Thursday, August 30, 2007

SciFoo Lives On Upgrade and Wiki

There have been a few additions to the SciFoo Lives On area on Nature Island in Second Life.

The area has been divided into 36 numbered plots and most posters from the first two sessions have been moved to fill the first 10 spots. Posters for future sessions will be added sequentially as they are created. (Thanks to Eloise and Beth for help with this!)

This makes the area much more appealing and permits regular poster sessions where people can meet at any time to present and discuss. I have been a huge fan of the effectiveness of poster sessions in Second Life after my first experience. We will still do talks at the scheduled sessions but afterwards groups can break out to posters from any previous SciFoo Lives On session.

I have also created a wiki to keep track of dates and topics of past and future sessions. Presenters are welcome to record their names (Second Life and Real Life), affiliations and presentation titles next to their poster number.

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Monday, August 27, 2007

SciFoo Lives On Medicine 2.0 Session

Our second session of SciFoo Lives On took place today on Nature Island in Second Life (SLURL).

The topic was Medicine and Web 2.0, as suggested by Bertalan Mesko (Berci) at the last session.
We had a very good turnout, with about 30 people. Many returned from last week's session but there were many new faces also.

Berci ran the session with me and helped out all week with getting our presenters set up with posters and general navigation. He also had the first poster with lots of great resources for blogs and wikis by and for doctors, medical students and anyone interested in medicine.

Other presenters were from Tiromed (linking doctors and medical students in mentorship relationships) and Biowizard (a service to rank and comment on medical articles).

I had a one page summary of our collaborators who do docking and those who will be testing our compounds for anti-malarial or anti-tumor activity. I was very pleased that our testing collaborator Dan Zaharevitz from the National Cancer Institute was able to join us and talked a bit about the potential benefits of doing drug development in the open. There is a lot more to be said about about that and we'll probably set up a session on that topic alone at SciFoo Lives On in a while.

Deepak Singh could not make it so we didn't look at his poster. But we'll do a session soon on Video in Science and make sure that he can attend and present.

It was good to see Cameron Neylon show up as well. I've recently blogged about his discussions of Open Notebook Science.

Next week on Tuesday September 4, 2007 at 16:00 GMT we'll be doing a session on Definitions and Open Science. Contact me or Berci if you wish to put up a poster and see you there!

All the posters are still available for viewing. (SLURL)

Here is the transcript (this is a good place to find links to the stuff that was discussed):

