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Science 2.0

Science 2.0

For people interested in Science 2.0 and Open Science, especially the use of online tools to do science in new ways.
Daniel Mietchen
A possible way to go global (>7 countries) with some Open Science projects (be this blog 3 descendants or a reform of the peer review system)? Source: European Science Foundation. Largest drawback: They foresee 15 months for the review process, not really the time frame for _supporting_ innovation. Deadline for proposals: Oct 22, 2009. - http://www.esf.org/activit...
"An ESF Research Networking Programme is a networking activity bringing together nationally funded research activities for four to five years, to address a major scientific issue or a science-driven topic of research infrastructure, at the European level with the aim of advancing the frontiers of science." - Daniel Mietchen via Bookmarklet
Good grief, 15 months of review. This sounds like a possible way for a big open science consortium to be funded - if one can strip away the typical EU verbiage. I could represent Australia (where we have our own funding), but we'd just then need "Canada, China, Israel, Japan, Korea, Russia, USA and others". - Matthew Todd
in 15 months we could be past the singularity already :) - Jean-Claude Bradley
I'm all for it! Let's do some brainstorming! - Björn Brembs
OK, http://etherpad.com/pqDktXauOD is ready for brainstorming to start. - Daniel Mietchen
Additional development of interdisciplinary research methods would be useful, particularly if there is a focus on the learning and sharing aspects. - Mike Chelen
made a few comments and quickly skimmed the call. No harm in working something up though - we could use some of the old network proposal we wrote a year or ago...http://docs.google.com/View... - Cameron Neylon
Bah, I meant to say - it would be a good thing to start putting together some of these - if nothing else we can re-use the text until some of them get funded. Wasn't meaning to be negative. - Cameron Neylon
Cameron: advocacy for data repository, semantic publication, and community commenting could be influential and interesting - Mike Chelen
It might be interesting to see if writing this in public would get the attraction of funders with shorter review periods. - Daniel Mietchen
Daniel: :-) witty witty, drop them a line - Claudia Koltzenburg
Bill Hooker
"Via web application software, data citation standards, and statistical methods, the Dataverse Network project increases scholarly recognition and distributed control for authors, journals, archives, teachers, and others who produce or organize data; facilitates data access and analysis for researchers and students; and ensures long-term preservation whether or not the data are in the public domain." - Bill Hooker via Bookmarklet
More of a checksum though (just thinking lots of very nig data sets coming)? And wouldn't it be better to piggyback on a DOI at least (e.g., http://DOI_stem/your_extension)? - Chris via twhirl
Regarding DOIs: any connection here to the STD-DOI project for archiving primary datasets and assigning DOIs to them to make them citable? Example dataset citation: Kamm,H; Machon, L; Donner, S (2004): Gas Chromatography (KTB Field Lab), GFZ Potsdam. doi:10.1594/GFZ/ICDP/KTB/ktb-geoch-gaschr-p (from http://www.std-doi.de) - 'Mummi' Thorisson
Absolutely I'm campaiging for it myself (not this specifically though I was very pleased to stumble on it) -- just gave this (http://tinyurl.com/nvyb57) talk at ISMB on Thursday (just the last couple of slides are the relevant ones). So I'm all for it and liked the mention of standards, just that DOIs are so close to being widely-enough used already that it seems a shame not to build on that. - Chris via twhirl
Meeting peopl efrom the British Library on Monday to talk about this very kind of thing and amongst the (MI) standards people and at www.rin.ac.uk we've been talking about it quite a bit -- the principle more than the exact mechanism, which for easy-bridging reasons seems to make sense as a kind of vestigial journal as a vehicle... - Chris via twhirl
@ Mummi, good lord that's rather interesting isn't it -- no relation to me at all no. The BL group I'm meeting also have a guy that's a big DOI advocate and his talk mentions some kind of euro registry? http://tinyurl.com/mkuhvq slides 6+ (DOIs) and 12+ (JRA) - Chris via twhirl
@ Mummi again btw the timeline and a little mistake (multi-threading mayhem) made my post immediately after yours a little odd-sounding. As I later said I've nothing to do with the German project I was speaking in another context. - Chris via twhirl
@Chris, sorry my bad, I was being unclear which didn't help! I meant to say earlier whether there was any relation between the Dataverse thing and the German (based/funded..?) international TIB project. - 'Mummi' Thorisson
@Chris Thanks for the PDF, very helpful to know about this JRA initiative which I don't know yet if is an extension/expansion of the TIB thing, or modelled after it. Will read property around this in PDF + elsewhere ! BTW I'm tangentially interested in this topic, from the perspective of genome-wide association study datasets and ways to archive them and cite them. - 'Mummi' Thorisson
Okay. I'll try to give a bit more info about the JRA thing once I have it. Incidentally, on association studies (QTLs too?) I ought to mention one of the projects we have registered at MIBBI for reporting QTLs and association studies: http://mibbi.org/index... - Chris via twhirl
Mike Chelen
"OSCAR3 (Open Source Chemistry Analysis Routines) is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries." - Mike Chelen via Bookmarklet
Berci Mesko
Top 20 Websites Every Scientist (or engineer) ought to know | Zangani - http://www.zangani.com/node...
