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scienceapps

Feel free to discuss / post links relevant to social web apps for scientists.
Michael Habib
The Research 2.0 Concept Model above is an evolution of the Academic Library 2.0 Concept Models developed for my Master's Paper (http://mchabib.com/2006... ). While the original model primarily focused on academic library services for students, the new model focuses on services for researchers. Like in the original models, the top represents communication spaces grounded in physical space, while the bottom mirrors this in the online realm. Two ends of the spectrum are informal communications and formal communications. My argument is that Research 2.0 falls somewhere between these extremes. A full presentation is located here: http://www.slideshare.net/habibmi... - Michael Habib
The above Scholarly Identity 2.0 Concept Model takes the series of concept models one step farther, but with a slightly different twist. The divide between online and offline scholarly communication is largely meaningless, so has been discarded. The spectrum in this case is more specific with one end being entirely user-generated content and the other traditional scholarly... more... - Michael Habib
Michael - interesting stuff. Do you have that paper you mentioned published by now (blog post is dated mid-2006). I would like to mention some of this in my thesis and cite your publication of course. - 'Mummi' Thorisson
some comments here http://ff.im/aXOKZ, - so what's your thesis about, 'Mummi' Thorisson? - Claudia Koltzenburg
Thesis located here: http://hdl.handle.net/1901/356 and the title is "Toward Academic Library 2.0: Development and Application of a Library 2.0 Methodology" - Michael Habib
Claudia - the overall theme is data publication and the role of data standards, federated database networks and digital identity in facilitating/encouraging data sharing. The context is research into correlation between genotype and phenotype, or medical genetics/genomics more generally. Have a look at this review published last year that i co-authored with my supervisor: "Genotype-phenotype databases: challenges and solutions for the post-genomic era" - http://dx.doi.org/10... - 'Mummi' Thorisson
Nice. Thanks Michael!! - 'Mummi' Thorisson
The second (right) model above on identity is the more interesting of the two. If you are going to look at just one.... - Michael Habib
Interesting social status implications here, especially with the second model. The more robust both sides of the scholar2.0 identity components (UGC + trad), the "deeper" the 2.0 identity (think tag clouds as the metaphor here). Or, perhaps color combos is a better metaphor, with schol.identity2.0 being a mix of UCG (say, "yellow"), trad (say "blue") and combo being "green" -- the shade... more... - Mickey Schafer
Aaron
Open access to science journals - c/o of a new feature built into researchgate. ResearchGATE launches SelfArchiving Repository Scientific Online Network ResearchGATE blazes a new route into the world of Open Access Boston, September 15th 2009. The last few weeks have been big here at ResearchGATE (www.researchgate.net), the world's largest online...
Cameron Neylon
Ben Woodcroft
A Grease Monkey script for getting rid of the annoying frames from Wiley HTML fulltext webpages - http://userscripts.org/scripts...
Please post only to relevant groups. I don't see how this is related to Ruby or bioinformatics. - Neil Saunders
I didn't find it, I made it. But I agree, it isn't properly filed. apologies. - Ben Woodcroft
Iddo Friedberg
Microsoft tried to patent studying evolution - Ars Technica - http://arstechnica.com/science...
Somewhat bizarre article on how MS filed to patent sequence clustering two years ago. For those of us using OpenOffice, there is the additional weirdness of MS granted a patent for using XML to store documents, while being sued for intellectual infringement of the same. Hat tip to Andor Kiss - Iddo Friedberg from Bookmarklet
And here is the patent application. http://www.freepatentsonline.com/y2009... - Iddo Friedberg
See also this article in Science: http://bit.ly/2VHMKH - Enro
Maxine
Reflect: augmented browsing for the life scientist : Article : Nature Biotechnology - http://www.nature.com/nbt...
