Sunday, September 30, 2007

InChI Rezzer in Second Life

Hiro Sheridan has just significantly upgraded the capabilities of his molecule rezzer in Second Life. It is available on the Chemistry Corner on Drexel Island. (SLURL)

Simply start it up and paste an InChI or InChIKey in the chat box and the rezzer will query web services provided by ChemSpider and Rajarshi Guha to look up the molecule, carry out a quick minimization then draw the structure in 3D. Here is a video that Hiro made to demonstrate:

This type of automation is moving us toward a world of ubiquitous realistic chemistry and smart chemical environments.

There was a time when I accepted spending an afternoon in the library looking up the synthesis and properties of a compound using dozens of books and lots of walking around. Today I fully expect to be able to do the same from anywhere in the world without leaving my computer.

Most chemists today have low expectations of chemical information in their environments. They see a 2D image of a molecule on paper or an online pdf and they just accept that. Peter Murray-Rust has been advocating for years that things don't have to be that way. Egon Willighagen, Rich Apodaca and Antony Williams are currently building tools that will change expectations, once chemists experience the difference.

What Hiro has done here is change the expectation of the organic chemistry experience in Second Life. When you come across a molecule in world, the bond angles and distances better be the same that I am teaching. Starting this term, my students will expect it - and I will expect it from them for their Second Life assignments.

Tuesday, September 25, 2007

ONS Case Studies

We had about a dozen participants at the Open Notebook Science Case Studies SciFoo Lives On session yesterday.

I talked about using a free and hosted blog (Blogger), wiki (Wikispaces), referral tracker (Sitemeter), mailing list (Google Groups), molecule database (ChemSpider) and raw data visualization (JSpecView) for managing UsefulChem.

Cameron Neylon described the use of blogs to track research in his group. In his approach each post is an object with a unique ID. His system will probably be more amenable to being read by automated agents and ultimately I would like to see something similar with the UsefulChem wiki experiment pages, although for the time being, we'll stick to freeform lab page entry that is easy to be read by humans. Cameron is now in the process of representing our experiment pages with his system and it will be interesting to see how it comes out. At the very least we are both learning from the exercise about how science is done and recorded in different fields by different researchers.

Jeremiah Faith also presented his system based on LaTeX. Jeremiah first used it privately to keep track of his research and then recently made it public. His lab notebook is now 400 pages. His advisor had no problem with letting him open his notebook to the world. It made me wonder if it would be worthwhile keeping a list of "Open Science Friendly" faculty on the SFLO wiki for students now looking for postdocs. I think there are probably several researchers who are not interested in actively pursuing some form of Open Science but would not have an objection to members of their group indulging in the practice.

Here is the transcript of the session.

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Sunday, September 23, 2007

Open Notebook Science Case Studies SFLO Session

Just a reminder that the ONS case studies session on SciFoo Lives On is tomorrow Sept 24, 2007 at 9:00 PT/12:00 ET/16:00 GMT.

The idea here is to get our hands dirty and look at the guts of our operations. What is working/what is not -what technologies are we using and where you can get them.

Cameron Neylon and I will be presenting but we hope there will be lots of discussion.

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Tuesday, September 11, 2007

Video in Science SFLO transcript

We had 3 talks yesterday at the Sept 10, 2007 SciFoo Lives On session on Video in Science. There were about 16 people and the discussion was lively with a lot of Q&A about the major services presented: Bioscreencast, SciVee and YouTube.

I was also pleased to see Lali, the researcher I met over the weekend who put up the first poster in the Chem/BioFoo area. She has blogged about her experience entering Second Life as a scientist and trying to understand what can be done there that is meaningful to her interests.

Also see other reports of this session:



