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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.
Zzzoot: The Future of Science: Semantic Web Applications in Scientific Discourse - http://zzzoot.blogspot.com/2009...
Andrew Su, Yaroslav Nikolaev, wembley and 7 other people liked this
"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
Do any of you know anything about science outreach/science educator type positions? I'm a high school science teacher (degree in chemistry, picked the teaching cert. up after college) who thinks she'd be more useful as a science outreach educator. I have no idea how to make this happen, however, so I'm asking anyone I can come across.
imabonehead, FFing Enigma (aka Tina) and Bicentennial (Franc) liked this
"Living with my personal genome" by Jim Watson. Future Medicine - Personalized Medicine - 6(6):607 - Full Text - http://www.futuremedicine.com/doi...
Mr. Gunn and 'Mummi' Thorisson liked this
Thanks, corrected
- Steve Koch
Meeting with two Media Arts majors at UNM, discussing ideas for collaborations on science outreach. Thinking that a video explaining Open Science to the general public may be a good idea?
Daniel Mietchen, Lisa Green, Pawel Szczesny and 6 other people liked this
Definitely!
- Mr. Gunn
We were mulling over a few ideas: (1) Like I mentioned in the title of this post: A combined video / screencast to explain what scientists are doing nowadays to make progress towards open science. Audience would be general public and scientists. Could use friendfeed as a starting point and then show things like open notebook science, etc...
- Steve Koch
(2) Making a 5 minute video explaining the Open Notebook Science we're doing in Junior physics lab here. Target audience: other science instructors around the globe who'd be interested in using our experience to add open notebook science to their own courses.
- Steve Koch
(3) (This what inspired our meeting, but then we thought up 1 and 2 above while talking) Making science videos explaining the research in our lab. Target audience: general public.
- Steve Koch
(4) (This just occurred to me, we didn't talk about it): We could collaborate on making high-quality protocols videos. Something like in JoVE, but produced locally. I like all of these ideas and glad I met these students!
- Steve Koch
Very cool, Steve. What can I do to help?
- Mr. Gunn
Why don't you make a similar video explaining Open Science to scientists? I bet you will find a larger (or smaller) audience.
- Paulo Nuin
I agree it would be larger or smaller :). @Mr. Gunn, thanks! I don't know what help -- the barrier now is to know what to do. Which of those #1-4 seem most worthwhile to you and most in need of digital media experts? #4 is the easiest for me to imagine, since I actually know what I'm trying to convey. #1 is the hardest, since I'm not sure how to coherently explain that.
- Steve Koch
I am going to put a bit in my NSF CAREER budget for these projects. Talking with the students today, it seems like they could get academic credit for the project in the Media Arts programs, and also get access to the equipment. So, even there, I'm not sure what I'd need to budget for.
- Steve Koch
And BTW: Both of these students took my Physics 102 "Conceptual Physics" course and did very well. So, this is cool validation for the whole teaching/research synergy idea.
- Steve Koch
What is Open Science?
- Paulo Nuin
I'll give this some thought, Steve. I've got my hands busy right now in terms of developing a presentation, but of course you're welcome to reuse any of my or Mary Canady's slides.
- Mr. Gunn
@Paulo: what I mean by the term is the application of the free-as-in-speech principles of Free/Open Source Software to the entire enterprise of science. The Blue Obelisk folks refer to ODOSOS (http://blueobelisk.sourceforge.net/wiki... Open Data, Open Source, and Open Standards); to this I would add Open Access (publishing) and Open Licensing, to give the "five pillars" of Open Science.
- Bill Hooker
Hmm. Open Data, Open Source, Open Access, and Open Standards are all forms of open licensing, aren't they? Or is there something specifically called Open Licensing that I'm not aware of?
- Michael R. Bernstein
What I mean by Open Licensing is CC-style explicit permissions for re-use in copyright, and things like Science Commons' MTA or CAMBIA's BiOS licenses for stuff that's covered by patents. So yes, that's all part of Open Foo, but I think there's more to Foo than just the licensing and more to licensing than Data/Source/Access/Standards.
- Bill Hooker
Ah. Open Content covers CC licenses, I'm not sure what to call MTA and CAMBIA BiOS.
- Michael R. Bernstein
Other possibilities might be to include a citizen science project as an example of what can be done with greater collaboration -- such projects are good entryways into outreach since they seem to make science "closer" to a non- or emerging scientist. You could even go so far as to tailor portions of your own projects to younger audiences (K-12) -- and by doing so entice classrooms of...
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- Mickey Schafer
Sounds like a great idea and one I'm all in favour of. An idea, Steve. You might want to alert SciVee's Prof Phil Bourne http://www.scivee.tv/user/phil as I'm pretty sure he'd be [1] interested and [2] willing to lend a hand in hosting/promoting this type of project.
- Graham Steel
Hey Mickey, Thanks for those ideas! Definitely interesting to me and will think about it. @Graham -- thanks for that link, I will definitely contact him when we have a clearer idea of what we're wanting to do.
- Steve Koch
If you're looking for additional inspiration, try googling "digital ethnography" -- you should get to the Kansas State stuff (both their blog/web pages and youtube videos) -- you may or may not like the science-y part (anthropology -- the first video ever produced in the series was fairly annoying to me, though the subsequent ones are quite interesting), but they have some great teaching experiments using web re/sources that you might find useful.
