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Peter Miller › Comments
Duncan Hull to Duncan's feed, The Life Scientists, Semantic Web for Health Care and Life Sciences IG
The Semantic Biochemical Journal experiment « O'Really? - http://duncan.hull.name/2009...
Mickey Schafer, Hope Leman, joergkurtwegner and 19 other people liked this
"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....
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- Duncan Hull
from Bookmarklet
Am I missing something here? I only seem to see a few popups when mousing over references?
- Cameron Neylon
Interesting though getting started wasn't entirely transparent. Figs are interactive (pink background and menu) so, for example, data from Fig 9 can be replotted. Tended to spawn popups at an alarming rate. Fig. 13e appeared unable to load into popup.
- Peter Miller
@Cameron, you need to download the Utopia client to get the full effect http://www.getutopia.com the animations are embedded in the PDFs and viewable within the client. It's not a browser based thing (yet).
- Duncan Hull
Done that, looking at both the paper online in enhanced version and pdf I'm not seeing any visual cues or anything that take me anywhere much. Do I need to have the utopia client running as well? Ok you need to open the pdf in Utopia. That's really not immediately obvious I have to say, particularly with the "enhanced online version" getting billing front and centre. Ok I could have read the instructions but its only the mention that Utopia is a "pdf reader" that tells you what to do. Could be clearer.
- Cameron Neylon
Have to say that the idea of a semantically enhanced pdf I have to download and open up in a particular viewer seems to be somewhat missing the point :-)
- Cameron Neylon
Also seems odd that the enhanced online version doesn't at least include the links that are in the enhanced pdf
- Cameron Neylon
@Cameron I see your point, I'd like to see a more web friendly version but there are some limits to what you can do in a web browser (especially when it comes to sequence alignment and molecular visualisation)
- Duncan Hull
Yes, and that is all fair enough - you need to start somewhere but you'd think the links could be translated across pretty easily (e.g. Caspase-3 in paper 1, fig-1 legend is linked in the PDF to a wikipedia entry, why not in the online version?). Bring on HTML5 is what I say :-)
- Cameron Neylon
@Cameron ... and yes, its an "experiment" too (normaly caveats apply!). The thing to look for is the little Utopia Documents icon embedded in the text once you've opened up an article (e.g. the review) in Utopia documents. Thanks for the rapid feedback...
- Duncan Hull
Yep, found it eventually. I'd suggest changing the instructions to be much more explicit. i.e. Download Utopia, then download pdf, then open in Utopia. Most people will have pdfs set to autoload in something else so its not an obvious path - particularly to people used to plugins and overlays. Heh, next quetions can I leave a comment on the journal article to suggest this....mmmm.....that would be a "no" then... ;-)
- Cameron Neylon
Dear Santa, Please can you provide Utopia for Ubuntu/Debian/Linux. Thanks :)
- Allyson Lister
I just skimmed it initially - didn't note the requirement for this odd piece of software. Puts paid to it for me, I'm afraid.
- Neil Saunders
From Philip McDermott: "ubuntu version in the works but just slightly delayed for launch. I'd have thought it'll be available next week sometime"
- Allyson Lister
The idea of a specialized PDF reader for this means it's just a proof of concept at this stage. I'll mention it to the Mendeley people and see if they might like to incorporate some of this into their internal PDF reader.
- Mr. Gunn
@Mr. Gunn thanks...
- Duncan Hull
@Mr. Gunn thanks. Be interesting so know what they think of it, feel free to put them in touch with us :o)
- Philip McDermott
I think that the initial confusion of PPLs website has confused a lot of web-oriented users. Try grabbing the app, the paper, and working through it, and you should get a feel for what we're trying to do. We're not saying web-based is bad, it's just that this is a little different.
- Philip McDermott
@Philip see also commentary here http://digitalcuration.blogspot.com/2009...
- Duncan Hull
As I understand it the PDF reader software is just an initial client for the backend which lets you annotate whatever - and from where all the annotations are fetched. If (when?) it gets opened up you could extend the existing client to read other files, write your own client, write a Firefox plugin, whatever...
- Euan
@Euan yes that's right (and you put it much better than me). As for opening it up, you'd have to ask the Utopia team... it would make a lot of sense.
- Duncan Hull
I like the concept of the Utopia reader. But the integration of references could have been done better. Why not use DOIs instead of linking to a Google Scholar search?
- Martin Fenner
Dear Santa, like @Allyson I really hope your reindeer's can still pull the Linux version, too.