[9:00] You: hi everybody
[9:00] You: thanks for coming
[9:00] Vishwaroop Baroque: hello horace
[9:00] WhiteWizard Chemistry: I am on a crummy wireless connection, so tend to get stuck *grins*
[9:00] You: we have 3 speakers today
[9:00] You: on the use of video in science
[9:00] You: after the talks if you want to hang around to look at posters
[9:00] You: I'm sure presenters will stay
[9:01] You: please get us started Berci
[9:01] Berci Dryke: thank you, Jean-Claude!
[9:01] Berci Dryke: Nice to see so many participants again!
[9:02] Berci Dryke: our first speaker is Deepak Singh from Bioscreencast who is also the author of the blog
[9:02] Berci Dryke: Deepak, please present your service!
[9:02] WhiteWizard Chemistry: Thanks Berci
[9:02] Zaldar Rhode is Online
[9:02] WhiteWizard Chemistry: Hi Folks ... today I wanted to spend a few minutes talking about video in science and why we started Bioscreencast
[9:03] WhiteWizard Chemistry: Actually Hari aka Vishwaroop, who is in here is the main culprit
[9:03] Vishwaroop Baroque: hi guys ...its good to see you all here
[9:04] WhiteWizard Chemistry: In recent years, thanks to broadband, RSS and Flash, multimedia on the internet has really taken a huge leap. I think YouTube pretty much personifies this
[9:04] WhiteWizard Chemistry: But also live shows like the Chris Pirillo Show, which I believe will be the next step
[9:04] WhiteWizard Chemistry: And science has taken steps in this direction. You have the Nature podcast, which will hopefully include video some day
[9:05] WhiteWizard Chemistry: and SciTalks captures presentations, often from the Google Tech talks and other scientific conferences
[9:05] WhiteWizard Chemistry: Then we have JoVE and SciVee. I will let SciVee describe their service
[9:05] WhiteWizard Chemistry: But essentially I see JoVE and SciVee as a wonderway way to present science somewhat formally through video. And I am looking forward to creativity :)
[9:05] Visitor Counter 1.8: Welcome Hilena Capalini. You have been counted.
[9:06] Visitor Counter 1.8: Welcome Icabad Vallejo. You have been counted.
[9:06] WhiteWizard Chemistry: Bioscreencast on the other hand is a service that is inspired by Jon Udell and his use of screencasting, which some people in this room already use for teaching and other purposes
[9:06] Vishwaroop Baroque is Offline
[9:07] WhiteWizard Chemistry: A lot of us have knowledge, often better than can be found in manuals and instructional web pages. We can share it and add to it. Video is just a means to do so, a powerful one.
[9:07] Berci Dryke: please give us time with the slides, we have to load them :)
[9:07] Zen Zeddmore is Online
[9:07] Zaldar Rhode is Offline
[9:07] WhiteWizard Chemistry: Sure thing
[9:08] Visitor Counter 1.8: Welcome Krystine Qinan. You have been counted.
[9:08] Troy McLuhan: If you hover your cursor over the slide image, that increases its load priority
[9:08] WhiteWizard Chemistry: Bioscreencast is essentially one way for anyone who knows how to use a piece of software or a web service to capture their actions on screen, add a narrative and share with their peers
[9:09] WhiteWizard Chemistry: The hope is that if you ever wanted to find out how to learn to use a piece of software or share your expertise, you could easily upload something there and others could consume it, comment on it, and perhaps add their own take
[9:09] WhiteWizard Chemistry: So what you are seeing now is the front page. It's your typical web 2.0 site
[9:09] WhiteWizard Chemistry: :)
[9:10] WhiteWizard Chemistry: Right now everything is converted to Flash, so that you can play it on any machine
[9:10] WhiteWizard Chemistry: You can also request screencasts about a specific subject and people can vote on that
[9:11] You: have you had requests ww?
[9:11] WhiteWizard Chemistry: Again the hope is that others in the community who have expertise in the field could upload something
[9:11] Habermas Aya: What do you call 4 identical sisters again?
[9:12] WhiteWizard Chemistry: Anyway ... I will stop talking here and take questions.
[9:12] WhiteWizard Chemistry: Horace .. yes a few. Vector NTI is the #1 request
[9:12] WhiteWizard Chemistry: So any Vector NTI geeks feel free to post something
[9:12] WhiteWizard Chemistry: (bit of a lag at this end)
[9:12] You have offered friendship to Habermas Aya
[9:12] WhiteWizard Chemistry: Is everyone clear about what a screencast is? It is essentially screen capture, but in video form
[9:13] You: what software do you use for screencasting deepak
[9:13] Vishwaroop Baroque is Online
[9:13] WhiteWizard Chemistry: Horace .. I happen to have a free version of Camtasia thanks to a conference, but there is Camstudio (Free). Also Hari uses IShowU (I think)
[9:14] WhiteWizard Chemistry: Vishwaroop do you have anything to add?
[9:14] You: I use Camtasia because we have it at Drexel
[9:14] Berci Dryke: just a question: can we edit our screencasts?
[9:14] Troy McLuhan: Four identical sisters... hmm.... maybe a quadraisosorora?
[9:14] WhiteWizard Chemistry: Not yet ... you could probably upload a new version
[9:14] You: clones
[9:15] Samara Barzane is Offline
[9:15] WhiteWizard Chemistry: Some day hopefully .. :)
[9:15] Sumney Zenovka is Online
[9:16] Vishwaroop Baroque: sorry I dropped out- im back now..harijay co-culprit
[9:16] WhiteWizard Chemistry: Currently we have screencasts for OWL, UniProt and Galaxy there which might interest the bioinformatics crowd ... would love to see other types
[9:16] WhiteWizard Chemistry: like Horace's NMR one
[9:16] You: yes screencasts can be useful for explaining science
[9:16] Vishwaroop Baroque: Or the Unprot one from elizabeth phan
[9:17] Habermas Aya: It seems this slide is pointing to wikis
[9:17] WhiteWizard Chemistry: Ah yes forgot that
[9:17] Berci Dryke: If I would like to create screencasts, about how much it would cost to me?
[9:17] WhiteWizard Chemistry: we have a wiki too .., where we have information on how to do screencasting etc
[9:17] WhiteWizard Chemistry: It could cost you as much as nothing
[9:17] Berci Dryke: and the software?
[9:17] You: there is a 30 trial version of Camtasia
[9:17] Berci Dryke: oh
[9:17] You: 30 day
[9:17] WhiteWizard Chemistry: Camstudio is free as well
[9:18] Habermas Aya: do you use the wiki structure to create and collaborate via videos?
[9:18] You: but Camstudio has some problems
[9:18] Habermas Aya: A video wiki
[9:18] Vishwaroop Baroque: The screencast apps arr all listed onour wiki several of them ( esp for windows and linux ) are free..the few othe rones we have played with run from $20 to $300
[9:18] WhiteWizard Chemistry: The wiki is more of a knowledgebase right now, but you could. One problem is that not all wiki platforms support embeding
[9:19] WhiteWizard Chemistry: I think wikispaces supports video as does mediawiki which is what we use (Hari correct me if I am wrong)
[9:19] You: yes wikispaces supports
[9:19] Habermas Aya: yes wikispaces has great multimedia support
[9:19] WhiteWizard Chemistry: The cool thing is you could host your videos on bioscreencast and just embed them on your wiki
[9:19] WhiteWizard Chemistry: or any other website
[9:20] Vishwaroop Baroque: We are using mediawiki- the choice was based entirely to ease its adoption as a container for linked screencasts
[9:20] Habermas Aya: yes and wikispaces provides it as a service
[9:20] You: how many videos do you have now?