Evangelos Pafilis1,3, Seán I O'Donoghue1,3, Lars J Jensen1,2,3, Heiko Horn1, Michael Kuhn1, Nigel P Brown1 & Reinhard Schneider1 European Molecular Biology Laboratory, Heidelberg, Germany. NNF Center for Protein Research, University of Copenhagen, Denmark. These authors contributed equally. e-mail: contact@reflect.ws IntroductionTo the editor: Anyone who regularly reads life science literature often comes across names of genes, proteins or small molecules that they would like to know more about. To make this process easier, we have developed a new, free service called Reflect (http://reflect.ws) that can be installed as a plug-in to web browsers, such as Firefox or Internet Explorer. Reflect tags gene, protein and small-molecule names in any web page, typically within a few seconds and without affecting document layout. - Maxine from Bookmarklet
Would be nice to integrate this with http://bit.ly/15HcyO for simple creation and maintenance of wiki pages like those at http://bit.ly/vX9tW (especially beyond mammals and beyond Wikipedia). - Daniel Mietchen
I think this is a fantastic tool for end users, but Daniel's comment about integration with the Gene Wiki just made me think it could also be great for developers. _If_ there were an API, that is. Does Reflect relate a recognized term back to a specific database entry or identifier (e.g., Ensembl/Entrez Gene ID), and if so, can I as a developer get access to it? I'd love to parse all Gene Wiki articles and establish wiki links to other gene pages do de-orphanize them. Would be really cool... - Andrew Su
... actually, we'd thought about doing a similar thing with the WikiProfessional Concept Web Linker API (but haven't spent the time to figure it out yet) or the NCBO OBA http://www.bioontology.org/tools... (but not sure it does genes/proteins real well yet). For its simplicity and apparent accuracy, I'd love to try this out with Reflect... - Andrew Su
Short answers: 1) We do relate the recognized terms to database identifiers; for example, mammalian proteins are specified by their Ensembl identifiers. 2) There is not an API on the production Reflect server, but we are currently working on a SOAP API - it should be ready for you to play within a couple of weeks :) - Lars Juhl Jensen
ugh, no REST interface planned? Given my frozen-in-time programming skills, SOAP is a code word for me to pass it off to a real programmer. ;) - Andrew Su
There may also be a REST interface. If we make this then it will be build on top of the SOAP interface (i.e. all REST calls will be translated to SOAP calls). I hope that we can do this in an automated manner based on the WSDL. In any case, this implies that the REST interface will be made only after we are done with the SOAP interface. - Lars Juhl Jensen
Maxine
Sharing this as it is a slightly less specialist post than some of the posts I've read about Google Wave (ie people like me can understand it). - Maxine
Cameron Neylon
Stubbleblog » Blog Archive » Passively Updated Microblogging For Business - http://www.stubbleblog.com/index...
The enterprise version of what we should probably doing to record data analysis and data production properly - Cameron Neylon from Bookmarklet
Maxine
Join the Science Online London group for this year's (2009) UK conference in August. http://friendfeed.com/solondon Also on twitter at http://twitter.com/soloconf . (via http://friendfeed.com/science...)
Maxine
Vine, Disaster Tech From Microsoft - O'Reilly Radar - http://radar.oreilly.com/2009...
Quote: "Last week Microsoft will start inviting users into Vine, a public-service tool that will be especially useful during disasters. In case of an emergency or everyday life, Vine will be a multi-platform, ad-free method of staying in touch with networks. Once Vine is launched it has the potential to become a very powerful communication platform. Last week I had a phone call with Tammy Savage, the GM of Microsoft’s Public Safety Initiative. Vine's primary goal is to connect you with a small group of people, reach them wherever they are, and allow you to determine what conditions are like where they are. Vine will do this by letting you connect to it as you desire. Initially that means Facebook, LinkedIn, email, SMS, and the Vine Windows client. " - Maxine from Bookmarklet
Maxine
Quote (by Tony Hammond): "We're pleased to announce that Nature.com now has an OAI-PMH interface. This service implements the Protocol for Metadata Harvesting from the Open Archives Initiative. This means that the Nature.com platform can now be queried by item, by title or by date range and that structured data records will be returned. All articles from over 150 titles can be accessed and dating back to 1869 for Nature magazine." - Maxine
Maxine
From Allan Sudlow http://network.nature.com/groups... (links at source URL): The British Library is developing something called the Research Information Centre in collaboration with Microsoft. This is a web-based collaborative environment in which research teams can find, manage, share and...
Maxine
On Facebook Opening Up - John Battelle's Searchblog - http://battellemedia.com/archive...
Quote: "The announcement, expected Monday, means developers can build services that access the photos, videos, notes and comments users upload to Facebook, with users' permission. That's a big change for the social-networking site, which has exercised tight control over the look and feel of its service and how developers can interact with it. What I cannot figure out is whether this means Facebook is going to solve its linking problem. I've complained about it before, but the big issue with Facebook, to my mind, is that it does not play well with others when it comes to linking on the open web. In fact, it's damn hard to even link *inside* Facebook, never mind sending links *from* other services (IE Twitter) into your Facebook status feed (you can't)." - Maxine from Bookmarklet
That's one of my main issues with it, too, besides the annoying interface and all that. I can't believe they'd get by without links, the most important things on the web. - Mr. Gunn
novoseek
"Access Points in novoseek". Find in this detailed information page how Access Points work in novoseek. Thanks to this, you should be able to explore more of the content and create very specific requests. We are very interested in having your feedback on it. Thank you - http://novoseek.com/AccessP...