- joergkurtwegner
Besides, how does it compare to the interactive ICM in PLoS ? http://ff.im/acHs9
- joergkurtwegner
Heading to the airport shortly via MAX train then on to Santa Barbara-let the holiday begin :)
Have a good one, Robin :)
- Peter Miller
Thanks, Peter! Wishing you a wonderful holiday as well :)
- Robin Ashford
from email
NPG changes direction in Second Life - http://network.nature.com/people...
Bora Zivkovic, Steve Koch, Graham Steel and 3 other people liked this
Well, I've expressed interest in participating in some fashion in the revamped Second Nature. Not quite sure what that might amount to but I did raise the possibility of running that SL/Web 2.0 science education event there. Seemed appropriate.
- Peter Miller
I regard this a good news, because it may throw more impetus behind finding better alternatives to Second Life.
- AJCann
I don't think it invalidates the platform so much as the business model.
- Peter Miller
hopefully this will lead to an exploration of the many powerful and exciting virtual world platforms, instead of limiting activity to only SL
- Mike Chelen
Well, OpenSim is the obvious way to go though concurrency and scripting bumps the price up significantly. Beyond that, Wonderland and Edusim, I guess. Both look great in demos. Problem comes when you try to get a local install. Some talk incidentally about a degree of convergence between these three.
- Peter Miller
the main issue for me is will there be the critical mass of people on these new networks - if not I'm not sure it is worth the investment of time
- Jean-Claude Bradley
The question is whether there are a large number of people amenable to using virtuals worlds but averse to SL. My guess is that aversion to SL is often a cover for aversion to virtual worlds generally. OpenSim (in the guise of Reaction Grid) is gaining some traction: the physicists from MICA just setup an outpost there (iirc). However, if you find SL UI clunky, OpenSim's no better, just cheaper.
- Peter Miller
I'm all for virtual worlds, as long as the usability is good (so not SL then). You'll have to convince my university that there is an acceptable security risk so that the ports required are not blocked (so not SL then).
- AJCann
Our students get on with SL OK. And hundreds of universities use it globally. When you've found the perfect VW that isn't SL, let me know and I'll buy you a virtual beer. Good luck.
- Peter Miller
So remind me, why did NPG pull the plug?
- AJCann
It was a financial decision - note they are not shutting down the islands - just the programs that took a lot of resources to run (like the talks).
- Jean-Claude Bradley
There are too many imponderables here. I don't know how Second Nature did their inductions but some folk gave them positive feedback: http://bit.ly/Iy0Gj
- Peter Miller
Have now linked this thread with the source (since they are directly related).
- Graham Steel
Possibly worth mentioning that there is a user interface redesign underway for SL. Having said that, there are also 14+ third-party clients and latterly a $3 implementation for the iPhone. For all its imperfections, all manner of people manage to use SL, including the blind and people with cerebral palsy. http://www.youtube.com/watch...
- Peter Miller
Ah, just seen that RezEd.org is indeed starting to use the Flash-based Smallworlds. Lots of interest too in the forthcoming Lego Universe virtual world. I doubt that either will be an easy sell to the average university administration or learned society but they may have niche uses.
- Peter Miller
RT @sorry_afk: Destruction of the time space continuum - thanks to Mashable. iPhone in an iPhone. You MUST see this. http://mashable.com/2009...
lol, there are still just a few of us who don't have iPhones :)
- Peter Miller
So long, and thanks for all the fish - http://tidalblog.blogspot.com/2009...
Andrew Lang liked this
Second Nature certainly did have a positive impact for us.
- Andrew Lang
Heck, yeah. I was forever in awe of cool dudes like Hiro Sheridan when they turned up to advise or demo stuff.
- Peter Miller
Sorry to hear that Metaplace is closing down its current operation -- have good memories of Rocking The Metaverse's gig in the Summer
AJCann liked this
As in not like. This is a shame. Any other free, Metaplace-like web alternatives to SL? (Software installation (client or server) not possible - has to work in browser, and IE at that).
- AJCann
Not sure -- at the end of the day someone has to pay for staff and servers. Place to go looking might be RezEd.org. Bear in mind that SL will actually run off a USB stick -- not sure whether the open source version OpenSim does. Although people are working on web browser versions of OpenSim, I suspect these will still require an install. Land in OpenSim tends to be much cheaper -- not sure whether you might be able to blag some from ScienceSim (Intel).
- Peter Miller
Ports SL requires are blocked at UoL, so it's a non-starter. Any other system which uses same ports would be similarly blocked. I'm looking for a lightweight, Lively/Metaplace-type in browser environment.
