Konrad Förstner › Likes

"There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia (http://www.getutopia.com) and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses: Blogs for biomedical science Biomedical Ontologies – OBO etc Project Prospect and the Royal Society of Chemistry The Chemspider Journal of Chemistry The FEBS Letters experiment PubMedCentral and BioLit [2] Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3] The Elsevier Grand Challenge [4] Liquid Publications The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it? The Semantic Biochemical Journal project with Utopia Documents [5] The review asks what advances these projects have made and what obstacles to progress still exist.... more... - Duncan Hull from Bookmarklet

Besides, how does it compare to the interactive ICM in PLoS ? http://ff.im/acHs9 - joergkurtwegner

mmmm - yes - the one thing that bothers me about this is basing it on ResearcherID I have to admit... - Cameron Neylon

"A proposed author ID system is gaining widespread support, and could help lay the foundation for an academic-reward system less heavily tied to publications and citations." - Pedro Beltrao from Bookmarklet

This looks closer to reality than ever. 23 organizations supporting the idea with plans to have working code within 6 months based on Thomson Reuters' ResearcherID. - Pedro Beltrao

Currently even two operating systems - Android and Chrome OS - which might become on at some point. - Konrad Förstner

Yes! At the Beagle Project we're always harping on this - it's a big problem - the 'icons' make people feel disconnected from the possibility of genius and alienate young would-be scientists. - Karen James

The reverse also seems to be true - grant reviewers being alienated by the young guys' ideas. - Daniel Mietchen

Clever! Until I saw there are 1,371 pages to go through :-) Would be good if they would allow you to drill down from general types into more specific ones. - Jan Aerts

@Jan Yes admitedly this is not really useful at the moment, but if/when it gets indexed by google swirl, or when they put something similar together...? - Yann Abraham

Wow, that's really weird. - Ruchira S. Datta

What is strangest to me about this story is how did a supervisor get all the other authors to go with the fake results ? - Pedro Beltrao

I was introduced to it today. It allows interaction/liveblogging/commenting in a way similar to FF, but an advantage I see is that it can also aggregate tweets based on the hashtag, and these can get archived through a function called twapper that gets set up when one sets up the cloudspace. It is not open source at this time, but I am told that will be happening in the near future. I am not sure I can assess its functionality/advantages/disadvantages on my own :). I also don't see in it the ability for it to take in my feeds from other social network sites, but that might result in keeping the space of discussion cleaner. The space is by definition open, there is no option to create closed discussions within the site. My understanding is that it was created originally with funding from the UK goverment as an open collaborative educational tool. Any thoughts? - Kubke

I am sorry, my error. The cloud is the individual element (where the session liveblogging would be done). The cloudstream is the stream of clouds (it tells you what is happening within the cloudscapes you are following) - Kubke

"Number of efforts across the board, including chemistry and biology. The extreme side of the "open science" world is Open Notebook Science http://en.wikipedia.org/wiki... In general you are required to put enough into the methods section of a paper to be able to reproduce the results, but as the computational side gets more and more complex and supplementary data sets get bigger and more complicated, the need to make the raw data and (if possible) code available for people to reproduce the results becomes almost a necessity. A number of folks are thinking along the publishing side as well. Theres PLoS One (http://plosone.org) and Cell has been doing some very interesting prototyping on the "paper of the future". People have already mentioned JoVE and OpenWetWare. It will happen, but it's going to take a few years. Too many years of established practice." - Deepak Singh

Another point in the discussion: "Perhaps, in the case of data-intensive work, grants should be given in pairs: one research team gets paid to collect the data, and another team gets paid to analyze it." ( http://news.ycombinator.com/item... ) - definitely yes, though two teams may not be sufficient, so the allocation procedure should be flexible. Fundscience have stated that they plan something like this, but they still haven't started out yet. - Daniel Mietchen

Daniel - I can't see that working very well - most scientists I know want to analyze their own data at least to the extent that they are capable - let alone permit others to do so. An exception to that is where core competences of collaborators don't overlap. But I do see a future like that when machines publicly report their experimental results - Jean-Claude Bradley

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

For computational modeling to become more widely used in biological research, researchers must be able to exchange and share their results. The development and broad acceptance of common model representation formats such as SBML is a crucial step in that direction, allowing researchers to exchange and build upon each other's work with greater ease and accuracy. The BioModels.net project is another step: an international effort to: 1. define agreed-upon standards for model curation 2. define agreed-upon vocabularies for annotating models with connections to biological data resources 3. provide a free, centralized, publicly-accessible database of annotated, computational models in SBML and other structured formats - Pierre Lindenbaum

:) Server side code is there for a reason. - Lindsay is in 20-ten

drupal computed field http://drupal.org/project... allows raw php so there is no hard limit on what can be programmed - Mike Chelen

Doesn't seem to cover small molecules? Just yet another identifier and database to link to for every protein...? - Noel O'Boyle

I'll try to remember to ask Mark about that tomorrow... - Egon Willighagen

Steps of evolution :)) cool :)) - Özgün Çağrı AYDIN

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

I really like this paper. Breath of fresh air. - Cameron Neylon

Required reading for every grad student. - Bill Hooker

Scenarios like this shouldn't need to occur any more. We're working on an automated experiment. we have a sourceforge page for experimental and evaluation software and will publish everything in JoVE, together with a large base of sample data for testing and comparison. Anything important we missed? - Björn Brembs

How hard can it be? Everything is linked together by "in reply to...". - Neil Saunders

when I "like" something in Friendfeed, it goes to Twitter so I can share with the network there. When I use Twitter's RT, no one in my network sees it. Big difference. - Karoli

Pullquote: "How many species inhabit our immediate surroundings? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling." - Lars Juhl Jensen

Yes, absolutely. :) - Konrad Förstner

"Every weekday, thousands of researchers around the world access the Arabidopsis Information Resource (TAIR), which contains the most reliable and up-to-date genomic information available on the most widely used model organism in the plant kingdom. But now, to those users' horror, TAIR faces collapse: the US National Science Foundation (NSF) is phasing out funding after 10 years as the data resource's sole supporter (see page 258). TAIR's plight is emblematic of a broader crisis facing many of the world's biological databases and repositories. Research funding agencies recognize that such infrastructures are crucial to the ongoing conduct of science, yet few are willing to finance them indefinitely. Such agencies tend to support these resources during the development phase, but then expect them to find sustainable funding elsewhere." - Michael Nielsen

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

Blog post and github repository showing how to turn emacs into a very cool Rails IDE. - Neil Saunders

Superb - Rajarshi Guha

very good :) - Pedro Beltrao