, i don't have time for google wave, i don't have time for google wave
Claudia Koltzenburg liked this
better stop lying to yourself now: google owns you ;-)
- Yann Abraham
noooo, i have to resist (and do some work today, too) :)
- Endre Sebestyen
@yannabraham two days(?) after Egon sent the invitation.
then it sounds like something dodgy is going on on my side :-(
- Yann Abraham
I think @robsyme sent out my invitation two days ago, but haven't got the email yet either.
- Jan Aerts
Note sure I would like to see my e-mails replaced by #wave.
luddite :)
- Frank
did you have a chance to test it yet?
- Yann Abraham
Les soutiers de l'université http://www.lemonde.fr/societe... Quel commentaire sera le plus affligeant ? La compétition est serrée
Effectivement les commentaires sont, comment dire... enfin ca vole haut quoi!
- Yann Abraham
Ten Simple Rules for Chairing a Scientific Session - http://www.citeulike.org/user...
Khader Shameer liked this
PLoS Comput Biol, Vol. 5, No. 9. (25 September 2009), e1000517. Alex Bateman, Philip Bourne
- Yann Abraham
Le twitter de Martine - http://twittermartine.blogspot.com/
via @Julien89, toutes mes excuses ainsi qu'a @yokofakun
- Yann Abraham
ah bon ? moi ?
- Pierre Lindenbaum
To all those people asking about Wave invites a) I don't know if/how many we get b) please form an orderly queue :-)
bala chandar, Peter Miller, Mr. Gunn and 12 other people liked this
Since I have seen lots of people asking, but nobody offering, I conclude that the new invites haven't gone out yet. Has anybody actually received a new account today yet?
- Matt Leifer
i've seen someone tweeting that he has 8 invites. don't know if it was fake or not. now i start forming the queue :)
- Endre Sebestyen
Is this the queue :)
- Kubke
Are we forming the queue here then? If so, here I am :) Thanks! (allyson.lurena at that gmail email account)
- Allyson Lister
The BBC suggest that each account gets 5 invites (http://news.bbc.co.uk/1...), but I read on Techcrunch yesterday that each account got 8 nominations (not invites, merely suggestions...). There's obviously no definitive info out there. Anyway, if there's invites going, and this is the queue, count me in :) (sjcockell at googlemail)
- Simon Cockell
I saw some comment about release at 4pm BST but no idea where that came from or if it is accurate
- Cameron Neylon
Queuing...
- Yann Abraham
This totally reminds me about how I got my googlemail account. Consider me enqueued :)
- Dan Hagon
I hereby formally join THE Wave queue :)
- Graham Steel
queuing: bjhaugen@gmail.com
- Brian Haugen
Hi. rich.bradshaw at that gmail thing.
- Rich
Me? barton.michael@gmail.com
- Michael Barton
And me (but you already knew that...).
- Jan Aerts
I will queue belatedly, but hope for an account of my own :D dan.swan at the googleplexes mail servers
- Daniel Swan
Queuing up in orderly fashion.
- Jill O'Neill
queuing. this is like Wimbledon.
- Sarah Kendrew
guess I'll also get in line. google acct: michael.kuhn
- Michael Kuhn
Tapping foot in line: rvidal
- Ricardo Vidal
News is popping up everywhere that the invites are rolling out, but I do not believe it...
- Egon Willighagen
Invites for sale on ebay already...
- Ricardo Vidal
Lines right up: tseng.ben
- Benjamin Tseng
Waits patiently in line. wordsforliving@gmail.com
- Jannifer @wordsforliving
Crossing my fingers...brian.j.krueger@gmail.com
- Brian Krueger - LabSpaces
Those Ebay buyers are going to be sorely disappointed when they find that it's not an invite but rather a nomination, which I read a Google's way of saying "we'll know if you try to let in a SEO or spam account".