- AJCann
Looking at RezEd, I noticed someone trialling Smallworlds. 2.5D like Mp and Lively, zero install but somewhat commercial and, I suspect, kids-oriented.
- Peter Miller
That's a lot less evil. Etherpad back online and being open-sourced. http://etherpad.com/ep...
Robin Ashford liked this
And now the source actually is open, the deadlines are still effective.
- Peter Miller
RT @mlindenSL Cool! Sydenham Crystal Palace - Pompeiian infl. on Victorian design/architecture. http://slurl.com/secondl... (history by UoBristol)
Not sure M Linden got the slant quite right in his tweet. As I understand it, it's a recreation of the Pompeian court within the original Crystal Palace. On the other hand, he's been there and I haven't ;).
- Peter Miller
#cfbweb2 Now multitasking -- also listening to Martin Bean (VC, OU) in SL -- as a male, cannot end well ;)
Most noteworthy aspect was that the OU is producing a complete module for delivery by iPhone. Packed sim and voice held up OK for a change. Possibly first UK VC to present in SL?
- Peter Miller
My predictions for last year were, erm, not that accurate, even if a few were inter-dependent. Worth trying again? http://tidalblog.blogspot.com/2009...
Yes Peter, please do. I still can't believe they don't have real html on a prim.
- Andrew Lang
Yes, it's astonishing how long it is taking: maybe it's because they changed tack to go with the media plugin rather than a one-size-fits-all solution. I wonder also whether it's a lower priority because they have the separate Immersive Workspaces integration with the 2D web. Mind you, edu is maybe best described as a priority *niche* anyway and the mainstream presumably aren't that bothered with html-on-a-prim. Patience is wearing thin though.
- Peter Miller
Classroom rewards 'do not work work' - http://www.telegraph.co.uk/educati...
Jo Young, Peter Miller, beatrice cherry and 2 other people liked this
Reward schemes reduce intrinsic motivation.
- AJCann
from Bookmarklet
Curious -- how many children are born with "intrinsic" motivation? Or is this something that is environmental?
- Mickey Schafer
Intrinsic versus extrinsic.
- AJCann
yes, learning can be both intrinsically and extrinsically motivated--and I believe this is true for everyone with variation depending on what has to be learned. But I've also encountered the terms as personality dimensions, and it isn't clear in the article which one was being used.
- Mickey Schafer
Yesterday, I overhead a very interesting conversation during which a school counselor was advising a parent with a failing child to remove all things of value to the girl and make her earn it back by achieving passing grades. This included _everything_ the girl liked from clothes and shoes to electronics to time with friends. She quipped after that she frequently has to teach parents how to be parents since today's generation was ill-informed. I found her horrifying.
- Mickey Schafer
@Mickey: that sounds like a recipe for leaving home at 16 and never going back to me. Horrifying indeed.
- Bill Hooker
There is some truth to this - when I have students play games for prizes, the reward (usually a chemistry book) is not the central motivation but it does make it more fun for the very best students to compete a bit. Similarly, with our ONSChallenge where students do labwork, the cash prize is small enough to not be the primary motivation but again it makes things more interesting.
- Jean-Claude Bradley
Jean-Claude, I agree that external motivation is quite useful. Nor does it have to be a big deal! I have premed students who once commented with enthusiasm that they would like get smiley stickers on their papers -- I was amazed. Didn't invest in stickers, but have thought about why this would be the case. In writing, the work is very personal and I get to see so many different sorts of...
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- Mickey Schafer
I also suspect we over-romanticize the intrinsic nature of learning in children. Yes, they do like learning, and they are curious, and the natural process of hypothesizing and testing that occurs can be rewarding (to a normal child). But this isn't the same process being used in school. And getting a kid to study for something like a spelling test in the first grade has very little to...
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- Mickey Schafer
Mickey good points. I experimented with different rewards and didn't find that much difference between a $5 reward and a video ipod - there is a type of student that responds to this type of competition so why not make their experience more enjoyable even if not all students respond?
- Jean-Claude Bradley
Doesn't this relate to Dan Pink's TED talk where tasks requiring significant thought were indeed adversely affected by a reward system?
- Peter Miller
That's a good point, Peter. And it gets at a real conflict in public education. Tasks that require significant thought are often intrinsically rewarding; James Paul Gee makes this point about computer games that are really quite complex, require hours of play to finish, and which kids readily engage in. In the public sphere, especially a test-driven one like the U.S., such tasks don't...
