Pedro Beltrao › Likes

Nucl. Acids Res. (9 November 2009), gkp944. Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by docking techniques. Current database version (August 2009) contains 25 559 experimental and modeled 3D structures for 771 organisms spanned over the entire universe of life from viruses to humans. Data are organized in a relational database with user-friendly search interface allowing exploration of the database content by a number of parameters. Search results can be interactively previewed and downloaded as PDB-formatted files, along with the information relevant to the specified interactions. The resource is freely available at http://gwidd.bioinformatics.ku.edu. 10.1093/nar/gkp944 Petras Kundrotas, Zhengwei Zhu, Ilya Vakser - 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

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

LOL! - Christian (Simply X)

"It’s really gratifying to see the social discovery of science generated by the simple act of keeping your references public on a Web page." - Duncan Hull

Replied on the blog but will try to give this a go ASAP...but probably not today... - Cameron Neylon

Thanks Cameron. That would be very much appreciated. I made a fair bit of progress yesterday - it's a case of sticking applets within Gadgets. It now pretty much works. However, the applets periodically, and mysteriously, disappear. Any debugging tips from anyone?!? - Neil Swainston

With mentions of @phylogenomics, @girlscientist, @sciencebase and @dgmacarthur - Noah Gray from Bookmarklet

Yes, Maxine, he certainly has. He didn't link to the earlier posts, but he used to be quite firmly in the "blogging is a waste of time, now get back to the bench" camp. - Mr. Gunn

it's either a huge increase or huge decrease in the open access fee for nature publishing, depending if you consider their old price to be infinity or zero :D - Mike Chelen

See, this is one of the reasons I like FriendFeed so much. The "like" does so well what the "re-tweet" does so poorly. - Chris Lasher

A clean restful API with reasonable limits. Don't make it too opaque and restrictive - Deepak Singh

Hi everyone, I'm a Product Manager that works for Rafael. Curious to hear your thoughts on if you have a search and query API for our SD or Scopus content, what is a max number of results you'd like to receive to build a good app? Are there any APIs from our content you'd really like? - Michelle Lee

The university has also dismissed 3.2% of its non-faculty workers. The value of the endowment dropped 27% in the fiscal year ending Aug 31. - Hilary

Yes, we do that. Quite a bit. :) - D0r0th34

Yes, yes. Very much like. - Neil Saunders

Very nicely summary of the problem. Really, the whole concept of a journal article about software is stupid. What does an academic article do? Alert people to a new finding/discovery. But in the case of software - well, the software is the finding. And people are "alerted" by finding it on the web, downloading it and using it. As Bosco says, the sole role of an article here is a CV tick - hence the hybrid approach. Non-academic programmers must find all of this very odd. - Neil Saunders

Hopefully nobody takes this too seriously - as it's offensive. - Louis Gray

There's got to be a joke about the social media term of "followers" here, somewhere. - Steve Lynch from twhirl

"So, I’ve just started a new job and moved home. There is loads to blog about but little time to do it. Before it’s too late, here are some first week impressions from a newbie starter at the European Bioinformatics Institute (EBI) on the Wellcome Trust Genome Campus. The Genome Campus owes its existence to the pharmacist Henry Wellcome, pictured over on the left. When he died in 1936, his legacy founded the Wellcome Trust, set up with money from his success as a pharmaceutical manufacturer and salesman. Today, the trust is the largest charity in the UK, funding innovative biomedical research and spending over £600 million each year. A large part of this legacy is being (and has been) spent on the Wellcome Trust Genome Campus, home to the Wellcome Trust Sanger Institute (WTSI) (aka “The Sanger”) and the European Bioinformatics Institute (EBI) an outstation of the European Molecular Biology Laboratory (EMBL) based in Hinxton, Cambridgeshire. Cambridgeshire life: Good and Bad It’s a bit... more... - Duncan Hull from Bookmarklet

Continued....Hmm. I wonder if a goatee beard (bristles not shown) counts for Movember? Fav comment from folks at work today was "Mr Steel, what is that thing on your face?" You up for a Movember challenge, my good fellow ?? - Graham Steel

Scientists are all about doing new things but actually we're very conservative about the way that we do them," said Cameron Neylon - Frank

BBC: British Broadcasting Cameron (neylon) - Duncan Hull

Jmol (the applet, application, and embedded in Bioclipse) - Egon Willighagen

pymol or rasmol are my *favorites* although jmol has a dear place for being a web-based utility - Mike Chelen

Mark Pilgrim's excellent book "Dive Into Python" was republished on Amazon.com, under the terms of his GNU Free Documentation License. This is driving his publisher nuts. I'm surprised it doesn't happen more - why aren't books by Doctorow, Lessig et al immediately republished by other publishers? - Michael Nielsen

@Matt: I really like your idea. In some sense, every open content license is transitional, pending even more openness, so I agree that such compromises can help. That's part of the genius of CC in the first place, after all. Before CC, there were very few gradations in pre-written licenses; you could go all rights reserved, BSD-style or GFDL, and that was about it. Now, you can specify if attribution is needed, if derivative and commercial uses are OK, etc., and I think we are far more open for the options. - Christopher Granade

cool idea: a wedding gift w/ built-in GPS: it'll only open at a specific location, and it only tells you the distance to wherever that is - Michael Kuhn from Bookmarklet

Genius. "At one point a friend of the family, a charming gentleman from up the street, said to me with a thick accent, “You are — how you say in English? — a BASTARD!” That one comment made this whole project worthwhile." - Bill Hooker

(e) technobabble! - Jan Wessnitzer

Thanks for the comments and the links :) Agreed about the goatee. I don't mind the technobabble, since it does provide some laughs and doesn't generally get in the way of the stories. (In particular I like the occasions where someone proudly explains that they used a recursive algorithm to do something -- news which is received with awe from the other characters...) - Mark Longair

"Making the Right Moves: A Practical Guide to Scientific Management for Postdocs and New Faculty" (should the time ever come) - Michael Kuhn

It is a very interesting read. I received a copy from HHMI last year. - Khader Shameer

Definitely an essential read - the questions to ask when interviewing candidates to hire is really helpful. - Jason Stajich