Andrew Su › Likes

Oh, now that's an interesting idea, Karen. - Graham Steel

I'd like something similar for the review process. Instead of having to register for each journal/publisher managing logins and passwords for each, have a clearing house that manages reviewer information that the journals subscribe to. - John Hogenesch

"extremely normal in all respects"--doubt this phrase would appear in anyone's recommendation nowadays. :) - Ruchira S. Datta

You owe me 30 min Paulo. That's how long I just wasted, without even realizing it, reading letters on the linked site. :-) - Bill Hooker

Yeah, i "liked" for the linked site (not reddit, obviously). One for the feed reader. - Neil Saunders

Much more interesting than the traditional approach, which seems to be a hybrid of the Microsoft and Google approaches. - Michael Nielsen

(ego) A while ago it was requested to use Open Access when possible to get the papers. After three of us tried to navigate the DOI, PubMed, and various publication systems we pretty much gave up on trying to figure out how to do it with all of the different systems and numbers. Enter another bioinformatician from CEPH, who not only partially solved the problem but shared his method, which I can use to accomplish something similar. - Pierre Lindenbaum

Genome Biology, Vol. 10, No. 11. (2009), R130. Online gene annotation resources are indispensable for analysis of genomics data. However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list. Here, we introduce BioGPS (http://biogps.gnf.org), a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform. Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, Serge Batalov, Christopher Hodge, James Haase, Jeff Janes, Jon Huss, Andrew Su - Neil Saunders

one of those authors seems familiar :-) - Neil Saunders

congrats ! Where will be your future job ? - Pierre Lindenbaum

How can I not like this :-D - Lars Juhl Jensen

In addition to "Literature, Sequence, Structure...", how about "Expression" with a link to BioGPS? just a thought... ;) - Andrew Su

Oh, that's terrific. - Neil Saunders

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,... - Neil Saunders

re transfer: if you are in human or mouse, you probably won't see so much transfer. but if you go to e.g. chimp, you'll see a lot of transferred evidence - Michael Kuhn

"For those who want to take a glimpse at where science and scientific discourse are going, take a look at some of the papers at this workshop" - Bill Hooker from Bookmarklet

several of the links are broken - this is the correct link to the Mons slides http://esw.w3.org/topic... - Jean-Claude Bradley

I'd really like to see that refactored as a collaborative Google Wave gadget. - Dan Hagon

@Neil: WikiPathways is intended exactly for that type of collaborative pathway creation. WikiPathways pathway format is based on, and developed in cooperation with, http://www.genmapp.org. So admittedly it's not a widely supported standard, but at least it wasn't a complete new invention. SBML / SBGN support is on its way. Re Google Wave: unfortunately, all this work predated Google Wave by several years... - Martijn van Iersel

The title is a bit generic, isn't this what Phil Bourne's been doing? - Ruchira S. Datta

That's awesome Mat! What would be the next step to processing our Ugi product library on the TDI kernel? - Jean-Claude Bradley

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

Better late then never ;-) - AJCann

I actually like the single loop in the video, falls well into place in a way :-) - Claudia Koltzenburg

"Also, in another subproject of the same grant, we plan to develop a JBrowse version of the GBrowse_syn synteny viewer developed by Sheldon McKay, so you can browse syntenic regions of homologous genomes side-by-side." definitely convinced me that a letter is in order. - Paul J. Davis

Thanks for posting! - Mitch Skinner

Cameron Neylon -- not as annoying as Scoble, but a great Friendfeed evangelist nevertheless - Benjamin Tseng

Jo's original post is here: http://tinyurl.com/ykq2yj3 Mine's coming on Monday. - AJCann

I think I am finally beginning to get my head round this. Got my self a desktop notifier, the iPhone skin for my itouch is really clear, picking up some new subscriptions and dumping my tweeters back into the twitterverse :-) - Jo Badge from iPod

[Image: "network" by Simon Cockell, link to original source for attribution] In particular, what are you using to view networks in a dynamic way? Cytoscape seems the behemoth for visualizing biological networks, but have you used other solutions? A group mate and I have been discussing how we could *really* use a JavaScript library that rendered as SVG in a web browser. This would allow us to call for more data from our databases and present data on the fly and only-as-needed. He's convinced we could start writing one; I'm concerned it's a lot more difficult than he thinks, but we're both fishing for other ideas. - Chris Lasher from Bookmarklet

Thanks, Chris! I certainly hope it enables some folks to do interesting science instead of just looking pretty, though. =) - Donnie Berkholz