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- Mickey Schafer
People, remember that we need to be attracting more people to the benefits and rewards of making the effort of deep thinking and problem solving. We could and should considering using a reward system to draw young people (and by 'young', I mean from pre-school to college) into situations where they need to challenge themselves by thinking deeply. When they are at that place, we can...
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- Jason Miller
Very interesting point, Jason, but figuring out how to draw a young child into complex activity, especially in a public school setting, is damned difficult. My kids are in a science/tech magnet precisely b/c the educational tasks are deeper and often collaborative. This particular program also screens more for motivation to learn than sheer "IQ" -- the academic requirements for selection are "B" grades and above, but the clincher is whether the kid wants to work.
- Mickey Schafer
And while I agree that drawing a greater population in is really important, my observations after a year of volunteering is an unpleasant truth: kids are not equally talented. They are not all cut out for complex work whether b/c of personality or ability. I would argue that bribing the talented is a crucial undertaking since many of those will not pursue careers in STEM b/c those jobs...
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- Mickey Schafer
Mickey - I agree with what you're saying. One think I'm sensitive to (and it sounds like you are, too) is where and how we look for talent. If we're looking for talent in white-bread communities, then we're doing something wrong. If we're looking for talent in _all_ communities, especially in those that have historically been underrepresented in STEM, then we're doing something right. This will bring new challenges and frustrations, but that is a Good Thing. Don't you think?
- Jason Miller
Absolutely -- I spend summers working with under-represented populations and have been puzzling for years about how to get these students more connected to all the possibilities out there. The difficulty that most vexes me, and which I've never found/read/overheard a way to counter is the cultural differences. And this isn't just about color: it's more a factor of education and SES. As...
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- Mickey Schafer
Team:Calgary/Second Life - 2009.igem.org - http://2009.igem.org/Team:Ca...
Peter Miller liked this
You have arrived at the sixth segment of our tour or the Second Life portion of our iGEM project. The Second Life team has built an island aptly named "Synthetic Biology Interactive" to serve as a tool to be used by future iGEM teams as an educational resource. Through interactive learning, students will be able to experience many different aspects of the iGEM: from big-picture applications to Biobrick construction to crucial lab techniques. Let's now move on to the human practices component by clicking HERE.
- Robin Ashford
I'm pretty sure they're going to write this up -- great to see students so actively engaged.
- Peter Miller
3-D Maps, Camera Phones Put ‘Reality’ in ‘Augmented Reality’ http://www.wired.com/epicent... (in 1-2 more yrs should be great)
Peter Miller liked this
Simpler approach based on 2D maps: http://www.youtube.com/watch... . Interesting that they can't name a killer app. As with VWs, I guess we'll know it when we see it :)
- Peter Miller
What the Google Web will look like in 10 years - http://royal.pingdom.com/2009...
Peter Miller liked this
No mention of Google's O3D initiative: http://code.google.com/apis...
- Peter Miller
odd to me that there's a whole genre of remixes of the Valkyrie speech by Mr. Hilter, but no page collecting/ linking them all
Peter Miller liked this
and none citing the others as an influence...?
- Cameron Neylon
I love the SL one but it is probably opaque to non-users and dating rapidly.
- Peter Miller
EtherPad Blog: Google Acquires AppJet - http://etherpad.com/ep...
Nany, Dan Hagon, Richard Akerman and 3 other people liked this
"We are happy to announce that AppJet Inc. has been acquired by Google. The EtherPad team will continue its work on realtime collaboration by joining the Google Wave team."
- Daniel Mietchen
from Bookmarklet
"If you are a user of the Free Edition or Professional Edition, you can continue to use and edit your existing pads until March 31, 2010. No new free public pads may be created. Your pads will no longer be accessible after March 31, 2010, at which time your pads and any associated personally identifiable information will be deleted."
- Daniel Mietchen
OK, now I have to start using Wave?
- Peter Miller
Etherpad was immensely more functional for realtime collaboration than google docs . This development was predictable..considering that wave is still so hard to grock
- Hari
I think the key for casual users of wave is that robot that email you when there is an update - Cameron gave me that trick. It was broken for a few days last week but seems fine now. Otherwise it is hard to keep checking wave for updates as part of your workflow. BTW - is there a way to get email alerts when wikipedia pages change?
- Jean-Claude Bradley
What is the address of that robot? Strange, though, that the supposed replacement of email doesn't work without it - let's hope this is just transitional.