"Top 20 Websites Every Scientist (or engineer) ought to know" - Berci Mesko via Bookmarklet
scienceblogs has interesting posts and provocative discussions - Mike Chelen
The person who made that list obviously has never used researchgate. - Brian Krueger - LabSpaces
Brian: is that not what it does, or does it not do it well? - Mike Chelen
Mike Chelen
"17th Annual International Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology The talk specific feeds will be created each day shortly before the start of the first presentation. Find talk specific blogs by searching here for the authors, the title of the talk or the talk identifier as given in the program (like HL03 for the 3rd Highlight paper) The feeds can also be accessed on the conference pages in the according sections: SIGs, Keynotes, Proceedings Track, Technology Track and Highlights and the last few blogs are shown on our web-portal page." - Mike Chelen via Bookmarklet
Daniel Mietchen
Scientific findings in a digital world: What is the genuine article? at the British Library on 22nd July (18.00 - 20.30) - http://network.nature.com/groups...
"Looking Good on Paper The gold standard of the peer-reviewed scientific paper has barely changed in form since its inception over 300 years ago. However, with more and more scientists communicating research findings in digital format in many different ways does the notion of the scientific ‘article’ itself remain relevant? Is the traditional research paper still the optimal format for the dissemination of the outputs of scientific research? If not, what are the alternatives? Video Killed the Methods Section More and more scientific findings are ‘born digital’. The traditional format of research article is being transformed into a multi-media digital object with linked content, video, audio, datasets and reader annotation. This raises new possibilities and challenges. How should these newer types of content be peer reviewed? Are researchers really able to make the most of them? Does a link to a dataset or image always provide sufficient context to enable informed re-use or validation?... more... - Daniel Mietchen via Bookmarklet
Anybody planning on going there? They do not foresee live streaming but would allow microblogging. - Daniel Mietchen
I'm not sure that I can go - its a long (and expensive) detour on the way home... - Cameron Neylon via twhirl
Can't help you with the "long" part but I'm working on the "expensive" one. - Daniel Mietchen
Sounds like a great discussion! Sadly it is too far away for me. Does anyone know what the format is? It says that John Wilbanks will introduce the topic but doesn't say how the discussion will proceed from there. - Lisa Green
Up to five people who commit to microblogging from the event will have free entry. Please sign up here or let me know via email. - Daniel Mietchen
D'oh! I already registered :) Looking forward to it! - Fiona Bradley
Looking like I might be able to make it after all. Woot! - Cameron Neylon via twhirl
Steve Koch
The All Results Journal ... conversation revisit? http://friendfeed.com/the-lif... I received an email invite for SAB on the physics journal today. Found our old FF discussion from back when Shirley was invited (link above)...wondering if peeps have any updated opinions?
Bill Hooker
New (to me) blog: Social media for scientific, technical and medical communities, by Andrew Spong. - http://stwem.com/
Matt Leifer
Do any of the online reference management sites (e.g. Mendeley, citeulike, Zotero, etc.) has a usable and *well documented* API? I'm want to integrate reference management and sharing into my site and I don't want to reinvent the wheel. Also, how well does bibtex import/export work on these sites?
