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Yann Abraham › Comments
The iceman of Ladakh | Athar Parvaiz - China Dialogue - http://www.chinadialogue.net/article...
Never ever underestimate the cleverness of Man!
- Yann Abraham
Visualization of large microarray experiments with space maps - http://www.citeulike.org/user...
BMC Bioinformatics, Vol. 10, No. Suppl 13. (2009), O7. Nils Gehlenborg, Alvis Brazma
- Yann Abraham
Space Maps: Knowledge-Supported Visualization of Large High-Throughput Gene Expression Data Sets - http://www.citeulike.org/user...
In Intelligent Systems for Molecular Biology 2008 (July 2008) We have developed an interactive visualization method for gene expression profiles from high‐throughput gene expression data sets with hundreds to thousands of samples. Our method integrates biological knowledge in form of hierarchies derived from ontologies. A sample hierarchy is employed that describes the relationship of samples to each other and to ontology concepts. This information allows us to combine expression levels into biologically relevant aggregates and it enables the investigator to interactively control the amount of data presented. Samples are mapped to the sample hierarchy based on their description so that leaf nodes represent samples and internal nodes represent ontological terms. Based on this structure we can compute an average expression value for each gene and ontology term in the hierarchy. Each gene is visualized as a rectangular “gene map” similar to a tree map [1] whose structure is defined by...
- Yann Abraham
Getting Started in Text Mining - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 4, No. 1. (25 January 2008), e20. Bretonnel Cohen, Lawrence Hunter
- Yann Abraham
Visualization of genomic data with the Hilbert curve - http://www.citeulike.org/user...
Pawel Szczesny liked this
Bioinformatics, Vol. 25, No. 10. (15 May 2009), pp. 1231-1235. In many genomic studies, one works with genome-position-dependent data, e.g. ChIP-chip or ChIP-Seq scores. Using conventional tools, it can be difficult to get a good feel for the data, especially the distribution of features. This article argues that the so-called Hilbert curve visualization can complement genome browsers and help to get further insights into the structure of one's data. This is demonstrated with examples from different use cases. An open-source application, called HilbertVis, is presented that allows the user to produce and interactively explore such plots. Availability: http://www.ebi.ac.uk/huber-s... Contact: sanders@fs.tum.de Supplementary information: Supplementary Data are available at Bioinformatics online. 10.1093/bioinformatics/btp152 Simon Anders
- Yann Abraham
Should You Be Tweeting? - http://www.citeulike.org/user...
Cell, Vol. 139, No. 3. (30 October 2009), pp. 452-453. Twitter needs no introduction. This "microblogging" service has gained tremendous popularity in the 2 years since its launch. Yet, most scientists are steering clear of it. Laura Bonetta speaks to some who have found value in tweeting. Laura Bonetta
- Yann Abraham
How to visually interpret biological data using networks - http://www.citeulike.org/user...
Nature Biotechnology, Vol. 27, No. 10. (01 October 2009), pp. 921-924. Networks in biology can appear complex and difficult to decipher. Merico et al. illustrate how to interpret biological networks with the help of frequently used visualization and analysis patterns. Daniele Merico, David Gfeller, Gary Bader
- Yann Abraham
BioMart Central Portal--unified access to biological data. - http://www.citeulike.org/user...
Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), pp. W23-27. BioMart Central Portal (www.biomart.org) offers a one-stop shop solution to access a wide array of biological databases. These include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase and PRIDE; for a complete list, visit, http://www.biomart.org/biomart.... Moreover, the web server features seamless data federation making cross querying of these data sources in a user friendly and unified way. The web server not only provides access through a web interface (MartView), it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services. The website is free and open to all users and there is no login requirement. Syed Haider, Benoit Ballester, Damian Smedley, Junjun Zhang, Peter Rice, Arek Kasprzyk
- Yann Abraham
"Il y en a assez de l'obscurantisme scientifique" Malheureusement, ce n'est pas du second degré ... http://actu-chretienne.blogdirigeant.com/2009...
Pierre Lindenbaum liked this
au secours...
- Yann Abraham
Bon, ça colle, mais ce n'était pas le lien que je voulais mettre, je me suis gouré d'onglet !!!!!
- Tom Roud
heard about the airport scene in Modern Warfare 2 on @buzzoutloud and obviously had to check it out. pretty sick indeed http://www.youtube.com/watch...
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This reminds me of the beach scene at the end of Broken Angels.
- Alexander Kruel
I'm missing a "not like" button in FF. Appalling.
- Pierre Lindenbaum
@Pierre A lot of people watched this movie and liked it: http://www.heatvisionblog.com/2009...
- Alexander Kruel
This would probably be a good James Bond movie, but to me the point of a game is to have fun and this is... not (at least it is a bit too realistic and twisted for my gamers' taste)
- Yann Abraham
Using R in Taverna: RShell v1.2 - http://www.citeulike.org/user...
BMC Research Notes, Vol. 2, No. 1. (16 July 2009), 138. BACKGROUND:R is the statistical language commonly used by many life scientists in (omics) data analysis. At the same time, these complex analyses benefit from a workflow approach, such as used by the open source workflow management system Taverna. However, Taverna had limited support for R, because it supported just a few data types and only a single output. Also, there was no support for graphical output and persistent sessions. Altogether this made using R in Taverna impractical.FINDINGS:We have developed an R plugin for Taverna: RShell, which provides R functionality within workflows designed in Taverna. In order to fully support the R language, our RShell plugin directly uses the R interpreter. The RShell plugin consists of a Taverna processor for R scripts and an RShell Session Manager that communicates with the R server. We made the RShell processor highly configurable allowing the user to define multiple inputs and...
- Yann Abraham
should I go climbing tonight, and then tomorrow to make it 3 in a row, that is the question
climb Ian, climb (the wall is calling you)
- Yann Abraham
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...
Fulaan, inna Hebel, 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.
- Fulaan, inna Hebel
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?
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
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