- Daniel Mietchen
Daniel the robot can be added to any wave as wave-email-notifications@appspot.com
- Jean-Claude Bradley
There's also an XMPP jabber bot that sends you an IM when a wave is updated, that's what I use.
- Mr. Gunn
Thanks, Jean-Claude; put it on some waves and will see what this gives.
- Daniel Mietchen
Noticed that the bot was already on most of the waves I have been on for weeks, but not a single notification reached me so far. Back on topic: Etherpad will remain operative until at least when they release their source code. http://etherpad.com/ep... .
- Daniel Mietchen
Daniel - if the bot is working it shows up at the very top of the Wave - it might be set to OFF and it will give you a link to activate it. If you see a broken image it is not working at all
- Jean-Claude Bradley
Thanks - got the activation links in some waves, though not in others. No broken image.
- Daniel Mietchen
Got my first notification. Thanks, Jean-Claude.
- Daniel Mietchen
Prohibition - http://scienceoftheinvisible.b...
'Mummi' Thorisson, Andrew Perry and Cameron Neylon liked this
Whether they agree or not they're not going to be able to stop a back channel going on. Which was your point surely? Read a clueless article yesterday about brands having to make a choice about whether going online because they might encounter negative content about their brand. Well duh - the content is going to be out there anyway - engage or don't those are the choices.
- Cameron Neylon
Yes, but since I've assumed a sort of responsibility for guiding the process, it would be nice to avoid a car crash rather than picking up the pieces.
- AJCann
Ah, I see your dilemma...
- Cameron Neylon
For me the issue is whether or not to have the/a back-channel visible on screen next to or behind a speaker. If the speaker wants it, then fine. If they do not, then that is their choice. The fact that a proportion of the audience may be watching and contributing to the back-channel on their own device seems to me to be a different issue, where I think that it's a free country.
- Seb Schmoller
@Seb And conference organizers who have tried to block the backchannel have also felt the wrath. Of course the easy way to do it is not to have wifi and a building which blocks the 3G signal :-) As a compromise, how about letting speakers choose whether they want the backchannel (which in the context of #altc2010 means Twitter, I guess) visible or not?
- AJCann
@ Alan. Exactly. That's the point I was trying to make. No pressure on speakers to have it visible. No pressure not to. A bit of "caveat" info to help them decide. (Practically speaking we'll have to think through where Elluminate's back channel might fit in.)
- Seb Schmoller
Might I suggest no screen, but a moderator who can pass on info to the speaker as an alternative. I have used this in my classroom and in presentations.
- Terry Elliott
I couldn't understand why there was a permitted back channel via elluminate at ALTC2009 but not via twitter, I assume because elluminate was moderated?
- Jo Badge
I think the speaker should be able to see the backchannel but not the audience unless they have their own kit (backchannel of limited use if you can't contribute). I've seen talks in SL (where backchannel is in chat) derailed by inexperienced speakers becoming overly engaged with a minority using the backchannel. Using a moderator is good if there is an inexperienced speaker or very noisy backchannel. Of course, in SL the audience also chooses when to change your slides unless you're careful. ;)
- Peter Miller
seen this? http://scienceblogs.com/terrasi...
- Jo Badge
Yes, I saw that. Sigh. Twitter banned. But not facebook, Posterous, Wordpress, Friendfeed. etc. FAIL.
- AJCann
The Dark Side of Digital Backchannels in Shared Physical Spaces - nice summary http://gumption.typepad.com/blog...
- AJCann
EtherPad to Shut Down After Google Acquisition of Parent Company AppJet - http://etherpad.com/ep...
My guess is that this is going to integrated into Google Wave for making it a more useful document editor :)
- Nash
It's back and will be available until open-sourced according to their blog.
- Peter Miller
Link to my IBM World Community Grid in Second Life posts for @bettinac & IBM team: http://robinashford.posterous.com/tag... (great meeting all!)
Peter Miller liked this
Glad it went well and sorry I couldn't stay longer.
- Peter Miller
Was glad to see you there, Peter. The tour inside went very well and some even stayed to visit the AIDS.gov Facing AIDS display on the deck. All in all, it was a good day on Karuna for WAD, even though griefers were working to disrupt things during the second half. (LL had to close the island to the public by 5:00 to gain control over the griefing but by then we were pretty well finished.)
- Robin Ashford
from email
Sorry to hear about the griefers -- similar problem at Helen Keller Day. Sometimes I am lost for words when it comes to the behavior of others but you have to take the positives as well.