[9:00] You: welcome
[9:00] You: lets get started
[9:00] You: looks like we have a lot of people from last week!
[9:00] You: basically this week's session was proposed by Berci
[9:00] You: we've got 5 posters
[9:00] You: about Medicine and web2.0
[9:01] Adastar Galsworthy is Offline
[9:01] You: please feel free to participate in the discussion
[9:01] Cary Flanagan: bling off
[9:01] Emile Pintens is Online
[9:01] You: berci I'm handing it off to you
[9:01] Berci Dryke: thank you, Jean-Claude!
[9:01] Berci Dryke: Welcome in this week's session
[9:01] Adastar Galsworthy is Online
[9:01] Rakerman Yellowjacket is Online
[9:01] Berci Dryke: as web 2.0 is based on feedback, please feel free to interrupt me whenever you have a question
[9:02] Berci Dryke: I'd like to say a few words about my slides
[9:02] Berci Dryke: I planned to talk about these tools/services/sites
[9:02] Berci Dryke: medicine and web 2.0 has a special realationship
[9:02] Berci Dryke: web 2.0 should ease the work of physicians/medstudents and scientists as well
[9:02] Berci Dryke: I should start with medical blogs
[9:02] Touch me for a Free BioWizard T-Shirt!: Thanks! - 5
[9:03] Berci Dryke: wyou know well we have about 100 Million blogs these days
[9:03] Berci Dryke: and 3-500 medical blogs
[9:03] Adastar Galsworthy is Offline
[9:03] Berci Dryke: we have a list of English medical blogs here:
[9:03] Berci Dryke:
[9:04] Berci Dryke: they're ranked by the number of comments, posts, feed readers and Technorati links
[9:04] Berci Dryke: physicians nowadays must face the fact that their patients do have a blog
[9:04] Berci Dryke: and write about their own doctors
[9:04] Adastar Galsworthy is Online
[9:05] You: how many of these are doctors?
[9:05] Berci Dryke: it's hard to tell an exact number or percent
[9:05] Berci Dryke: I would say about 20 %
[9:05] Berci Dryke: that's why it's crucial to have a standard code of blogging ethics
[9:05] Berci Dryke: actually, we have two
[9:05] Berci Dryke: the HONcode accreditation
[9:06] Berci Dryke: and this:
[9:06] Touch me for a Free BioWizard T-Shirt!: Thanks! - 6
[9:06] Berci Dryke: the second is a community of bloggers who take blogging very seriously
[9:06] Berci Dryke: an other important question is anonymity
[9:06] You: are they mostly anonymous?
[9:07] Adastar Galsworthy is Offline
[9:07] Berci Dryke: Horace: no!
[9:07] Berci Dryke: Just a few of them wouldn't like to write their names online
[9:07] You have offered friendship to Melvina Palen
[9:08] Melvina Palen is Online
[9:08] Berci Dryke: maybe because of the fear that they can write something bad about their boss/employer
[9:08] Clay Cazalet is Online
[9:08] Berci Dryke: so blogging for medical professionals makes it easier to share knowledge and experience
[9:08] Hiro Sheridan is Online
[9:08] Berci Dryke: we don't have to wait for a conference or a future puiblication to be able to discuss a new diagnostic tool/procedure e.g.
[9:09] You: any doctors in the house?
[9:09] Berci Dryke: we do havce
[9:09] DoctorAnn Buchanan: Yes
[9:09] You: do you blog doc ann
[9:09] Hilary Serevi is Online
[9:09] DoctorAnn Buchanan: I have started one, but am stumbling with it a bit at the moment.
[9:09] You: docann are you worried about liability
[9:10] DoctorAnn Buchanan: Yes, it is a concern.
[9:10] You: would biowizard like to start?
[9:10] Berci Dryke: that's why we need an accurate blogger code of ethics
[9:10] Visitor Counter 1.8: Welcome Hilary Serevi. You have been counted.
[9:10] Berci Dryke: just a minute, Horace
[9:10] You: sure
[9:11] Berci Dryke: yes,medical wikis
[9:11] Berci Dryke: Wikipedia is created for laypeople
[9:11] Berci Dryke: but we do need medical wikis, where only credentialed professionals can edit the articles
[9:12] Berci Dryke: the best example for that is Ask Dr Wiki
[9:12] Berci Dryke: a wiki created for and by physicians
[9:12] Berci Dryke: an othet important tool for physicians is a medical search engine
[9:13] Berci Dryke: Google can't select among the sources, so we needed search engines that only search among peer-reviewed sources
[9:13] Berci Dryke: so when you search for a term like diabetes
[9:13] Berci Dryke: you don't have to run through some forums and ads
[9:13] Berci Dryke: it's useful for laypeople and for professionals as well
[9:14] Berci Dryke: you know well these web 2.0 based sites (Youtube, Flickr, etc)
[9:14] Berci Dryke: these can be considered as medical resources as well
[9:14] Berci Dryke: on, you can find hundreds of medical cases (with fascinating images)
[9:14] Berci Dryke: on, you'll find medical videos created ny physicians
[9:15] Berci Dryke: and Second Life, let me say a few words about it
[9:15] Berci Dryke: the Ann Myers Medical Center
[9:15] Berci Dryke:
[9:15] Berci Dryke: we had our first medical training 2 weeks ago