For instance, if you want to earch for the gene "alpha synuclein" using the GenBank ID CR457058. The link structure should be this one http://www.novoseek.com/AccessP... - novoseek
Richard Akerman
A new tool for managing search for academic resources. Author is looking for comments. - Cameron Neylon - Richard Akerman
Maxine
Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development: June 10-13, Sicily, Italy - http://www.nettab.org/2009/
Sam Huleatt
Just wanted to let folks know that there is a new version of Workstreamer available. Last summer there was some interest in checking out our early-stage prototype. We've re-tooled it quite a bit and I think you'll be impressed. If you're interested in checking it out: sam@workstreamer.com Thx!
Maxine
ExecTweets - John Battelle's Searchblog - http://battellemedia.com/archive...
Quote: "This morning marks the launch of ExecTweets, a platform my company has built working with Microsoft, its sponsor, and Twitter. I'm proud of the work here, it reflects a lot of thinking about how to use conversations like Twitter to fuel what I hope is a value-added experience. In this case, we're filtering for business-realated content from senior execs in various industries, like retail, healthcare, government, and more, and we've created a platform for community conversation, voting, input, and recommendations. (FM blog post here)." - Maxine from Bookmarklet
JB says: "We hope to do a lot more projects along these lines, please let me know what you think, and how we can improve them." - Maxine
It's Twitter, except with Microsoft ads and the assumption that "top business execs" have more to say of more interest, impact and importance than others. What are the odds any of those executweeters are going to respond to you? So it's broadcast, with authority attached to position and power, and ads. How very "new media". - Richard Akerman
Dave Ploch
Maxine
CrossTech: Citation Typing Ontology - http://www.crossref.org/CrossTe...
Maxine
Google Gets Real Time Thanks to A Neat Hack - John Battelle's Searchblog - http://battellemedia.com/archive...
Cameron Neylon
ClaimID is not only an OpenID provider; you can also post a list of your papers there. Cool. - http://claimid.com/jandot
Discussion on functionality of ClaimID - reshared to start aggregating all the openID stuff here - Cameron Neylon
I use ClaimID! http://claimid.com/maxine. Don't say I'm up with the online trends, for once! You can link to people there but I have only found a few other users I know, so if anyone has a claim id account, maybe they could post it here. - Maxine
ClaimID does provide good services, and I need to avail myself of them. However, like many web2.0 services there are no plans for the long-term. Will as service like this be a req't in a research infrastructure? Is it a public good? - Bill Anderson from twhirl
@Maxine: did you find the bookmarklet? - Jan Aerts
Don't think so, Jan. - Maxine
Cameron Neylon
PublicationsList.org enables researchers to maintain a reliable, professional looking, web-based listing of their academic publication record. - http://www.nextgenerationscience.com/resourc...
Service that provides a "publication record on the web" doesn't offer OpenID but would be close to what was proposed if it did - Cameron Neylon
Cameron Neylon
A specialist OpenID service to provide unique researcher IDs? - http://blog.openwetware.org/science...
The main discussion on my original blog post on an OpenID based system - aggregating into one place - Cameron Neylon
Maxine
Kindle Above the Level of a Single Device - O'Reilly Radar - http://radar.oreilly.com/2009...
Maxine
How FriendFeed uses MySQL to store schema-less data - Bret Taylor's blog - http://bret.appspot.com/entry...
Hope Leman
Time Slider Screencast--can someone explain what this and how it works? I came across via Michael Nielsen'ss bookmarks
Cameron Neylon
ResearchGATE with a new look and fancy graphs - http://my.biotechlife.net/2009...
ResearchGATE gets a facelift - Cameron Neylon
Cameron--would you please put a Twitter button on your fascinating blog so that we can foloow you more easily and send news of posts by your around the Web? - Hope Leman
Maxine
The miners strike again - but these are text miners… | Professor Douglas Kell’s blog - http://blogs.bbsrc.ac.uk/index...
Michael Habib
Elsevier Launches SciTopics—Now a Fully Developed Research 2.0 Resource - http://newsbreaks.infotoday.com/nbReade...
why do PR and reporter people still love putting 2.0 after everything? - Richard Akerman
because they can't count to 3.0? (ducks) - Cameron Neylon
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