Hi Matt, we don't have a *public* API yet, but we're planning to introduce one. We'll also enable reference management/sharing my simply pasting some code into your side, much like embedding a YouTube video. Apologies if that info doesn't help you much for now! - Victor / Mendeley Team
I can't really tell you about usable APIs, but the bibtex features (export and import) seem to work really nicely on citeulike. Sorry I can't be of more help! - Allyson Lister
Zotero is a firefox browser plugin. References are stored in an sqlite db on your hard drive. Their api allows you to create additional Firefox plugins to extend its base functionality. I wrote a plugin to add an extra menu item that allows our users to export to our wiki...took about a day. It exports to bibtex if you want. If you're more advanced, you can just write SQL to read/write from the db, but that's obviously not recommended. - Fitzgerald Steele
Connotea (http://www.connotea.org/wiki...). Bibsonomy (http://bibsonomy.org/) also has an excellent API. - Euan
Thanks for the responses! - Matt Leifer
2Collab has an API, you could try emailing or tweeting them for more info http://twitter.com/2collab - Richard Akerman
Have you done any more work on this? I got a tweet follow up on this today...I'd love to hear about the approach you've taken.. - Fitzgerald Steele
I will send the 2collab API info. if you are still interested. - Michael Habib
Citeulike appears to have a rest based API if you can figure out what the necessary URLs are - Michael Barton
As far as I know, most of the sites/software have decent BibTeX export/import options. In any case, I'd just check the reference management comparison tables at wikipedia (http://en.wikipedia.org/wiki...) or Martin Fenner's Reference Manager Overview graphic (usually up-to-date) (http://network.nature.com/people...) - Ricardo Vidal
Somehow I missed all the responses after my initial thank you comment. I'm not actively working on this at the moment, but I am still interested in the available APIs. FYI, I would need an API that allows for upload of bibliographic records rather than one that just returns the results of search queries. - Matt Leifer
Mike Chelen
"The Eclipse Open Healthcare Framework (OHF) is a project within Eclipse formed for the purpose of expediting healthcare informatics technology. The project is composed of extensible frameworks and tools which emphasize the use of existing and emerging standards in order to encourage interoperable open source infrastructure, thereby lowering integration barriers. We currently provide tools and Frameworks for HL7, IHE, Terminology, Devices, and Public Healthcare Maintenance." - Mike Chelen via Bookmarklet
Daniel Mietchen
You can still nominate yours. - Daniel Mietchen via Bookmarklet
Great article! Thanks! - Gayle Jackson
Hmm, should really be called Rock Stars of Medicine though. - Matt Leifer
Andrew Andrew Maynard wrote an insightful blog about this on 2020 Science http://2020science.org/2009... - Lisa Green
Yes, Lisa, that's a good one. - Daniel Mietchen
technically, that's an insightful "post" on a usually also insightful blog, Lisa </pedant mode off> He does make some good points - science celebrity is of a different flavor that pop celebrity. - Mr. Gunn
Heh excellent point Mr Gunn! I am embarrassed by my sloppiness. That embarrassment should keep me on my toes. at least for a few weeks ;-) - Lisa Green
pedant, not peNdant. Notice how I'm not switching that mode off... :-) - Bill Hooker
yikes, Bill! There's gotta be a name for the phenomenon of making a stupid mistake while pointing out something about someone else(which I since corrected, in case you're wondering). If you're feeling biblical, you could call it the "beam-in-thine-own-eye' syndrome, I suppose. No worries, though, Lisa. I try not to point out things like that in general, but blog/blog post is the one thing that makes me twitch. - Mr. Gunn
Hilary
(7/22) John Wilbanks on 'Scientific findings in a digital world: What is the genuine article?' - TalkScience@the British Library: http://www.bl.uk/onlineg...