[9:15] Berci Dryke: as a medical student, it was one of the most incredible lectures/trainings in my life
[9:15] Berci Dryke: we got a patient history as a notecard
[9:16] Berci Dryke: then some images (tissue, microscopic, etc)
[9:16] Berci Dryke: and we had to discuss (with the other medical students coming from around the world) the case
[9:16] Berci Dryke: while the physicians helped us how to answer the questions
[9:16] You have offered friendship to DoctorAnn Buchanan
[9:16] DoctorAnn Buchanan is Online
[9:17] Berci Dryke: it was interactive, interesting and (I really believe) it was the beginning of a new era in medical education
[9:17] Stargazer Blazer is Online
[9:17] Touch me for a Free BioWizard T-Shirt!: Thanks! - 7
[9:17] Berci Dryke: to learn/study without boundaries, it's just perfect
[9:17] Troy McLuhan: Where is it in SL? Is it open to the public?
[9:17] Berci Dryke: you can ask your questions about this project to DoctorAnn or Cary
[9:17] Berci Dryke: I give you a link
[9:17] DoctorAnn Buchanan: Yes, it is on "Hospital" Island
[9:17] Berci Dryke:
[9:18] Adastar Galsworthy is Online
[9:18] DoctorAnn Buchanan: Is this the new location Berci?
[9:18] Berci Dryke: I think so
[9:18] DoctorAnn Buchanan nods
[9:18] You have offered friendship to Zen Zeddmore
[9:18] Berci Dryke: any questions ab out it?
[9:18] Miss Dawes: Can I ask who your tutors where - were they doctors? If so, how did they feel about the tutorial?
[9:19] Berci Dryke: DoctorAnn, pleas
[9:19] Berci Dryke: e
[9:19] DoctorAnn Buchanan: Yes, the physicians are leading the "courses".
[9:19] Touch me for a Free BioWizard T-Shirt!: Thanks! - 8
[9:19] DoctorAnn Buchanan: We are in the process of collaborating with Sprott-Shaw college and Sloodle to develop a curriculum
[9:19] Zen Zeddmore is Online
[9:19] Miss Dawes: How did they feel about mastering SL? It'd be a new skill - and one they'd perhaps not use elsewhere. Was that a problem?
[9:20] DoctorAnn Buchanan: Each physician is presenting a case to the students
[9:20] You have offered friendship to MrFlakes Rodenberger
[9:20] DoctorAnn Buchanan: So far, only a few have had any issues, but those of us who have become proficient are assisting
[9:20] DoctorAnn Buchanan: Additionally, the Sprott-Shaw tech team is helping
[9:21] Berci Dryke: Miss Dawes: I don't think so: to learn more about a specific disorder by history and images and links is much better than to sit in a real life room and listening to a doctor
[9:21] DoctorAnn Buchanan: We currently have white boards, a file system, video and audio for training
[9:21] Miss Dawes: We are thinking of using SL in PG medicine teaching - but I am worried about training the clinicians to use SL.
[9:21] Berci Dryke: we had to find out the disorder
[9:21] You have offered friendship to Miss Dawes
[9:21] Miss Dawes is Online
[9:22] Adastar Galsworthy is Offline
[9:22] Berci Dryke: just to move on: NHS, CDC, Red Cross all have their sites in SL
[9:22] DoctorAnn Buchanan: Actually, most of our physiciansm nurse educators and scientists have learned it rather quickly
[9:22] Berci Dryke: and at last, I'd like to introduce you two medical communities:
[9:22] Ummo Femto is Offline
[9:23] Visitor Counter 1.8: Welcome MrFlakes Rodenberger. You have been counted.
[9:23] Berci Dryke: first, Lauren from, then Max from, but they'll introduce themselves and their sites better
[9:23] Berci Dryke: thank you for the attention!
[9:23] Troy McLuhan: Will these slides be posted online?
[9:23] Adastar Galsworthy is Online
[9:23] DoctorAnn Buchanan: Berci, will you ahve these slides available for download?
[9:24] Berci Dryke: these slides have already been posted online (an extended version with 67 slides)
[9:24] Berci Dryke: here:
[9:24] DoctorAnn Buchanan: Excellent, thank you.
[9:24] You: we can put a link from here also
[9:24] Berci Dryke: I'll Jean-Claude
[9:24] Berci Dryke: any questions?
[9:24] Cameron Niekerk: Is there a big enough community to support Wiki and digg type sites?
[9:25] Berci Dryke: good question! the number is growing, more and more medical professionals use these sites
[9:25] Berci Dryke: and Biowizard are the perfect examples
[9:25] Vidal Loon: I believe there is. Other examples of communities based on even more specific topics have been set and are growing with the help of wikis.
[9:26] Samara Barzane is Offline
[9:26] Miss Dawes: Sorry but I'm still wondering about the training of clinicians/physicians to give tutorials in SL? You say that's not a problem? Is that right?
[9:26] Morrhys Graysmark: How can Second Life extend the idea of these sites? Can the "sites" be turned into 3-D places in SL? With model instruments, animations?
[9:26] Berci Dryke:, a radiology wiki is getting some sponsors as well
[9:26] Berci Dryke: Morrhys: I think just some of them
[9:27] You have offered friendship to Cameron Niekerk