[9:20] Troy McLuhan: How is Bioscreencast funded?
[9:20] Habermas Aya: My people have found Wikipedia impossible
[9:20] WhiteWizard Chemistry: about 60-65?
[9:20] Berci Dryke: (the Camstudio link in the wiki is broken)
[9:20] WhiteWizard Chemistry: No funding
[9:20] WhiteWizard Chemistry: we are pretty much doing this from our own pockets
[9:20] WhiteWizard Chemistry: it's still very much an "after hours" project :)
[9:21] You: the problem with Camstudio is the Flash convertor is poor
[9:21] Habermas Aya: so the subject is screen casts, captures of computer screens?
[9:21] Habermas Aya: no conferencing?
[9:21] WhiteWizard Chemistry: yes .. habermas .. its about sharing how you use software or webservices. At least thats our current goal
[9:22] Sumney Zenovka is Offline
[9:22] Habermas Aya: have you rejected flash animations for any reason?
[9:22] Vishwaroop Baroque: Sorry for that broken link..its fixed now
[9:22] WhiteWizard Chemistry: I am not sure I understand the question?
[9:22] You have offered friendship to Katharine Martinek
[9:22] Vishwaroop Baroque: Camstduio is one of the better featured FREE screencasting apps for windows
[9:23] Habermas Aya: It seems to train software usage a flash animation is rather interactive
[9:23] You: can you upload the avi from Camstudio?
[9:23] Habermas Aya: I have used them for 10 years to make help systems on software
[9:23] Berci Dryke: I'm downloading it right now (you made me curious)
[9:23] WhiteWizard Chemistry: ah yes .. but then the barrier to creation is higher. We want to keep it informal
[9:23] WhiteWizard Chemistry: and it is a great idea
[9:24] WhiteWizard Chemistry: I don't think we would reject a flash animation
[9:24] Vishwaroop Baroque: Yes you can upload avi from camstudio our curent file size limit is set at 100MB so even a half hour screencast can be uploaded
[9:24] You: so it is fine then - the problem with Camstudio is their Flash convertor
[9:24] Lali Ewry: Can I make a request?
[9:24] Katharine Martinek is Online
[9:24] Lorri Momiji is Offline
[9:24] WhiteWizard Chemistry: sure thing
[9:25] Lali Ewry: I want to learn how to use R
[9:25] Lali Ewry: the statistics program
[9:25] Lali Ewry: :)
[9:25] WhiteWizard Chemistry: Anyone up for some R screencasts :)?
[9:25] Berci Dryke: :)
[9:25] Lali Ewry: hehe
[9:25] Habermas Aya: sure
[9:25] WhiteWizard Chemistry: or flash animations
[9:26] Berci Dryke: if there aren't any new questions, we should move to the next poster
[9:26] WhiteWizard Chemistry: Thanks everyone
[9:26] Vishwaroop Baroque: Well Lali it would be good to add the request to our request page
[9:26] You: thanks deepak
[9:26] Berci Dryke: Thank you, Deepak, I'm sure you'll get a lot of questions after the session :)
[9:26] Lali Ewry: I will check it out
[9:26] You: I'll be tyou have some converted people now :)
[9:26] WhiteWizard Chemistry: I sure hope so .. its fun
[9:26] You: I just have 2 slides here
[9:27] You: in my lab we have been using YouTube to record experiments
[9:27] You: often the students don't realize what is important to note in their notebook
[9:27] You: so I encourage them to link from our lab wiki to youtube
[9:27] You: these are examples
[9:28] You: one is an reaction flask
[9:28] You: and the other is a chromatography technique called the chromatotron
[9:28] You: these are not edited or produced in any way
[9:28] You: just rapidly done - the context would be in the wiki notebook
[9:29] You: sombody clicked it:)
[9:29] You: good - this slide shows what Deepak was saying about screencast of the analysis of a reaction
[9:29] You: I am analyzing NMR data
[9:30] You: and the bottom one is a video of docking our molecules in Second Life with Hiro's help
[9:30] You: by the way notice that the bottom recording has over 5000 views in the past year
[9:30] WhiteWizard Chemistry: Wow .. wonderful!!!
[9:30] You: so this might also get a way to get younger students interested in science
[9:31] You: since they are already on YouTube
[9:31] Berci Dryke: fantastic!
[9:31] You: any questiosn?
[9:31] Habermas Aya: How is the data structure, just ou wiki?
[9:31] Berci Dryke: but there isn't any scientific category in Youtube, I don't know why...
[9:31] You: true - this is under howto
[9:32] Lali Ewry: I am really curious about the NMR one, one of my colleagues is working on NMR metabolite analysis
[9:32] You: by the way if you click on my picture at the top it takes you to the usefulchem keyword search on youtube
[9:32] Habermas Aya: yes what is the metadata structures collaboration to get this informaiton out there
[9:32] You: Habermas - you mean how do people find it?
[9:32] Habermas Aya: Yes, finability and distribution
[9:32] Habermas Aya: not just search though
[9:33] Habermas Aya: 5,000 is what a film of a kid eating worms gets in a day lol
[9:33] You: well they are linked directly from our lab notebook wiki, where the context is fully explained
[9:33] You: so most people would find it through there probably
[9:33] Habermas Aya: and is that on wikispaces?
[9:33] You: yes on wikispaces - it rules!
[9:33] Habermas Aya: yes I have been a fan for a while
[9:33] You: CC license by default
[9:34] Habermas Aya: do you also use or any bookmarking technology with tagging?
[9:34] You: i played around a bit with delicious but it didn't fit my needs enough to go wild on it
[9:34] You: so far....
[9:34] Habermas Aya: How about MySpace of FaceBook
[9:34] Habermas Aya: or
[9:35] You: I have been dragged into FaceBook lately
[9:35] You: by many of the people here:)
[9:35] You: I like it actually
[9:35] Habermas Aya: as do 100,000 people a day
[9:35] Troy McLuhan: LOL I feel the same way about Facebook... dragged in
[9:35] Habermas Aya: I feel the same way about SL
[9:35] You: yes SL was a though sell for me
[9:35] WhiteWizard Chemistry: Tag*Raises hand * guilty as charged
[9:36] You: until I attended a class of my colleage Beth Ritter-Guth
[9:36] You: once I saw that it actually worked I knew that I wanted to use it to teach
[9:36] WhiteWizard Chemistry: Horace sold me on SL
[9:36] WhiteWizard Chemistry: at Scifoo
[9:36] You: then I attended a poster session and became a convert of that
[9:36] Habermas Aya: Yes the problem with SL is findability
[9:36] WhiteWizard Chemistry: Horace .. what do you think are the barriers to video getting more commonly used the way you are leveraging it?
[9:36] Habermas Aya: which is the problem I see with these video silos
[9:36] You: yes Haber you have to have a reason to go to SL
[9:37] You: the barrier may be more related to the PI encouraging use
[9:37] You: of their students in the lab
[9:37] You: I think many students are open to it
[9:37] Habermas Aya: yes but the key to science teaching is going to be getting beyond the lab
[9:37] Berci Dryke: if there are no more questions, can we move on to SciVee's poster? (time is running fast)
[9:37] You: thanks Berci
[9:37] Berci Dryke: thank you, Jean-Claude!
[9:38] Habermas Aya: thank you
[9:38] You: scivee is busy...
[9:38] Berci Dryke: the speaker is sleeping :)
[9:38] You: sleeping on the job
[9:38] WhiteWizard Chemistry: :)
[9:38] Morrhys Graysmark is Online
[9:38] SciVee Chemistry: Quick question before I start… how are the slides forwarded?
[9:38] Berci Dryke: Apryl, please present SciVee to us!
[9:39] Berci Dryke: just click on the board
[9:39] You: mouse clic
[9:39] Vishwaroop Baroque: Sciveee is a great development in the science video space