A discussion with John Wilbanks addressing: " * In an age of digital content and communication, does the notion of the scientific ‘article’ remain relevant? Is the 300-year old approach to structuring findings – from abstract to references – still valid in the era of the multi-media research object? * How should new types of content such as video protocols and embedded datasets be peer-reviewed, and does it matter? * Will opening access to the outputs of scientific research really improve innovation? * Does more access to research data and information necessarily mean we are better informed? * When it comes to communicating research findings, what are the fundamental building blocks and what is the wallpaper?" - Hilary
See also http://ff.im/4A4qx on this. - Daniel Mietchen
Cesar Sanchez
JACS Beta: testing ground for the ACS Publications web platform - http://pubs.acs.org/JACSbeta/
JACS Beta: testing ground for the ACS Publications web platform
Michael Nielsen
JISC (UK) and funding for new technologies in higher education - http://michaelnielsen.org/blog...
Interesting comment from Andy McGregor about UK funding for new technologies in higher eduction, thought it might be of interest to many here. Here's an excerpt: "I work for an agency in the UK called JISC (http://www.jisc.ac.uk) that is set up to support education and research in higher education by promoting innovation in new technologies. We fund a lot of innovation projects in the area of scholarly communication, and it struck me reading the post how much of the work we are funding relates to the points you make in your article We have funded 40 rapid innovation projects these are short agile projects that have just started and are designed to experiment and try out solutions to user problems, similar to start ups you mention in your post. A couple which sprang to mind as I read your post and are worth mentioning are a way to manage and publish data sets which uses a notecard metaphor: http://www.jisc.ac.uk/whatwed... and a way to use bayesian filtering... more... - Michael Nielsen via Bookmarklet
JISC is one of the most innovative funders in this space in the UK (or indeed internationally). I dislike the way and the mode in which they fund (very short notice calls, far too little money) but nonetheless they have imagination an actually act on it in a way that other UK research councils rarely do. I have the usual sour grapes from not getting things which I thought were important funded obviously but even so the idea of the Rapid Innovation call was very cool. - Cameron Neylon
How much is far too little money? - Michael Nielsen
tends to be limited to around £50k which isn't enough to employ a new person. Which means in turn that if you don't have local staff on rolling contracts that you can bring up then you can't play. Have been a couple of exceptions recently, but that was no good because they gave the money to something else. It can be a very difficult game to break into from the outside of the existing community. - Cameron Neylon
I wonder if you could talk with JISC about using the 50k to start spinoffs? YCombinator (Reddit, Backtype,Scribd and loads of other companies) typically starts companies with about 15k US, for 5-10% equity. The result is fantastically talented and motivated developers, with real ownership over the project (and thus determination to make it work). Of course, the money doesn't last long, but it's long enough to see if there's a there there, so to speak, and to attract further money. - Michael Nielsen
Perhaps, although startups isn't really their remit. They are more focused on infrastructure for higher education so projects often have to use pieces of previously funded services. Thinking more and more that the only way to get those kind of things started is to get right out of the academic sector. - Cameron Neylon
Hope Leman
Templeton Positive Neuroscience Awards Request For Applications http://www.posneuroscience.org/awards...
@Bjoern: includes grants for investigations into "free will"... - Bill Hooker
Noah Gray
Only 57% of medical research news reported on the front pages of newspapers referred to published studies - http://www.plosone.org/article...
From PLoS ONE; article concludes that "Medical research news should be clearly referenced and state the evidence level and limitations to inform the public of the maturity and quality of the source." Many (including myself) have been calling for this kind of disclosure for years...Astonishing that even after 3 yrs, almost 1/4 of the front page stories never passed muster in peer-review!!!!!!!!! - Noah Gray via Bookmarklet
Not surprising at all. A lot of the stories I've seen in MSM are "exclusive" access pieces. I guess that's the drawback of trying to get a story no one else has. - Brian Krueger - LabSpaces
Mike Chelen
Fwd: Citizen Scientists: Prof. Eric Paulos investigates ways to measure pollution with cell phones. More: http://www.pri.org/busines... (via http://friendfeed.com/carnegi...)