[9:27] Berci Dryke: medicine in SL is not represented enough to convert those sites into SL world
[9:27] MrFlakes Rodenberger: PubMed gets 1M daily visits; the community is absolutely present online
[9:27] Cameron Niekerk is Online
[9:27] Berci Dryke: but this is not a community, to be honest
[9:27] Ummo Femto is Online
[9:27] Berci Dryke: if Pubmed would be more interactive, then we could call it a community
[9:27] Berci Dryke: Ummo: please say a few words about
[9:27] DoctorAnn Buchanan: Yesm Morrhys, is I may answer your question.
[9:27] DoctorAnn Buchanan: if
[9:27] Morrhys Graysmark: Please.
[9:28] DoctorAnn Buchanan: We have and are in the process of building equipment that will be linked to sites and from which the student will make an analysis
[9:28] Ummo Femto: Hello, thanks for your attention while I briefly discuss
[9:29] You have offered friendship to Bor Boram
[9:29] Bor Boram is Online
[9:29] Ummo Femto: BioWizard is a tool used for life scientists looking to simplify their research
[9:30] Ummo Femto: as this slide indicates, we have a host of features
[9:30] Troy McLuhan: Hold down ALT then click-drag your mouse to zoom
[9:31] Adastar Galsworthy is Offline
[9:31] Adastar Galsworthy is Online
[9:31] Ummo Femto: Bertalan referenced Digg earlier, and as you can see, we feature a a Digg model that allows users to rank PubMed articles
[9:32] Meditador Writer: sorry
[9:32] You: so like Connotea?
[9:32] Meditador Writer: i´m
[9:32] Meditador Writer: lost
[9:32] Melvina Palen is Offline
[9:32] Ummo Femto: to the left you will see that their are 18 disciplines to which these articles are organized
[9:32] Melvina Palen is Online
[9:33] Meditador Writer: pardon
[9:33] Ummo Femto: Meditador, how can I help you find your way?
[9:33] Meditador Writer: i´m just listening
[9:33] Ummo Femto: from my brief glance, I think Connotea is more like a reference tool,
[9:34] Troy McLuhan: Like
[9:34] Meditador Writer: my first time
[9:34] Ummo Femto: The current slide shows how our tool differs from PubMed
[9:34] Adastar Galsworthy is Offline
[9:34] Ummo Femto: the difference largely being that we have the interactivity that PubMed lacks
[9:35] Adastar Galsworthy is Online
[9:35] You: so you are linking and discussing articles?
[9:35] Berci Dryke: and rank them
[9:35] Teo Lorenz: can you flip the slides a little slower please? they take longer to rez for me
[9:35] Ummo Femto: correct, with a host of products to search on
[9:35] Ummo Femto: yes, I apologize about the slides, I think other users are clicking on them while I speak
[9:36] Clay Cazalet is Offline
[9:36] Emile Pintens: sorry about that...i am guilty
[9:36] Zen Zeddmore: As 3dPrinting tech matures and we see more implants and organs "printed", does SL in that context provide a means to transfer data, view docking problems, collaborate editing the article remotly, etc?
[9:36] Ummo Femto: BioWizard also offers aggregated news based on the 18 disciplines in the left hand column of the screen shot in the current slide
[9:36] Adastar Galsworthy is Offline
[9:37] Teo Lorenz: oh! i might have even don that myself once - I thought it would give me URL or something.
[9:37] You: zen we have done some docking
[9:37] Meditador Writer: Odes
[9:37] Hiro Sheridan: :)
[9:37] Meditador Writer: Does Bip
[9:37] Morrhys Graysmark: Do you see "articles" moving toward taking advantage of virtual 3-D worlds, by publishing 3-D enabled models as part of scientific papers?
[9:38] Visitor Counter 1.8: Welcome Itep Blanco. You have been counted.
[9:38] Meditador Writer: Has Biohazrd stuff in clinical analysis?
[9:38] Ummo Femto: BioWizard does not currently have a 3D presence in Second life, but as the web evolves beyond 2.0, welcome every consideration
[9:39] Morrhys Graysmark: Thank-you.
[9:39] Troy McLuhan: I think SL is, for now, far more useful as a place for people to discuss things real-time, rather than a "place for 3D models"
[9:40] Ummo Femto: BioWizard's content is primarily that featured on PubMed
[9:40] Ummo Femto: In the interest of keeping this session brief, I'll wrap up my session
[9:40] Samara Barzane is Online
[9:40] Hiro Sheridan: leveraging web services to display 3d models in SL will come eventually :)
[9:41] Teo Lorenz: I think I read somewhere that Linden Lab does not envision the kind of 3D capabilities that are needed for any reasonable scientific modelling or simulations.
[9:41] Berci Dryke: thank you, Ummo!
[9:41] Ummo Femto: unless there are other questions pertaining to BioWizard
[9:41] Berci Dryke: Max, would you say a few words please about
[9:41] You have offered friendship to Cary Flanagan
[9:41] Tiromed Oppewall: Hello everyone! My name is Max and I am a co-founder and web admin of First, I’d like to thank Berci from for inviting me to speak.
[9:41] Cary Flanagan is Online
[9:41] Berci Dryke: you're most welcome!