- Mr. Gunn
Ok - it looks like I have eight - can other people on the sandbox confirm numbers and we can see about dividing these things up. Also can anyone who got their own invite delete the comment above?
- Cameron Neylon
I can confirm 8 invites... which are really nominations, it seems...
- Egon Willighagen
Line gets crowded ;-) pls count me in: yar.nikolaev [] gmail.com
- Yaroslav Nikolaev
I make it 17 names above - and I've seen at least three other requests (Richard Akerman, Mike Ellis, David Bradley). So not sure how to do this. My inclination is to prioritise based on people who will be able to put some direct effort into building (but not necessarily coding) things.
- Cameron Neylon
Can I just check whether Bjorn, Andy, and others with sandbox accounts have any free invites?
- Cameron Neylon
Would it be worth getting those interested in obtaining accounts to write a short abstract (say 100-200 words) about the sorts of projects they'd use their account for?
- Dan Hagon
According to http://twitter.com/larsras... no more invitations are being processed until tomorrow (Sydney time)
- Nick Lothian
To all those wondering what is going on here - we are trying to coordinate the invitations we have with the people who want them. Its a bit of a slow process.
- Cameron Neylon
Yes, Jan. There's a wave weve set up for tracking who's got them and who still needs them. Everyone from this thread (that I know - please don't spam this thread ;-)) has been added.
- Mr. Gunn
Since I haven't heard from Google, yet, I'll place myself in this queue for Wave invites. First name, last name, gmail. Thanks for organizing the process.
- Chris Lasher
Cameron - Thanks for your efforts to match requests to invitations. Hopefully there'll be enough to go around for everyone on this thread who asked for one. Btw, because I didn't mention it above, my gmail account name is axiomsofchoice.
- Dan Hagon
Jan, Wave makes the communication faster and more efficient in some ways but it doesn't help that much for human processes - like making difficult decisions. Also as far as I am aware the invitations I haven't sent haven't actually flowed through the system yet so you're not missing anything as yet...
- Cameron Neylon
Oh, I'll add myself late to the list. rni.boh at gmail (you know the rest...).
- Bob O'Hara
Would like to add myself to the queue as well ;-)
- bala chandar
I would like to add my name to the list too - mhanwell at gmail if there are any invites still out there.
- Marcus D. Hanwell
I have now been nominated for an invite (it's "in the mail"), so I've removed my comment above. Thanks @robsyme !
- Andrew Perry
I got mine too. Thanks
- Deepak Singh
Got an invite as well today, and removed my comment above. Thanks anyway.
- François Dongier
I disagree http://twitpic.com/jyhjx RT @gregtyrelle #Excel is the universal data analysis tool in science
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Michael Kuhn, Christopher Fields, Greg Tyrelle and 15 other people liked this
that picture has made my Friday
- Simon Cockell
I have seen this in real life, and when I offered to write a script to do it faster and quicker, that you could re-use again, the response was, "but why?
- Frank
which also reminds me of someone who was checking 7 different websites every week getting upto date information a certain identifier. When asked, if I wrote you a workflow to do the checking automatically and only alert you when the information you are looking for has changed, do you think that would be useful?, the response was "No, I do not".
- Frank
LOL - fantastic!
- Daniel Swan
Best picture I've seen all week.
- Chris Miller
ROFL!
- Yann Abraham
I stand corrected :) I haven been sent a word file with sequence data for a while. Must be the realization that pdf files are better for that kind of thing...
- Greg Tyrelle
Today's story: Bike meets car. Car smashes bike.
where you on the bike or in the car?
- Yann Abraham
on the bike, naturally.. :-)
- Daniel Jurczak
from a fellow cyclist to another fellow cyclist: Ouch! hope you are fine?
- Yann Abraham
I am, rented bike is not.. however, the old lady who ran the red light and hit me took care of everything..
- Daniel Jurczak
Improbable Research - http://improbable.com/ig...
Cass Johnston liked this
Priceless!
- Yann Abraham
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
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