- Mickey Schafer
Second Mickey's recommendation. Very interesting stuff - e.g., a short presentation at: http://www.youtube.com/watch.... I really like the idea of doing something of similar impact for open science. The longer 55 minute Library of Congress talk from the same channel is well worth watching, IMO.
- Michael Nielsen
That's spectacular!
- Steve Koch
STeve - It'd be really nice to have something similar for open science. Some visual ideas I like are to make a movie of the version history on, e.g., OWW, or the Polymath wiki; visualizations of the evolving network of relationships from, e.g., GeneWiki... I'll bet things like diseases gradually being understood are actually visible in the network of links on Wikipedia.
- Michael Nielsen
Steve - Jon Udell does an awesome Wikipedia movie at http://jonudell.net/umlaut.swf Things get really fun a couple of minutes in...
- Michael Nielsen
Hey Michael, that too is very cool. And I really like your idea of adapting that for OWW or the other sites. I don't know if the students I talked with are good at that or not. Looking at the things you linked me made me realize that if I'm going to be heavily involved (say as "producer" with the $), then I think I'm missing some talents to lead those kinds of things. So, maybe I'm not...
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- Steve Koch
Demonstration is a more effective way of explaining a concept than just explanation is anyway! Hmm. That could've been more elegantly expressed. In any case, Demo of what you are doing with some discussion of implications (pedagogical to philosophical) also sounds like a great project.
- Mickey Schafer
Hi All -- Met again with Noel and Leslie (the Media Arts peeps), and we've planned to start making the video on November 23. We're planning on short video showing what we're doing in Junior Lab with Open Notebook Science. General plan can be seen here: http://docs.google.com/Doc... and a list of potential interview questions is being generated here: http://docs.google.com/Doc...
- Steve Koch
Muchas excellentos
- Graham Steel
Liked: Shining a light on dark data - http://dmm.biologists.org/content... by Chris Patil (http://friendfeed.com/mycopha...) and Vivian Siegal (editor of Disease Models and Mechanisms).
Mr. Gunn, Greg Tyrelle, 'Mummi' Thorisson and 4 other people liked this
"We are increasingly keeping scientific records in electronic form; it would be straightforward to wrap our notebook pages describing an orphan result with a bit of searchable text, generate a web page, and submit the whole thing to a database. The act of conducting research would thus become practically synonymous with the act of disseminating the resulting knowledge. Along the way, we would have to spend some energy improving the records that we keep in order to ensure that our notebooks were more accessible to outside readers and less like the quirky private diaries they often become." Heh.
- Heather
.. and if this could result in a proper citable reference on the other end, that'd sweeten the deal :) See e.g. Jean-Claude Bradleys comment near the top of this thread, about 'dumping' data to Nature Preceding to get a reference + DOI in return: http://friendfeed.com/the-lif...
- 'Mummi' Thorisson
PathVisio / WikiPathways tool for creating and analysing biological pathway diagrams - http://www.pathvisio.org/
Ami Iida, Holly Rae, FFer, Daniel Mietchen and 8 other people liked this
I'd really like to see that refactored as a collaborative Google Wave gadget.
- Dan Hagon
Me too, re: Google Wave gadget. Then add SBML support, use SBGN in the display, support MIRIAM annotations and I can retire penniless.
- Neil Swainston
@Neil, there are a few other tools which support SBML and SBGN (see http://sbgn.org/Communi...). Wikipathways seem to be inventing yet another pathway format and dont provide a conversion to any other existing "standard". Shame as it would benefit everyone if they did.
- Frank
Thinking about it a little more, I'd really like to see the above refactored as a collaborative Google Wave Gadget. I've been involved in about five network reconstruction "jamborees" now, which involve flying loads of people around the World to sit in a room and discuss things that they could do with PathVisio (if it supported SBML...) or Payao. Anyways, this costs a fortune (see the...
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- Neil Swainston
@Neil: WikiPathways is intended exactly for that type of collaborative pathway creation. WikiPathways pathway format is based on, and developed in cooperation with, http://www.genmapp.org. So admittedly it's not a widely supported standard, but at least it wasn't a complete new invention. SBML / SBGN support is on its way. Re Google Wave: unfortunately, all this work predated Google Wave by several years...
- Martijn van Iersel
Fwd: Research 2.0 Concept Model - http://www.flickr.com/photos... (via http://friendfeed.com/habib...)
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io2a, Thomas Brox Røst, Mickey Schafer and 10 other people liked this
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...
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- 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...
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- Mickey Schafer
On the web: links to web-based resources for teaching about interpreting evidence (provided by NSTA): http://science.nsta.org/enewsle...
Fwd: Scholarly Identity 2.0: Matrix, Concept Model, and Presentation - http://mchabib.com/2009... (via http://friendfeed.com/habib...) (Full description of how these models interact and an overview of the presentation.
Mickey Schafer, maxilprof and Andreas Matern liked this
Early data from citeulike's automated article recommender http://blog.citeulike.org/...
Yann Abraham, Martin Fenner, Mr. Gunn and 16 other people liked this
"It’s really gratifying to see the social discovery of science generated by the simple act of keeping your references public on a Web page."
- Duncan Hull
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