Jean-Claude Bradley › Likes

That is a good point - the PubMed version of the article will take away from the article metrics. So we shouldn't take them too seriously but they are better than the dominant system in place right now. - Jean-Claude Bradley

I wouldn't say Ugi products form within minutes or seconds - at least the ones we do take hours or even days - Jean-Claude Bradley

I took that from a quote, "The exothermic U-4CR usually proceeds fast, within seconds or a few minutes at room temperature or below." from an article: Alexander Dömling, Ivor Ugi. Multicomponent Reactions with Isocyanides. Angew. Chem. Int. Ed. 2000, 39, 3181. I do agree with you that it does take longer than that for the product to precipitate. - David Bulger

interesting David - I don't think we are using unusual reactants - Jean-Claude Bradley

I am planning to use WebCite for my thesis. - 'Mummi' Thorisson

not that I know of Claudia - Jean-Claude Bradley

What do you want to store? Bits and bobs or lots of stuff? I use google doc for bits and prices dropbox is useful as it has an iPhone app. - Jo Badge from iPod

Anna -- I've also seen French tweets -- here's the product spec page: http://www.pogoplug.com/meet... -- voltage specs are "Power requirements: 100-240V, 50/60HZ" -- the rest relates to OS, internet, browsers, etc so should cross the ocean just fine. - Mickey Schafer

"Daniel Mietchen - Open Science Policy Director" Congrats, Daniel! - Mr. Gunn from Bookmarklet

You certainly got a point there but the site is indeed an umbrella platform for initiatives that go into very different directions, e.g. http://pyrn.ways.org/ and http://giraf-iffd.ways.org/ , and the parent site aggregates that content and provides the forum to discuss matters of interest across the different initiatives. - Daniel Mietchen

The basic structure for this part iii of the "what would X look like if invented today" series is in the mind map at http://www.mindmeister.com/3016825... , with background via http://friendfeed.com/search... . Main points: More flexibility in the models of funding, more attention to technological shifts in the way people (including scientists) communicate. Such has also been argued at http://ff.im/9GGRn and http://2020science.org/2009... . - Daniel Mietchen

thanks for the pointer, Daniel - Claudia Koltzenburg

1973 study of D2O on circadian rhythms. A good quote from introduction: "Many subsequent studies, the most important of which are those of Suter and Rawson (2) and Enright (3), indicate this effect of D20 is widespread: it lengthens r in unicellulars (1), green plants (4), isopods (3), insects (Caldarola, in preparation), birds (5, 6), mice, and hamsters (2, 5, 7, 8). The effect is clearly widespread and since no exceptions have been found in 12 cases, it is likely to be truly general. As several authors have noted, it therefore merits closer study as a potential clue to the physical nature of the cellular oscillation responsible for circadian rhythmicity." - Steve Koch

Thanks, Bora! - Steve Koch

"This result also provides the astronomers with a new, cost-effective way to search for planetary systems: by checking the amount of lithium present in a star astronomers can decide which stars are worthy of further significant observing efforts." - Andrew Lang

I wonder how much backlash they will get from students who really don't want to do it. - Jean-Claude Bradley

It is mandatory for the advisors - optional for the students. - Andrew Lang

thanks Andy - I didn't catch that - Jean-Claude Bradley

Interesting... that means that I find writing grant applications boring like ... well, that could be about right. Unfortunately, I cannot drop it... :( - Egon Willighagen

"We describe the system architecture and template design of "Scratchpads", a data-publishing framework for groups of people to create their own social networks supporting natural history science. Scratchpads cater to the particular needs of individual research communities through a common database and system architecture. This is flexible and scalable enough to support multiple networks, each with its own choice of features, visual design, and constituent data. Our data model supports web services on standardised data elements that might be used by related initiatives such as GBIF and the Encyclopedia of Life. A Scratchpad allows users to organise data around user-defined or imported ontologies, including biological classifications. Automated semantic annotation and indexing is applied to all content, allowing users to navigate intuitively and curate diverse biological data, including content drawn from third party resources. A system of archiving citable pages allows stable referencing with unique identifiers and provides credit to contributors through normal citation processes." - Mike Chelen from Bookmarklet

modules mentioned: leftandright http://drupal.org/project... biblio http://drupal.org/project... cck http://drupal.org/project/cck og http://drupal.org/project/og image http://drupal.org/project... imagex http://drupal.org/project... creativecommons_lite http://drupal.org/project... simplenews http://drupal.org/project... wysiwyg... more... - Mike Chelen