There are quite a lot of cell phone sensor network projects out there - I've been following the Urban Sensing project at UCLA for a while... http://urban.cens.ucla.edu/ - Hilary
Wonder if there are discussions between the different groups, either for direct collaboration, or to plan for interoperability of software and data. - Mike Chelen
I think Nokia is trying to address some of the interoperability questions through their SensorPlanet project: http://www.sensorplanet.org/ - Hilary
Ruchira S. Datta
Mike Chelen
Fwd: BOF: VizBi - Visualization of Biological Data 1pm Wednesday K1 (via http://friendfeed.com/ismbecc...)
Lasse Johnsen
Scientists kill cancer cells with trojan horse - http://www.reuters.com/article...
"Australian scientists have developed a "trojan horse" therapy to combat cancer, using a bacterially-derived nano cell to penetrate and disarm the cancer cell before a second nano cell kills it with chemotherapy drugs." - Lasse Johnsen via Bookmarklet
Ruchira S. Datta
Michael Nielsen
Is scientific publishing about to be disrupted? - http://michaelnielsen.org/blog... (via http://friendfeed.com/michael...)
Essay based on a talk I gave on June 11, 2009, at the American Physical Society Editorial Offices. - Michael Nielsen
How was it received? - Dave Bacon
With good humour and many interesting questions - the questions continued (lunch was brought in) for about 90 minutes or so. - Michael Nielsen
This is great. Really like the flow of the argument. - Cameron Neylon
Excellent essay - all read from my iPhone :) - Frank
Fantastic writeup. You should submit this to some print magazines (yes, I see the irony) - Chris Miller
Thanks Cameron, Frank and Chris! Reading a 6,000 word essay on an iPhone is a compliment I won't quickly forget :-) - Michael Nielsen
Add me to the iPhone readers list...great, great essay. - Noah Gray
oh, i wish i could write in the margins (or on it like PLOS does)- i guess i'll leave my comments in an incoherent jumble at the bottom like usual... - Christina Pikas
Uh, two separate threads. Commented at http://ff.im/4AnZc - Matthew Todd
Thanks Noah! - Michael Nielsen
Sorry about that, Matthew. Not sure how to stop FF creating two separate conversations for items that come through on my blog feed and are then reshared. - Michael Nielsen
NextBio
Matthew Todd
Apparently a panel on open access at the Lindau Nobel meeting http://twitter.com/lindaunobel
Bill Hooker
Reading machine to snoop on Web | Military Tech - CNET News - http://news.cnet.com/8301-13...
Not sure if this is good (will drive semantic web tech) or bad (who will get to use that tech?)... - Bill Hooker via Bookmarklet
BBN -- old skool. They pretty much invented the internet. But I don't remember them being major players in the comp. linguistics game... - Andrew Clegg
Cameron Neylon
Interesting Blog I hadn't come across before - via @CasesNetwork on Twitter http://wishfulthinkinginmedica...
Reflections on medical education in a digital world - Cameron Neylon
Mike Chelen
"InterMine is a powerful open source data warehouse system. Using InterMine, you can create databases of biological data accessed by sophisticated web query tools. Parsers are provided for integrating data from several common biological formats and there is a framework for adding your own data. InterMine includes an attractive, user-friendly web interface that works 'out of the box' and can be easily customised for your specific needs." - Mike Chelen via Bookmarklet
Mike Chelen
Carey Lumeng
You know you want it....HP reincarnates calculators on iPhone - CNET Reviews - http://reviews.cnet.com/8301-19... (via http://friendfeed.com/iphone-...)
You know you want it....HP reincarnates calculators on iPhone - CNET Reviews - http://reviews.cnet.com/8301-19512_7-10273119-233.html (via http://ff.im/4tWaK)
Given the UI flexibility of the iPhone, why recreate older, less intuitive HP calculator interfaces? - Steve Levin
@Steve: Nostalgia, I guess. - Christopher Granade
This would probably work better with a Bold and the clickable screen. I do miss the feel and thunk of pressing the keys on that thing. - Carey Lumeng
Noah Gray
PLoS ONE: 'A Principal Component Analysis of 39 Scientific Impact Measures' from Johan Bollen & colleagues - http://www.plosone.org/article...
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