Yann Abraham › Likes

Makes me think "I want a pet octopus ! I could teach it tricks". And then rethink with "Nah, just let 'em do their thing in the ocean". - Andrew Perry

They're quite playful creatures. If you happen on one while diving and offer your hand, they'll often grab it and wrap around it. Not a great survival strategy perhaps... - Neil Saunders

Did you have a look at Law's Laws? (from Andy Law, my ex-boss) http://bioinformatics.roslin.ac.uk/lawslaw... - Jan Aerts

Yeah, good stuff and familiar to us all :-) - Neil Saunders

Usually the inventor, and on first release... - Chris Rusbridge

If I have my story right I think this came out of a criticism from a review panel that the structures and computational bio department was not collaborating enough. They came up with the mycoplasma collaboration that Luis Serrano in particular was very excited about. 3 science papers is not a bad way to show results :). I still have to read them. - Pedro Beltrao

News and Views at MSB: http://www.nature.com/msb... - Pedro Beltrao

Editor's choice at Science Signalling http://stke.sciencemag.org/cgi... - Pedro Beltrao

Is there no end to the horror of the buzzword-ome? - Bill Hooker

So, should we come up with a new buzzfix then? So far, we had 'science', 'omics', ... who knows what next... I'm betting on complexity... so, proteoplex, bioplex, chemplex, metaboplex, ... not merely the individuals, but also the complexity between them. - Egon Willighagen

I like the complexity angle - we should register all those domain names - Jonathan Eisen

Call me cynical, but I think they've got it the wrong way around. - Neil Saunders

You know, there are funny parallels with drug discovery biology here, as well. More often, we're seeing new technologies come from startups (which come from an academic background) and not from established programs at larger companies. Is there enough of a market for short, clever bits of code that you could support a startup model in bioinformatics? - Mr. Gunn

Pete Sefton has some significant criticisms of the Wave document model - Cameron Neylon

I hope the #Google #Wave developers are listening... - Egon Willighagen

Aim to feed some of this in - or at least get some answers - we also have some other significant issues that need to be solved so will try to make a list soon. - Cameron Neylon

This is totally amazing! Need to get my hands on one of these programs and render! - Björn Brembs

Some of them look organic. - Andrew Lang

No contemporary communication paradigms function really well on it. And that's a Bad Thing. Sure it's "like" email, sure it's "like" IM, sure it's "like" Google Docs, but as the combination of all of those, none of those ways of thinking about it work effectively. I can't imagine it appealing to anybody but a very small portion of people on the net. And that's a Really Bad Thing. - Chris Lasher

You've got a point there, Cameron. Much of the criticism I hear about Wave is really just criticism of the knocked-together client. Not much interesting is going to happen with Wave until the serious developers start playing around with it and putting some really good stuff together. Whether or not that'll happen is yet unknown, but Wave is a pretty cool tech from a protocol standpoint.... more... - Mr. Gunn

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site http://www.Flickr.com and the bookmarking site http://www.CiteULike.org We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We... more... - Duncan Hull

Full paper available on the arXiv: http://arxiv.org/pdf/0905.0976 - Duncan Hull

I wonder how that has changed in the last, say, 100 years. Obviously it's higher now, but by how many orders of magnitude? - Chris Miller

His actual words: if you did nothing but read your whole life, you'd process 2GB text. Puts big data in perspective. - Neil Saunders from fftogo

Many of you know I've been working with Mendeley as a sort of ambassador/community liaison. I started this because I've always felt a little shut out from contributing to open science/open access/open data because I don't work for a publisher, don't really write code, and wasn't in a job where I could openly share data. This was a way to influence how things develop by promoting the people who "get it". - Mr. Gunn

Yes, I got the one you sent and I really appreciate it. I do plan to follow up when I get back into town. - Mr. Gunn

For the lazy people, just go directly to the action: http://bit.ly/4DXwZv - Lars Juhl Jensen

Maybe the fire truck had nothing to with the accident. Maybe grandma saw the Google Street View car and go so excited that she fell on her bicycle ;-) - Lars Juhl Jensen

Send me an email if you like one. - Egon Willighagen

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

love! - Ashwin Bharambe

I didn't like Computer Modern or Times. I used Century Schoolbook for my stuff, I think (\usepackage{newcent}). - Amit Patel

what's Eclipse? - laura

I've learned Java with eclipse. The editor, the code completion, etc... make the learning Curve exponential. - Pierre Lindenbaum

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 do better using these tools and those newer... more... - Duncan Hull