pretty slick - Jean-Claude Bradley

Two proposals for the Euroscience Open Forum 2010 have been submitted by Eurodoc and accepted on Nov 10, 2009: "What would science look like if it were invented today? " This will be a debate on how new communication tools such as wikis and other collaborative environments, blogs and microblogs can enrich scientific communication, how public post-publication peer review and contribution-based metrics can work. Special focus will be put on how young researchers can benefit from Open Access and Science 2.0 tools. More information on the topic can be found here. "New comparable data on young researcher's mobility patterns available: What are the consequences for European Research Policy?" This will be a presentation of the Eurodoc survey with special focus on mobility issues. In addition, Massimo Serpieri from the European Commission will report on other related studies. More information on the topic can be found here. Information on... - Daniel Mietchen

congrats Tony and Sean! very nice that's it is public - Jean-Claude Bradley

thanks for the link - I'm adding this under the compilation section of my cheminfo retrieval class http://getcheminfo.wikispaces.com/resourc... - Jean-Claude Bradley

fyi, I'm really enjoying these. There's no way I'd read through the registration list, but this way I get a good feel for who's coming. - Bill Hooker

Thank you. That's the idea: I assume many will not slog through the whole list, so this way, piecemeal, one gets introduced to everyone. - Bora Zivkovic

pq - "If the data obtained via crawlers and APIs can be used, only then does the lock-in of data go away. And, of course, the ideal foundation for such software is open source -- allowing users to publish and subscribe to information with as many data standards as possible. Some of these good fellows really exist". So the desire and necessity of gaining back control over data, or, as we Trekkies here dubbed it “Command your Data” is what will evolve the power of the open source idea into the cloud. - Graham Steel

How about an animated gif rotating it? - Ruchira S. Datta

Jmol has been up for discussion for a long time. I am not aware of any movement to support it at present. You might want to put the crystal structure hosted in Jmol elsewhere and make a link to it from the Wikipedia page rather than having it in the Wikipedia article itself. - Antony Williams

So, where can I get this from? - Noel O'Boyle

is it a commercial product? - Jean-Claude Bradley

doesn't look like it. Once again - look all you want, but no touching :) - Rajarshi Guha

Just caught this story on the way home -- audio not available until 3:00 EST (US) -- great conversation with biomedical researcher who was in grad school when he got called to Iraq -- returns with only part an arm, goes into prosthetics research. At end of interview (maybe 7 min in?) makes terrific statement on the lack of open data when the whole thing has been govt. funded -- and has a response to the "economically necessary" argument for propriety, commercial production. - Mickey Schafer

"November 10, 2009 When Marine engineer Jonathan Kuniholm returned to his industrial-design shop after a tour of duty in Iraq, one of his first projects was personal: He wanted to improve on the design of the prosthetics he'd been using since he lost part of his right arm in an ambush near Haditha. Kuniholm and his colleagues founded the Open Prosthetics Project, an open-source collaboration that shares its innovations freely." - Mickey Schafer

The new entries are listed in the Open Chemical Data room: http://friendfeed.com/openche... - Egon Willighagen

Earlier similar calls: http://ff.im/5s2Dc and http://ff.im/9hscn . - Daniel Mietchen

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

Personally, am not convinced of some of the assumptions, e.g. "...Both are unfortunate, but are parts of the current culture [reference to sharing early lab results]. Any network that hopes to succeed must adapt to the culture of the community, rather than trying to rewrite it." First, though likely rare, I think there are instances where culture gets "re-written" -- another perspective is that this form of communication provides an alternative to established routes. That is, does not replace them but adds to the diversity of communication means. - Mickey Schafer

were observations limited to sites specifically designed for scientists? perhaps to the exclusion of other significant mainstream platforms like facebook or twitter - Mike Chelen

"The problem was that I not only mistakenly assumed that students were already reasonably tech-savvy; I also made the mistake of thinking that poking around a site’s instruction pages and/or support forums (if they ran into trouble) would be a natural thing for them to do. It isn’t." - Rich Apodaca

it actually looks like a toe - Jean-Claude Bradley

My mistake Egon about the confusion with the book - yes we have one coming out soon. As for help with adding data from the Seidell book I think we have most of the relevant compounds. And it would require a chemist to translate the way names were done back then - also much of it requires conversion between g/100g solvent or g/100g solution to molar, etc - Jean-Claude Bradley

Is it really that easy? http://www3.interscience.wiley.com/journal... - Andrew Lang

@Andrew... no, it's not that easy... it's that *difficult*... the problem is so complex, it's very hard to do better... - Egon Willighagen

"...once any area becomes an information technology, it starts conforming to the exponential curves of Moore’s Law..." - Andrew Lang

great post - if we can figure out a way to automate the execution of the DoSol sheet it should go exponential - that is our bottleneck right now - Jean-Claude Bradley

"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

Tags: lostart Posted by: cwhooker - Bill Hooker