[9:39] SciVee Chemistry: ok thanks
[9:40] SciVee Chemistry: Hello all, thank you for tuning in today…. This is a fun and interesting opportunity to be here and we look forward to becoming more involved in many manifestations of Science Web 2.0 as we evolve.
[9:40] SciVee Chemistry: Our site is still in Alpha, but we are so grateful to all who have shown an interest in our project and look forward to meeting the many requests and suggestions that the scientific community has sent us.
[9:41] Vishwaroop Baroque: how many people are behinf scivee
[9:41] SciVee Chemistry: SciVee is operated in partnership with the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC).
[9:41] SciVee Chemistry: hi Vishwaroop Baroque, there are about 9 people
[9:41] SciVee Chemistry: may I answer allt he questions at the end?
[9:42] You: sure sv
[9:42] Berci Dryke: as you wish
[9:42] SciVee Chemistry: ok, thank you
[9:42] SciVee Chemistry: SciVee allows scientists to communicate their work as a multimedia presentation incorporated with the content of their published article.
[9:42] SciVee Chemistry: Other scientists can freely view uploaded presentations and engage in virtual discussions with the author and other viewers. SciVee also facilitates the creation of communities around specific articles and keywords.
[9:42] SciVee Chemistry: Science is conservative and new generations are the major motivators of change.
[9:43] SciVee Chemistry: Like all you hear today...
[9:43] SciVee Chemistry: Phil Bourne, SciVee co-founder, noticed that MOST of his students were spending a lot of time on YouTube when they should be working on their thesis projects. As a professor, he often caught them in the act watching videos.
[9:43] SciVee Chemistry: and here... :)
[9:43] SciVee Chemistry: It occurred to Phil that they could be using YouTube to do science. But the content on YouTube can be difficult to find and is mixed with a wide range of other materials.
[9:43] SciVee Chemistry: Plus the quality or scientific viability is not assured.
[9:44] SciVee Chemistry: SciVee is Phil's solution to this problem.
[9:44] SciVee Chemistry: It is a video website dedicated to scientific content. We ensure quality content by promoting the upload of videos related to peer-reviewed articles" (this is different from ensuring high *production* quality.
[9:44] Emile Pintens is Online
[9:44] SciVee Chemistry: futhermore, phil has noticed that the open access movement in scientific publishing was initially well-received but that the scientific community has made little use of the possibilities that it offers
[9:45] SciVee Chemistry: plos has very high quality content and by associating with them, we hope to be more reputable
[9:45] Cary Flanagan is Online
[9:45] SciVee Chemistry: sorry I didn't keep my slides up with my presentation...
[9:46] SciVee Chemistry: if you have any questions please feel free to ask
[9:46] SciVee Chemistry: :)
[9:46] WhiteWizard Chemistry: Scivee ... is the goal always to be associated with publications?
[9:46] Berci Dryke: thank you! who can upload videos?
[9:46] SciVee Chemistry: anyone that has scientific content
[9:47] You: are there any screencasts on scivee?
[9:47] Vishwaroop Baroque: So it is then a Youtube for the sciences
[9:47] SciVee Chemistry: another important thing to remember is that we have two types of video content
[9:47] SciVee Chemistry: we accept video content that is relevant to a published peer reviewed paper
[9:48] You: what about editorially reviewed lik Nature Precedings?
[9:48] SciVee Chemistry: we have been called the "YouTube for scientists" by SlashDot
[9:48] SciVee Chemistry: we have also enabled the upload of videos unrealated to a paper
[9:49] WhiteWizard Chemistry: I am actually hoping that scientists posting to scivee get very creative with how they leverage video
[9:49] SciVee Chemistry: I am not familiar with Nature Precedings, Horace but we can look into it afterwards
[9:49] Troy McLuhan notes that the SciVee "Terms of Use" are still ambigious. On the one hand, they apply the Creative Commons Attribution 3.0 License, but then they say "SciVee applies the Creative Commons license to all of the video content on this site in order to make the work freely available for non-commercial purposes." (CC Attribution 3.0 allows commercial purposes.)
[9:49] SciVee Chemistry: I totally agree with youWhiteWizard
[9:50] WhiteWizard Chemistry: Will the onus on video production always be with the scientist uploading the video?
[9:51] SciVee Chemistry: We are soon to have a meeting with Phil about the ambigiuity of the terms... and speak with a lawyer. :)
[9:51] Vishwaroop Baroque: How about quality control and accuracy of content
[9:51] Troy McLuhan: Great
[9:52] Habermas Aya: How narrow is scientist defined
[9:52] Habermas Aya: I work in the social research
[9:52] SciVee Chemistry: Quality Control is another great concern
[9:52] You have offered friendship to Atina Davies
[9:52] SciVee Chemistry: we hope that the community will be interested in keeping the quality high and reporting abuse, somewhat like wikipedia retains validity
[9:53] Atina Davies is Online
[9:53] Habermas Aya: But again how narrow is the concept of scientists
[9:53] WhiteWizard Chemistry: I think your initial approach (typing it to published content is one good way of maintaining quality)
[9:53] Habermas Aya: is this restricted to hard scienctists or social thinkers who deal with science
[9:53] Habermas Aya: For example if I was to destruct a sceintific study would it be part of the site?
[9:54] SciVee Chemistry: Yes that is why we have separated the peer reviewed publications of pubcasts from the community video section on our site
[9:54] You: do you have a limit on length?
[9:55] Vishwaroop Baroque: Have you contacted the authors of a ny recent papers ? how has the response been
[9:55] WhiteWizard Chemistry: Habermas .. I sure hope social science is permissible .. it should be
[9:55] SciVee Chemistry: Since we want to retain quality, it is important for us to have the peer reviewed paper + video combinations in specified channels
[9:55] Habermas Aya: My concern is the wikipedia refernce where bias is used to insure quality
[9:55] SciVee Chemistry: additionally, pubcasts allow the author to present information that cant be included in a traditional article
[9:56] WhiteWizard Chemistry: Habermas ... in theory you could self police if the community gets strong enough. I think that is critical for anything in this space. Wisdom of crowds and all that.
[9:56] SciVee Chemistry: we hoep to meet the demand to keep the quality as high as possible
[9:57] Katharine Martinek is Offline
[9:57] Habermas Aya: sounds good
[9:57] You: We are almost out of time - thanks SciVee!
[9:57] Berci Dryke: great presentations and posters!
[9:57] Habermas Aya: yes
[9:57] Troy McLuhan: I guess you could have a paper on some results from a fluid dynamics simulation, and you could show an animated visualization
[9:57] SciVee Chemistry: it is great to know that you are also concerned with the quality of the science presented on SciVee
[9:57] You: If anyone wants to stick around you are welcome to look at any poster here
[9:57] You: Thre is a Nature Precedings poster in the front
[9:57] Berci Dryke: thank you for participating in this session!
[9:58] Stargazer Blazer is Online
[9:58] You: check for the next sessions on the wiki
[9:58] SciVee Chemistry: thank you everyone