- Peter Miller
now approved :)
- Peter Miller
Sorry about the delay Peter. It appears that the ning has not been attractive for conversation and many have moved to blogging and microblogging, with a suitable tagging strategy. Comments on the value of ning are welcome but it appears the habits have developed in other tools. I have left the ning up though as an example of a web 2.0 technology 'left open' and we may discuss it on our day.
- Terry McAndrew
Well, that’s an interesting observation in itself. I can point to a few more-or-less successful nings but why some fly and others don’t is worth discussing. Peter
- Peter Miller
from email
Pathways from genome to phenome - anyone know of a similar but CC-licensed depiction? Fig. 2. of http://linkinghub.elsevier.com/retriev...
Vedran Rodic, Peter Miller and Khader Shameer liked this
Did you try http://krauthammerlab.med.yale.edu/imagefi...
- Peter Miller
Had forgotten about this one, thanks! I only tried http://biosearch.berkeley.edu/ and think they basically search the same dataset but the results are different, e.g....
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- Daniel Mietchen
Heh, and I didn't know the one that *you* used :)
- Peter Miller
Web 2 for bioscientists sounds interesting. Anyone interested in a parallel SL session for those who don't/can't travel? #cfbweb2
Kate Boardman and Jean-Claude Bradley liked this
possibly - what time are you planning the SL event?
- Jean-Claude Bradley
Well, I don't want to compete with the RL event so we could make it later if it suited you better? Opportunity to reflect on the twitterstream and present additional perspectives if nothing else.
- Peter Miller
sure the conf ends at 16:00 London time right?
- Jean-Claude Bradley
The CFB (Centre for Bioscience) was jointly in control of the agenda for this session, but since we can't access SL on the Leicester campus, we won't be able to participate I'm afraid. You guys go ahead without us ;-)
- AJCann
I use mobile broadband -- works fine for me if you just want to see inworld, i.e. project. But if we do something, it can be after 16:00 so it doesn't impact.
- Peter Miller
Jean-Claude (or anyone else), any thoughts? Question is whether we want it to have the same focus as the RL event, i.e. higher education, bioscience and Web 2.0, or whether we broaden it out. Assuming there is an extra VW perspective as well, could publicise it via inworld groups, SLED and the UK VW list. Presumably HEA Bioscience would offer it to their normal list? I'm thinking short papers, maybe some posters/demos? Pretty informal.
- Peter Miller
Well, don't all rush. :) As the topic is pretty germane to my current interests, I'm probably going to take this forward anyway in some fashion, even if not in the format above and with a more overt SL focus.
- Peter Miller
Peter - I would be willing to do a poster, a panel, whatever you like. Hopefully Hiro can make it too
- Jean-Claude Bradley
Jean-Claude, you and Hiro have an excellent story to tell but I am wondering whether the SL event might be better run at a later date so those travelling back from the RL meeting could attend both? There are lots of possibilities here...
- Peter Miller
The other option is to gather up the people and have them attend or present at the SciOnline conference - there will be a Second Life co-session on Jan 17
- Jean-Claude Bradley
I am not seeing a lot of interest. Daniel Livingstone volunteered a SLOODLE session, Lexi on SLED was interested in an open science dimension, HEA PhysSci said they would advertise their members but that's about it. Maybe "competing" SL-specific RL events are to "blame", maybe the science focus makes it too narrow. Running a session at VWBPE in March is another possibility. Let's give it a couple more days before pulling the plug.
- Peter Miller
StoryMachine, meet TiddlyWiki - http://tidalblog.blogspot.com/2009...
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Opensource Obscure liked this
Peter, is this still available in-world? I'd like to play with it
- Opensource Obscure
nevermind, I just found http://sites.google.com/site... that seems to give all details
- Opensource Obscure
the StoryMachine can be found here along with many other useful free tools http://slurl.com/secondl...
- Opensource Obscure
It's kind of a perpetual work in progress but there's a copy at http://slurl.com/secondl... TiddlyWiki aspect was never really finished and I haven't played with the whole thing for a while though, curiously, I was just about to when I read this.
- Peter Miller
from email
Getting real about our virtual future - http://communicatescience.com/zoonomi...
Peter Miller and Jean-Claude Bradley liked this
virtual worlds bigger than the web in 10 years? That is a stretch
- Jean-Claude Bradley
Did he say that? A bit apples and pears as comparisons go and increasingly meaningless as the two merge into one another.
- Peter Miller
Peter - first sentence : "Imagine an online phenomenon, that you can engage with today, but which in ten years time will be bigger than the web"
- Jean-Claude Bradley
Images of molecules « Freelancing science - http://freelancingscience.com/molecul...
