Marcin › Likes

There has been quite a lot of literature in recent years about why classification schemes such as SCOP and CATH present a skewed view of protein space. While these classification schemes can be very useful, they do present a picture of "fold continents" and "superfamily countries" that are separate from one another, while protein space seems to be more continuous. So I'm not sure the number of SCOP categories vs. time is the best way to address whether "Protein Space is Still Ripe For Exploration". - Mickey Kosloff

Continuing sushant's line, an additional question that arises is how "continuous" is fold space, that is, is there a series of intermediate (stable) folds between each two folds? Works from Ron Elber's group (http://www.ncbi.nlm.nih.gov/pubmed... and more recently http://www.ncbi.nlm.nih.gov/pubmed...) show that certain folds are 'sinks' and slight sequence variations can... more... - Nir London

"Whereas the first human genome cost $3 billion and took more than a decade to produce, Illumina charges $48,000 for the kind of sequencing Close got." - Mike Chelen from Bookmarklet

thanks. :) - Michael Kuhn

Well done! - Konrad Förstner

Nice indeed..... - Graham Steel

Graham - if there ever was an abbreviation subject to miscommunication that would be it :) - Jean-Claude Bradley

Now I just have to attend - Deepak Singh

it is important to make a distinction between Free Access Beer and Open Access Beer: http://tinyurl.com/qfrvvd - Bora Zivkovic

Feedback request. I try to make a visual overview of my experience so far and my future plans. Any comments regarding both, visual side and scientific/career side really appreciated. - Pawel Szczesny

it's a great idea, it looks great, and it's a great way to have a quick overview of your competences! congrats! - Adrien Joly

Chemspider, Talis Connected Commons, Neurocommons... - Cameron Neylon

Cameron: AFAIK all providers allow publication of derivatives (web and trad. print) but with onerous provider specific constraints. However, the common format for derivatives is jpg. This degrades the data structure in the imagery and means that re-users can not conduct reconstructive image analysis. Discussed this in a paper here: http://www.univie.ac.at/aarg... - Ant Beck

mammalian genomes have been losing mobile DNA elements since the kt extinction. Connection to extinction somewhat tenuous but interesting. - Iddo Friedberg

"...Gert Vriend at Radboud University Medical Centre in Nijmegen, the Netherlands, and his colleagues are writing software that they hope will eventually automatically re-refine, at the click of a mouse, all the data deposited in the PDB." - Wladimir Labeikovsky

:-) A lot of the work I did in grad school was done using WHATIF. Wonder how much he's added on to it in the last decade - Deepak Singh

Thank you for interesting news. - Marcin

"University College London (UCL) has become the latest institution to adopt an open-access publishing policy, adding to a rapid increase in such mandates over the past year." - Björn Brembs from Bookmarklet

Too much to think about to respond sensibly at moment but just one point is that there are two issues, one is the technical issue - can it be managed legitimately - and the other is the social confusion issue - how many people do you lose because they assume that you're not allowed? I would certainly make the assumption that I can't mix CC-BY, GFDP, and oDBL together so would walk away.... more... - Cameron Neylon

Required reading for anyone interested in Open Data. I would still say PDDL/CC0 makes things simpler by removing all question, but I *think* you may be right about clean interfaces making PDDL/CC0 not strictly necessary. - Bill Hooker

comment = {Found via a search in PLoS Biology for "kinesin." I only read the abstract but learned that Tetrahymena has two nuclei--one for sexual reproduction (MIC) and one for gene expression (MAC). This is fascinating to me, and hopefully someday I can learn about it. At this point, I have no idea what benefits this could have for the organism. I also wonder how it impacts DNA damage repair and genome stability. } PLoS Biol, Vol. 4, No. 9. (29 August 2006), e286. The macronuclear genome of Tetrahymena thermophila is sequenced and analyzed. Conservation in this single-celled ciliate of some features normally observed in only multicellular organisms sheds light on early eukaryotic evolution. Jonathan Eisen, Robert Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer Wortman, Jonathan Badger, Qinghu Ren, Paolo Amedeo, Kristie Jones, Luke Tallon, Arthur Delcher, Steven Salzberg, Joana Silva, Brian Haas, William Majoros, Maryam Farzad, Jane Carlton, Roger Smith, Jyoti Garg,... - Steve Koch

great, embedded wolfa looks great - Abhishek Tiwari

@Neil: regarding the exisence of core miciobiome: see http://bytesizebio.net/index... Jeffrey Gordon from WashU claims that there isn't much of a core micriobiome, at least for the gut. - Iddo Friedberg

"They bought minicows -- compact cattle with stocky bodies, smaller frames and relatively tiny appetites. Their miniature Herefords consume about half that of a full-sized cow yet produce 50% to 75% of the rib-eyes and fillets, according to researchers and budget-conscious farmers. "We get more sirloin and less soup bone," Ali said. "People used to look at them and laugh. Now, they want to own them." In the last few years, ranchers across the country have been snapping up mini Hereford and Angus calves that fit in a person's lap. Farmers who raise mini Jerseys brag how each animal provides 2 to 3 gallons of milk a day ... one animal needed less than an acre for grazing. Because the minicows could be grass fed, the couple were spending at least half the amount on feed than they would have on regular-sized animals. The minicows also reached their mature weight faster, so they could be sold for meat sooner." - Paul Buchheit from Bookmarklet

I think this is the sort of cow that White Castle uses for their little burgers. - Gabe

Congrats Pedro - nice work! - Jason Stajich

Congratulations! - Ruchira S. Datta

"Ever wanted to see the entire conversation surrounding a post? Now you can! This simple bookmarklet will load comments from Twitter, FriendFeed, Digg, Reddit, HackerNews and any blog mentioning the article and will load it in a handy sidebar" - Andrew Perry

The example says: "could not retrieve results". - Björn Brembs

Must be a temporary outage .. it worked for me ~ 24 hour ago. - Andrew Perry

Our mission is simple: To enable the public to fund pilot research projects. Accomplishing this goal has immense benefits. First we're providing research funds to a whole new generation of researchers that are our future. Secondly we're walking the public through the scientific process, from grant writing to funding, all the way to the results. Finally we are creating an ecosystem for scientists to collaborate with each other as well as the public on shaping future research projects. Tags: science.funding Posted by: cwhooker - Bill Hooker

Cool idea, it'll be interesting to see how this grows - Brian Krueger - LabSpaces

"Brick by brick, Lego has been building its way out of the near bankruptcy it suffered around the turn of the century. It has done this by a seemingly simple strategy — making awesome product after awesome product. Now it is releasing the almost ridiculously fitting Architecture series, beginning with the Frank Lloyd Wright Collection, six planned sets including the Guggenheim in New York and Fallingwater, the iconic cantilevered waterfall-house outside Pittsburgh, Pennsylvania." - Shirley Wu from Bookmarklet

mmm I'm notionally on holiday - this may require some negotiation... - Cameron Neylon

Website is due to go live Tuesday, after the bank holiday. There's barely enough funding for the conference itself -- there will be a small registration fee, and they didn't pay me anything last year! - Richard P Grant