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Saturday, September 08, 2007

ChemBioFoo Lives

Ding dong - one of my bells emailed me today.

Someone was at the gate of the BioChemFoo area on Nature Island in Second Life and wanted assistance with setting up a poster.

When I logged on I found Lali Ewry (a researcher) and Bronwen Pizzicato (from Nature Protocols) still waiting there. Since there were no posters yet in the ChemBioFoo area I took them over to the adjacent SciFoo Lives On section to show them examples of what posters can look like in Second Life.

Lali had some slides available so I gave her one of Hiro's boards and showed her how to upload, re-size and move the poster. (By the way Hiro's boards have the nice feature that, as a presenter, you can go backwards in your presentation and the boards reset to the starting slides after a few minutes of inactivity)

We took her board to the ChemBioFoo area and Lali positioned it at poster #1. She also put a bell so others could summon her to discuss her work on "Transcription of Inflammatory Genes in Crohn's Disease". There are wonderful images in that presentation about the mechanics of the disease and Lali is still adding more. She had some animations that have to be converted to still images before posting.

Lali's real name is Laura Ferrero-Miliani and she is at Herlev Hospital, Medical-Gastroenterology Lab 54O3 in Denmark.

This is a perfect example of what I had in mind for ChemBioFoo. In keeping with the SciFoo un-conference, the SciFoo Lives On area has some great posters to promote and discuss Open Science and new Science Communication Technologies. However, I think there needs to be a place to host domain-specific scientific discussion as perpetual poster sessions in Second Life.

This is actually very much in keeping with the format of the Nature journal itself. The articles are typically high level and are collected from various scientific fields. I am starting with Chemistry and Biology because I feel that these areas have a strong potential for improving human lives directly (in terms of affecting disease processes for example). Also these areas are most closely related to my domain specific research of organic synthesis and drug design. (And we only have 36 booths in this area for now). Of course I would be happy to assist anyone in creating a poster area with another scientific focus.

I often tell people that they should only enter Second Life if they have a good reason for doing so. By putting posters that are similar in format and content to those that the typical researcher is likely to find at the physical conferences that they attend is probably a pretty good way to attract traditional scientists to media platforms like Second Life. If they see a poster that is interesting they can ring the bell, talk with the presenter then decide how that experience compares with a physical meeting.

So I am asking for anyone interested in contributing to let me know (or Lali - she is trained now to help the next presenters after all).

My presentation is coming up - I have a few more slides to put together. Tony Williams from ChemSpider also sent me a presentation that I'll put up shortly.

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Thursday, September 06, 2007

Second Life Science Center

Troy McConaghy has set up a wiki to keep track of science initiatives in Second Life.

One really nice feature on there is a Google calendar for upcoming events. SciFoo Lives On sessions are listed there.

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Wednesday, September 05, 2007

Definitions in Open Science SFLO Transcript

We had our third SciFoo Lives On session yesterday (September 3, 2007).

The topic was "Definitions in Open Science" and there were two posters: mine on Open Notebook Science and Bill Hooker's on broader considerations. Richard Akerman also presented, using some of Bill's slides, where he was cited.

As I expected, there were fewer attendees than last week (about a dozen compared to over 30 for the Medicine 2.0 session). Defining terms is not exactly the sexiest of topics. As Bill mentioned, it is more interesting to do the work, rather than philosophize about it. I agree with him for the most part - in fact I think that defining terms from a top down way can be counterproductive, especially if we hold back doing work, waiting for standards and terms to be entirely established.

Terms are useful to succinctly communicate ideas and it is even fine for terms to be "fuzzy", as long as everyone communicating understands that. For example, the term "open science" is extremely broad and as such it is useful to describe categories (such as sessions here and at SciFoo).

Problems arise when people use terms with multiple meanings. For example "Open Source Science" may mean Open Source scientific software or science done openly. Even in the later definition, confusion can arise. For me, openly means that that the raw data should be available on the open internet but that is not an assumption shared by everyone. That's why I started using the term "Open Notebook Science".

A recent confusion over definitions has surprised many people. The term "Open Access" has had a fairly unambiguous definition: universal free online access to traditional journal articles. However, as Peter Murray-Rust has reported lately, the term has been abused my some publishers.

Next week - Monday September 10, 2007 at 16:00 - the SFLO session is "Video in Science". We should have a good turnout. For other sessions information see the SFLO wiki.

Here is the transcript:

[9:00] You: ok lets get started
[9:00] You: you will notice some changes from last week
[9:00] You: the posters are ordered and will remain there
[9:00] You: so that we can have poster sessions anytime
[9:00] You: there are bells on some of them
[9:01] You: they tell you if the presenter is online
[9:01] You: and gives you a way to summon them if youwant to talk
[9:01] You: I thought we would give the "poster session" a try in breakout groups after the talks
[9:01] You: we have a smaller set this week anyway - 3 speakers
[9:02] You: so this week is about definitions in open science
[9:02] You: I have 3 slides here to discuss my concern
[9:02] Hiro Sheridan is Online
[9:02] You: Bill Hooker and Richard Akerman will discuss their points in a few minutes
[9:03] You: the confusion has been (I noticed this at Scifoo also)
[9:03] You: that one person uses the term open science
[9:03] You: and the listener interprets it very differently
[9:03] You: there are many shades of open science
[9:04] You: the most closed form of science I think is the private lab notebook of a researcher
[9:04] You: then the traditional article is shared with the world but is not free
[9:04] You: Open Access has come to mean something very specific
[9:04] CW Underwood is Online
[9:05] You: that of standard articles made free to view
[9:05] You: well Peter Murray-Rust would have a lot more to say about that but couldn't make it
[9:05] You: finally on this plot the term that is of most interest to me
[9:06] You: is Open Notebook Science, where the reseracher's actual lab notebook is made public in real time
[9:06] Vidal Loon is Online
[9:06] You: I think it is important that ALL experiments are made public for ONS
[9:06] You: the selection of experiments when writing an article can leave one with the impression
[9:07] You: that the science is a lot simpler than it really is
[9:07] You: by doing ONS, people can also study how science actually gets done, messiness and all
[9:07] You: we do ours in a wiki
[9:07] You: but other people have interesting approaches
[9:08] You: Cameron Neylon is using a blog to record experiments
[9:08] You: any comments or issues you guys want to discuss?
[9:08] Troy McLuhan noticed that the blogs now support LaTeX markup - handy for math etc.
[9:09] Hiro Sheridan: I love the idea of how students can view the research process
[9:09] Berci Dryke: and how they can be tracked :)
[9:09] Hiro Sheridan: I wish I had that available when I was a student
[9:09] You: yes it is a way of interacting with my students that is handy
[9:09] CW Underwood: there's a caution to be voiced, though, about laws and sausages...
[9:09] Vidal Loon: tracked, corrected, discussed, etc
[9:09] Emile Pintens: Is everyone else hearing the side conversation?
[9:09] You: I leave comments in bold and italics and they can respond
[9:09] CW Underwood: there's a side discussion?
[9:09] Vidal Loon: wikis allow for all this and more.
[9:10] You: we're not using right now guys - maybe later in the breakout sessions
[9:10] WhiteWizard Chemistry: Agreed. My concern is that we might end up in a situations where different ways of recording science will not interact with each other and not be transportable
[9:10] Duriel Akula: from an evolutionary point of view it also makes the process modular. the importance becomes the individual experiments and not the paper
[9:10] Troy McLuhan: When I said blogs, I meant wikis
[9:10] WhiteWizard Chemistry: Troy that is excellent
[9:10] You: the standardization is an issue
[9:10] Hiro Sheridan: Horace do you want to mention how we used google docs to collaborate?
[9:11] CW Underwood: modularity is very important -- i think the future of the scientific paper as we know it is limited
[9:11] Emile Pintens: We have integrated wikispaces into Knowble as an FYI
[9:11] You: the way we are approaching it is to first worry about recording all the science
[9:11] Emile Pintens: It is a work in progress though..
[9:11] CW Underwood: i think science will (soon?) be reported experiment-by-experiment
[9:11] You: so we use free text with links to spectra and molecules
[9:11] You: but we are going to add automation to process much of that
[9:12] Hiro Sheridan: :)
[9:12] You: for example we now use InChI tags in all experiments
[9:12] You: to track molecules
[9:12] WhiteWizard Chemistry: How does this tie into Neil Saunders' desire for an open source electronic lab notebook? I can see one with specific modules for different science/data types
[9:13] Duriel Akula: i guess that goes a bit into the standards , microformats etc
[9:13] You: usually when people refer to open source electronic notebooks they mean open source software I think
[9:13] Clay Cazalet is Online
[9:13] CW Underwood: frankly, i haven't seen an ELN that does anything better than a wiki...
[9:14] You: from my experience i think a general purpose wiki works very well as lab notebook
[9:14] Duriel Akula: I cant speak for Neil , but I think he does mean a ELN system. that really does not exist per se.
[9:14] CW Underwood: though I haven't looked at the Neylon lab's attempt to use custom blog software as an ELN
[9:14] WhiteWizard Chemistry: The cool thing is that we are just at the start and there is such an opportunity here
[9:14] Vidal Loon: Wikis can be extended with many new functions. Mediawiki allows for extensions and these can make the wiki a better tool for science research information. One very good example of this is the work being done at OpenWetWare.
[9:14] You: the Neylon lab is based on a blog format
[9:15] You: ww I think that is the point
[9:15] You: there are lots of opportunities
[9:15] Rakerman Yellowjacket: I think eSciDoc may be working on an e-lab notebook
[9:15] You: to experiment with science
[9:15] CW Underwood: " experiment with science" -- that, after all, is what we do, no? :-)
[9:16] Duriel Akula: I am hoping one of the big guys comes out with a system for your scientists to manage their labs online, so that this can lift off
[9:16] You: I think scientists take a lot for granted in how science can be done
[9:16] Duriel Akula: *young scientists"
[9:17] You: Richard, would you like to say a few words before Bill?
[9:17] Rakerman Yellowjacket: sure
[9:17] Rakerman Yellowjacket: let me run some ideas up the virtual flagpole, as it were
[9:17] Vidal Loon: I personally think that these tools and much more can be weaved together to make a real "office" type of setup for the scientist to keep tabs on the info and have it available for other.
[9:17] Rakerman Yellowjacket: my perspective comes from software engineering and enterprise architecture
[9:18] Rakerman Yellowjacket: both of which have big aspects of technology planning based on requirements gathering
[9:18] Vidal Loon: there are just so many tools available to juggle data nowadays. it's a question of knitting them all together.
[9:18] CW Underwood: VL: as long as each module stands alone and doesn't lock anyone into anything, that's a great idea (don't like the idea of Office as model though...)
[9:18] WhiteWizard Chemistry: Agrees with Rakerman
[9:18] Rakerman Yellowjacket: so when I saw the discussions at SciFoo I thought it would be useful to apply that kind of thinking, to systematise the discussion
[9:19] Rakerman Yellowjacket: I found a lot of things were getting mixed together - desire for speedy publication, desire for recognition for grants/tenure/post-doc, and issues with the current scholarly communication system
[9:19] Rakerman Yellowjacket: so i think the key is to focus on what problem you're trying to solve
[9:19] Rakerman Yellowjacket: To me, when I hear the core of the discussions about open science
[9:19] Rakerman Yellowjacket: it's about making better *science* through collaboration and open sharing
[9:20] CW Underwood: better science, yep
[9:20] Rakerman Yellowjacket: that is quite different from some of the goals of open access, which address availability of science later on
[9:20] Rakerman Yellowjacket: so I would suggest focusing around the aspect of making better science happen through open communication