Jean-Claude Bradley liked this
Using Blender with pdb files
- Peter Miller
nice pic of one of Drexler's creations - I don't think any have been made yet
- Jean-Claude Bradley
Letter Positioning - Second Life Wiki - http://wiki.secondlife.com/wiki...
Alternative to XyText by Dedric Mauriac
- Peter Miller
Chemistry in Second Life paper in Chemistry Central Journal - http://usefulchem.blogspot.com/2009...
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ffcode, Mike Chelen, OpenSci Info and 5 other people liked this
My Xstreet account has seen a very sharp uptake on the number of people getting our stuff. I have had to log in to SL just to make sure my messages are not capped. I'm sure it will die down soon but pretty cool to see.
- Andrew Lang
where is the best place to find source code for these items, is http://opensledware.wikispaces.com/ still active? great article, congrats!
- Mike Chelen
Last time I checked the wiki was mainly taking spam. I think Desideria Stockton runs it and she's not been inworld a lot lately afaik
- Peter Miller
The final format just got published http://journal.chemistrycentral.com/content... which is nice because you don't have to download the pdf for the full text version
- Jean-Claude Bradley
Chemistry in Second Life - http://www.journal.chemistryce...
Mike Chelen, Berci Mesko, MD, Peter Miller and 3 other people liked this
Sheesh, 23MB PDF !
- Rajarshi Guha
It's all the pretty pictures.
- Andrew Lang
no substitute for images to describe Second Life projects
- Jean-Claude Bradley
Would be nice if one could transform a scene into something 3D portable... and I'd be happy if that would extend 100m or so, with the far scenery as images on the 100 circular wall around the scene... (tune 100m where you like)
- Egon Willighagen
could you use Jmol Egon to depict 3D scenes?
- Jean-Claude Bradley
Well, at least the molecular bits...
- Egon Willighagen
Not sure what is meant by "3D portable". SL certainly has its limitations though the Meerkat viewer and its ilk can be used to archive structures offline though I haven't tried it with any molecules yet. In principle the molecules can also be uploaded to OpenSim grids which can run standalone and, I believe, in a web browser too. You could use the VR room or a holodeck/holoemitter to provide a context. Great paper btw.
- Peter Miller
Ah, I should have said that using Meerkat works fine with the protein sculpted prims, at least as far as SL is concerned. Just tried it with one of the molecules generated using Andy's older molecule rezzer and that works fine too: 145 prims rezzed and linked in about a minute.
- Peter Miller
And just confirmed that you can upload said molecule in an OpenSim grid (Intel's ScienceSim to be precise).Not sure whether Andy has already done this, nor indeed whether any of his rezzers work in OpenSim. I suspect the molecule rezzed in the same sim position it was archived in -- which could be inconvenient though Meerkat shows your own content in the mini-map clearly enough.
- Peter Miller
@Peter. Great stuff - I've never tried OpenSim - didn't know you could transfer content. Cool.
- Andrew Lang
Short blog: http://tidalblog.blogspot.com/2009...
- Peter Miller
Final (pretty) version released, pdf only 5.7 MB :)
- Andrew Lang
KochNeylonSalvagno - http://www.flickr.com/photos...
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Anthony Salvagno, Jean-Claude Bradley and Steve Koch liked this
Is there a Downfall remix yet?
- Peter Miller
What is Downfall remix, Peter? I have however remixed the original 25.0kb image again and have come up with this http://www.flickr.com/photos... 'Open Science that Sizzles', kinda thing. I like it :)
- Graham Steel
One day people are going to collect "Steel Open Science" prints the way they collect old Soviet propaganda posters and early Beatles concert flyers.
- Bill Hooker
I LOVE IT -- fantastic remix, Graham!
- Steve Koch
danka....
- Graham Steel
Cameron visited our lab today! Here's a photo of Cameron discussing the tweezers with Anthony. I'm doing my best to suck my gut in.
Kubke, Victor / Mendeley Team, Claudia Koltzenburg and 23 other people liked this
Was an awesome day. Thank you so much for traveling and spending time with us today, Cameron! I learned a lot about science and means for carrying out open science. I'm energized about what seems like a very nice future protein-DNA collaboration. And I'm also energized about trying to implement some of the LaBlog and Google wave things you demoed for us.
- Steve Koch
I agree it was a great visit. I enjoyed showing you the version of the $100 spectrometer I'm working on and all the great conversation. I hope KochLab can start a collaboration with our friends across the pond.