[9:21] Rakerman Yellowjacket: then that leads to a clearer discussion of the kinds of tools that would support that
[9:21] Rakerman Yellowjacket: we have already seen a good discussion about using wikis
[9:21] Rakerman Yellowjacket: from a library perspective, I think one of the most useful aspects is to preserve more of the scientific work from the get-go
[9:21] You: yes Richard is right - first and foremost get the science done then worry about technology
[9:22] Rakerman Yellowjacket: often today data and failed experiments are lost from the record, even if they had some original ditgital format
[9:22] Rakerman Yellowjacket: we don't want the current science work to be a digital dark age when seen from the future
[9:22] WhiteWizard Chemistry: Scientists should worry about the science ... someone else should (working with the scientists) think about the technology that makes lives easier for scientists
[9:22] Rakerman Yellowjacket: I see some positive developments in terms of science communication
[9:23] Rakerman Yellowjacket: one example is eSciDoc, a project in Germany to develop end-to-end communication - from lab notebook to publication and beyond
[9:23] Rakerman Yellowjacket:
[9:23] You: As long as authors retain copyright - they don't have to worry about re-formatting their work :)
[9:23] Rakerman Yellowjacket: I also think Fedora Commons presents a lot of opportunities in this area
[9:23] Rakerman Yellowjacket:
[9:24] Rakerman Yellowjacket: as a mostly-technology guy these days, I'm interseted in gathering the best requirements so that the tools support the real goals!
[9:24] You: have you looked at the escidoc richard?
[9:24] Rakerman Yellowjacket: So I agree with WhiteWizard
[9:24] Rakerman Yellowjacket: What I'm concerned about is if we're not careful, often we end up with closed systems - like Facebook, or even Blackboard and WebCT
[9:25] Rakerman Yellowjacket: Horace I have seen the eSciDoc people present, I think they're doing great work
[9:25] You: I think redundancy is a way to safeguard getting locked in
[9:25] You: is their work open to anyone
[9:25] Duriel Akula: I would not mind to have a company making a profit with such a system
[9:25] Duriel Akula: as long as the data was open to anyone
[9:25] WhiteWizard Chemistry: and examples like Aordpress/Automattic provide excellent examples for profitable open source platforms
[9:26] Rakerman Yellowjacket: as far as I know, they plan to share the Scholarly Workbench once it is developed
[9:26] WhiteWizard Chemistry: oope Wordpress
[9:26] You: the company interface is interesting - for example ChemSpider
[9:26] CW Underwood: I don't mind who makes what money, but I'd like to see the software on SourceForge...
[9:26] You: is a company but giving out database for free
[9:27] Rakerman Yellowjacket: I think there are lots of different models, the main goal is that the information should be open to improve science collaboration and preservation
[9:27] WhiteWizard Chemistry: There are models oand made available to other developers to build on top of
[9:27] Rakerman Yellowjacket: Horace, do you want to move to Bill's presentation now?
[9:28] You: sure
[9:28] Duriel Akula: it actually an interesting business model, so much would be known about each groups reasearch that it would make ads much more valuable
[9:28] You: thanks Richard
[9:28] CW Underwood: heh, presentation?
[9:28] CW Underwood: I'm not sure what I can say that isn't in the slides
[9:28] CW Underwood: they are so full of text because I had no idea what SL was like
[9:29] You: do you have any thoughts Bill that have not been discussed?
[9:29] CW Underwood: I think the easiest way to go through it would be as questions for discussion
[9:29] CW Underwood: first question being: do we need/want to define Open Science
[9:29] CW Underwood: further than it already is (al la Richard)
[9:30] Hiro Sheridan: Do you think there is a need for an open-science format - some sort of xml data format?
[9:30] WhiteWizard Chemistry: I think that is a key point. We tend to get bogged down in philosophical arguments
[9:30] CW Underwood: i think that most of the tools are already available, if perhaps a bit clumsy
[9:30] CW Underwood: think of wikis and what JC is doing
[9:30] CW Underwood: a fully featured ELN suite might be slicker
[9:31] CW Underwood: but it would not capture any more science
[9:31] Hiro Sheridan: It would be nice to be able to mashs thing up though
[9:31] CW Underwood: and once it becomes available it will be able to slurp up the wikified content
[9:31] CW Underwood: Hiro's idea of a standard format is very important though
[9:31] Rakerman Yellowjacket: I think we are going to need lots of different formats depending on the discipline (for data interchange)
[9:31] You: yes that is the point Bill - reprocess info
[9:31] CW Underwood: wihtout standards and metatdata data interchange is virtually impossible
[9:32] Troy McLuhan: There is MathML in mathematics
[9:32] WhiteWizard Chemistry: It's why I like the idea of a core platform (s) that adhere to some simple standards and allow people to build on top of that
[9:32] Rakerman Yellowjacket: I do think standard formats are *essential* to enable more automated processing and interchange of science
[9:32] CW Underwood: so in answer to Hiro, I would like to see such a format, but I wonder if (say) XML + MathML and
[9:32] WhiteWizard Chemistry: and those standards exist, MIAME, etc
[9:32] CW Underwood: a few others that already exist (MIAME, etc)
[9:32] CW Underwood: would not do the job already?
[9:32] Clay Cazalet is Offline
[9:33] Duriel Akula: but a minimal standard would be .. to minimal. just to say that here goes science. there is little else that would be common to all
[9:33] Doolin Chemistry: I think the emphasis on standards is way overemphasized
[9:33] Rakerman Yellowjacket: Dr. Liz Lyon has done quite a bit of work in the UK on open scholarship as well as some work specifically on crystallography formats
[9:33] Rakerman Yellowjacket:
[9:33] You: the differences between fields makes it very difficult
[9:33] WhiteWizard Chemistry: I think they would ... we just need the hooks ... I think the standards should focus on interoperability and let the scientific standards stay with the individual scientific areas
[9:33] Doolin Chemistry: I think a very flexible infrastracture that allows for rapid prototyping is the most essential thing.
[9:34] CW Underwood: WW, yes, interoperability is the reason for having the standards -- that is the job they should do
[9:34] Doolin Chemistry: Scientists can always figure out what some other data is about as long as the formt is completely described.
[9:34] Rakerman Yellowjacket: I think it may be useful to work on the idea of "semantically aware science wiki"
[9:35] You: we would love to collaborate with people with standard models
[9:35] CW Underwood: Richard's got a point, we do seem to be coming back to wikis time and again
[9:35] WhiteWizard Chemistry: Rakerman ... I really like your line of thought
[9:35] You: we have all the data there in the wiki already - just tell us or add the tags/structure
[9:35] CW Underwood: perhaps that would provide a good starting platform
[9:35] CW Underwood: yup, great minds and allthat
[9:36] CW Underwood: speaking of wikis then
[9:36] CW Underwood: perhaps we can skip most of the verbiage on my slides
[9:36] Rakerman Yellowjacket: there's a project in this area - a commercial effort -
[9:36] CW Underwood: and go to what I think is the best point
[9:36] Hiro Sheridan: Ok next question, what is the role that journals such as nature have or should have with open science?
[9:36] CW Underwood: again comes from Richard
[9:36] Rakerman Yellowjacket: more info at
[9:37] Joanna Wombat is Offline
[9:37] CW Underwood: which is that we could get a "good enough" solution to the "define Open Science" (non)problem
[9:37] CW Underwood: using the NodalPoint wiki
[9:37] Joanna Wombat is Online
[9:37] CW Underwood: and that would be in keeping with the whole "small pieces loosely joined" approach