- Andy Maloney
from iPhone
I think I'm going to put some nuggets of information from today onto this thread. Here is a link to the Neylon, Ward, Towrie, and Parker Tus-Ter single-molecule proposal (linked in Cameron's open notebook; see PDF at the bottom): http://blogs.chem.soton.ac.uk/sortase... I think that the system they are studying fits...
more...
- Steve Koch
I started learning more acronyms having to do with open and linked data. RDF = Resource Description Framework http://en.wikipedia.org/wiki... There was some other acronym that I can't remember or find that Cameron was suggesting as a way of bundling an entire open data set of arbitrary format...lots of vowels, something like OAI... "open access...? NOTE...
more...
- Steve Koch
Cameron showed us some of the robots he and others have programmed for Google Wave. I learned that it's not crazily complicated to write a robot, and that you can use Google App Engine (http://code.google.com/appengi...) to host your code and run the robot. It currently runs Python and now Java. I still don't understand how it connects with Wave, but it solves a mystery to me of...
more...
- Steve Koch
(Coincidentally (or maybe not), right after waving with Cameron, Google Wave gave me my 20 invites to send out. Let me know if you need one!)
- Steve Koch
I'm sure Cameron and others have already said this in their many fantastic presentations and blog posts about wave. But I was happy to hear Cameron agree with my thinking that google wave + robots would be a very good way of handling data analysis workflows. When we process unzipping data, there are a few layers of software involved. I imagine each software application being run in the...
more...
- Steve Koch
Cameron's current LaBLog at Rutherford can be found here: http://biolab.isis.rl.ac.uk/cameron... Hopefully I'll be able to get access to this to see the edit features (I "requested" an account by logging in with my yahoo openid). I had previously been impressed by the notebook, but today was really wowed when I saw him edit a new entry. The particular things was the ability to...
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- Steve Koch
+1 for a Wave invite, please (pmiller@liv.ac.uk).
- Peter Miller
That's wonderful that Cameron visited your lab Steve! For all the usefulness of communication technologies nothing can replace a productive meatspace interaction.
- Jean-Claude Bradley
I had a great time - meeting and talking with Koch and the team. Lots of very cool stuff going on and lots of ideas that just seemed to bubble out of it. The meatspace interaction is really important but having that bit of background about what was going on and the context and trust built up here on Friendfeed amongst other places makes the whole discussion a lot quicker and more interesting.
- Cameron Neylon
Agree -- pre-meeting definitely made the in-person meeting very quick to start off. & @Peter Miller, sent the invite
- Steve Koch
Sounds like a fun (and productive!) day - thanks for sharing it with us, Steve. Also, I would appreciate a Wave invite (if you have any left!) - thanks! tom.tullius@gmail.com
- Tom Tullius
I hope to see some cool pics from this meet-up on Flickr :) Science builds upon Science especially in terms of ONS !! http://farm4.static.flickr.com/3358...
- Graham Steel
@Tom sent invite (fyi it takes several days to arrive) @Graham I think this is the only picture they got, unfortunately!
- Steve Koch
@Steve, Auch well. Best I can do with this 20.kB image is to B&W it, with a bit of res. conf.:- http://farm3.static.flickr.com/2620...
- Graham Steel
@Graham, I think I'm missing something. Is there a whole slew of cool open science photos on Flickr somewhere?
- Steve Koch
@Steve - I don't think there is..... yet. I take that back. Starter for 10 with http://farm4.static.flickr.com/3089...
- Graham Steel
Small number of people use the tags openscience - http://www.flickr.com/photos... and science2.0 - http://www.flickr.com/photos....
- Neil Saunders
Thanks for wave, Steve
- Peter Miller
Thanks, Steve
- Tom Tullius
from iPod
A few comments back, I was simply looking through this filter http://search.creativecommons.org/... with open science - At worst, some really cool Flickr/CC images for future usage for anyone.
- Graham Steel
It occurs to me that in virtually every photo of me online I'm wearing the same jacket and same shirt. Typical academic...
- Cameron Neylon
@Graham, loved that one: http://farm4.static.flickr.com/3089...
- Steve Koch
Cameron let me in on the mystery acronym: OAI-ORE "Open Archives Initiative" "Object Reuse and Exchange." http://www.openarchives.org/ore...
- Steve Koch
For images there are the ONS logos created by Andy Lang and Shirley Wu http://onsclaims.wikispaces.com/
- Jean-Claude Bradley
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