[9:37] CW Underwood: that seems to be coming to the fore in these discussions
[9:37] WhiteWizard Chemistry: Great place to have this discussion, but we might leave out non-life scientists
[9:38] You: the only time definitions become a problem is when people make assumptions
[9:38] CW Underwood: sure, but people do that all the time
[9:38] Joanna Wombat is Offline
[9:38] CW Underwood: look at the confusion over Open Access
[9:38] Clay Cazalet is Online
[9:38] CW Underwood: (Hiro: I think Nature is taking the lead as far as the role of journals goes)
[9:38] You: Nature Precedings
[9:39] CW Underwood: the first job for journals is Open Access, on which Open Science depends
[9:39] Duriel Akula: a good way to hammer some of the definitions would be to write them together and then try to all together promote them in the blogs or open letters
[9:39] WhiteWizard Chemistry is Offline
[9:39] CW Underwood: after that, Nature Precedings is a *wonderful* thing, a preprint server for life sciences
[9:40] You: actually it is more than pre-print because they take almost any format
[9:40] You: it could be instead-of-print in a lot of cases
[9:40] Troy McLuhan: There are already things like Precedings in other branches of science, notably
[9:40] Hiro Sheridan: yes
[9:40] You: Troy no arxiv is different
[9:40] CW Underwood: Horace: yes, Precedings goes further than arXive
[9:40] You: Arxiv has a format
[9:41] CW Underwood: Precedings could, for instance, capture failed experiments and observations too small to constitute a formal paper
[9:41] You: exactly bill
[9:41] Hiro Sheridan: good point
[9:41] CW Underwood: such things could be put into Precedings more or less directly from
[9:41] CW Underwood: a lab wiki or ELN
[9:41] Clay Cazalet is Offline
[9:42] You: yes we would like to do that when experiments reach conclusions
[9:42] You: but they did take some blog posts of mine
[9:42] CW Underwood: can you update a document on Precedings?
[9:42] You: about work in progress
[9:42] You: Yes Bill
[9:42] You: there are versions in Precedings
[9:42] Duriel Akula: my particular view would be that a preceeding would be a good place to post solutions, once they are found. giving a time stant and DOI
[9:42] You: actually Precedings has a poster here - 3 I think
[9:42] CW Underwood: ah, good, then you could add a story result-by-result
[9:43] Hiro Sheridan: does precedings have rss/subscription capabilities?
[9:43] CW Underwood: in fact, Precedings could almost do what JC's wiki does
[9:43] CW Underwood: except that we would not want to fill Precedings up with "history"
[9:43] CW Underwood: the side-comments and thinking out loud and so on
[9:43] You: well it does not have a wiki style version system I think
[9:43] CW Underwood: that will be so valuable to historians of science
[9:44] CW Underwood: studying Open Notebook systems
[9:44] You: I think people like Heather Piwowar are interested in that
[9:44] Hiro Sheridan: so really its a place to store data?
[9:44] You: Hiro they won't take massive data sets (yet)
[9:44] Rakerman Yellowjacket: the Google people are also interseted in hosting datasets for people
[9:44] You: they will take posters
[9:45] CW Underwood: Google is interesting as a data repository
[9:45] You: last time I checked Preceding took ppt, pdf, doc
[9:45] Hiro Sheridan: Maybe they need to be a little more 'social'
[9:45] CW Underwood: we seem to be more interested in tools than definitions
[9:45] CW Underwood: which I think is a good thing
[9:45] You: that was 2 weeks ago :)
[9:45] CW Underwood: it is about getting things done after all
[9:46] DrDoug Pennell is Offline
[9:46] Duriel Akula: we keep talking about the tools instead of definitions :)
[9:46] CW Underwood: so i'm not sure my slides are of much further use
[9:46] CW Underwood: perhaps we could move to the next person?
[9:46] You: Bill, people will read your slides when they visit
[9:47] Hiro Sheridan: Sorry guys I have to go, I'll catch up on the blog, keep it interesting :)
[9:47] CW Underwood: Horace, yep, that's what I was hoping -- there are a lot of links in there that may be useful
[9:47] You: Bill you are the last speaker - let me make some announcements
[9:47] CW Underwood: OK, i'm done
[9:47] You: next week Monday is video and science
[9:47] Hiro Sheridan is Offline
[9:47] You: I think the turnout will be good
[9:47] CW Underwood: be sure to get Deepak!
[9:47] You: and we have several speakers - Berci is helping out with that
[9:47] Berci Dryke: we'll get him for sure
[9:48] You: yes Deepak will be there :)
[9:48] Berci Dryke: Videjog, JoVe, SciVee, Bioscreencast all seem to be interested
[9:48] You: to my left there is another 36 poster area
[9:48] You: right now I'm collecting posters for a ChemFoo area
[9:48] You: if other fields want to contribute that would be cool
[9:48] Berci Dryke: anyway, I've been blogging live about this session (in case you're interested to hear back your thoughts :)
[9:49] Duriel Akula: other fields ? general science ?
[9:49] You: the idea is to have "regular science" posters and discussion
[9:49] You: to "draw out" the unconverted colleagues
[9:49] You: if we have posters in their areas maybe they will visit
[9:49] Troy McLuhan: Like a discussion about the Homologies of Pn3?
[9:50] You: exactly Troy
[9:50] You: I have some organic chemistry I want to share
[9:50] You: on the synthesis of our anti-malarials
[9:50] You: I can help anyone put up their posters - if you have it in ppt you are almost done
[9:51] You: we have special boards to make it easy
[9:51] You: we also now have bells
[9:51] Emile Pintens: JC, sorry I didn't get a ppt done on open innovation
[9:51] You: if someone visits you can set up your second life IM to forward to your email
[9:52] You: do control P then change the setting
[9:52] You: Emile you can add a poster
[9:52] You: if there any posters from previous weeks that you would like to see
[9:52] You: you can check them out - if the speakers are here they can discuss
[9:52] Emile Pintens: Where should I put it up, I'll try and get it done later today
[9:52] You: like a regular poster session
[9:53] You: you can also play with voice at posters
[9:53] You: if you have it
[9:53] You: you can mute people from adjacent plots if needed
[9:53] You: so any other questions/comments?
[9:54] Rakerman Yellowjacket: post the link to the scifoolives on wiki :)
[9:54] You: yes I'll put the link to the wiki shortly
[9:54] You: next to the big sign
[9:54] Berci Dryke: if you have suggestions for the future session, please leave your note on the wiki
[9:55] You: ok- lets checkout the posters then
[9:55] Rakerman Yellowjacket:

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Sunday, September 02, 2007

Ding Dong - Lets Talk SciFoo

If you wander around the SciFoo Lives On area, you will notice that some of the poster booths have bells.

If the text above them is green, it indicates that the presenter is somewhere in Second Life. The visitor can then just click on the bell to summon the presenter with a quick message.

If the text is red, the presenter is not in world. However, a message can still be sent and it will show up the next time they log in.

Now this can be problematic for users who created a Second Life account exclusively for the purpose of presenting or attending a SciFoo Lives On session since they are unlikely to login again and retrieve IM messages. There is a trick around that: in SL hit control-P and turn on the setting to forward IM to email.

This effectively transforms the SciFoo Lives On area into a perpetual session with the cumulative content of all prior sessions, which now include "Tools for Open Science" and "Medicine and Web 2.0". We are now getting ready for the "Definitions in Open Science" session on Tuesday Sept 4, 2007 at 16:00 GMT and there are still slots available to present.

The bells can be purchased for 150L (about 60 cents) on PixelTrix Island (SLURL) - thanks to Ron Comer for help in locating these!

The location and list of all upcoming SciFoo Lives On sessions can be found on the SFLO wiki.

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