[9:42] Tiromed Oppewall: I also want to say that I am a beginner with SL so I apologize ahead of time for my learning curve. I’d like to give a brief introduction about and then open things up for questions if that’s okay.
[9:42] Meditador Writer: sorry but does biohazard have material in clinical analysis?
[9:42] Hiro Sheridan is Offline
[9:42] Tiromed Oppewall: INTRODUCTION: is an international knowledge and mentor network for physicians and students of medicine.
[9:42] Tiromed Oppewall: Our vision was to create an online community that could help anyone during their journey from a premed to a practicing physician; we believe that this can only be possible if all user levels join and share their knowledge and experience with each other (i.e. premed, medical student, resident, fellow and physician).
[9:43] Tiromed Oppewall: We have been in beta for about 11 months: we have over 2600 members, represent over 70 countries and have formed several partnerships with medical associations, including the International Federation of Medical Students’ Associations, the largest medical student entity on the globe (please see
[9:43] Tiromed Oppewall: We have had tremendous feedback from the “prototype” website we have up and running, and continue to explore how we can make Tiromed a better service. Tiromed was founded by three practicing physicians and me (a graduated premed) in the U.S.
[9:43] You: does it help students find rotations?
[9:43] Tiromed Oppewall: . Web 2.0 plays a significant role in our development as we are trying to create a knowledge based environment where the community can collectively give back and share information with each other.
[9:44] Tiromed Oppewall shouts: Thank you for listening to my introduction, I’d be happy to take some questions from you.
[9:44] Tiromed Oppewall: we would ulitmatley like to build functionality that helps students find rotations nationally and internationally
[9:45] You: so there is discussion of the medical life?
[9:45] Tiromed Oppewall: the focus of tiromed was to faciliate discussion about the process of becoming a physician
[9:45] Berci Dryke: I'd have one: I'm a member of Tiromed. As a medical student from Hungary, how do you make it possible for me to do my residency training in the US? e.g.
[9:46] Meditador Writer: does have stuff in clinical analysis?
[9:46] Tiromed Oppewall: well, we will take tiromed to a place where there will be more information about redsidencies
[9:46] Tiromed Oppewall: we are working on this now
[9:47] Berci Dryke: how do you think you could improve the number of members?
[9:47] Berci Dryke: do medical professionals intend to join Tiromed?
[9:47] Tiromed Oppewall: we are less clinicaly and academic focused for now, more about progession throught th ephysican process
[9:47] Tiromed Oppewall: we are currently working with medical associations to provide network platforms to their members
[9:47] Emile Pintens: Tiromed, how do you plan on reaching more doctors to grow tiromed?
[9:48] Tiromed Oppewall: working with medical associations will definitely help us here
[9:48] You have offered friendship to Morrhys Graysmark
[9:48] Teo Lorenz: How do you validate the information (authorship/credentials) of material on Tiro*Med?
[9:48] Berci Dryke: what kind of features do you plan to create in the near future?
[9:48] Tiromed Oppewall: for an example see :)
[9:49] Tiromed Oppewall: Ted, we are looking into this now
[9:49] Tiromed Oppewall: Berci, we are listening to feedback from membership about how to improve
[9:49] Tiromed Oppewall: many members like the networking capability
[9:49] Morrhys Graysmark is Online
[9:49] Tiromed Oppewall: this may get more sophisticated
[9:50] Tiromed Oppewall: well, if that is it i encourage you all to check out the site and contact me, my name is max
[9:50] Tiromed Oppewall: thank you
[9:50] Berci Dryke: Horace, can we move on to the next board?
[9:50] Berci Dryke: thank you, Max!
[9:50] You: yes
[9:50] Berci Dryke:
[9:50] Berci Dryke: and
[9:51] You: I'll move on to a different angle on this - primary research
[9:51] Ummo Femto: thank you, Berci
[9:51] Berci Dryke: sorry, Cary :)
[9:51] Cary Flanagan:
[9:51] You: on this board you see our drug development efforts that we do in the open
[9:51] Berci Dryke:
[9:51] You: on blogs, wikis and mailing lists
[9:51] You: my group is in the middle - we are synthetic organic chemists
[9:52] You: but we have collaborators who do docking - like Rajarshi
[9:52] You: and people who do testing of the compounds we make
[9:52] Stargazer Blazer is Offline
[9:52] You: I did a lot of talking last week - I'd like to give one of our collaborators some time
[9:52] You: Dan, would you like to say a few words?
[9:53] Doolin Chemistry: Well it will have to be a few as I get used to this medium
[9:53] Morrhys Graysmark: :)
[9:53] Melvina Palen is Offline
[9:53] You: docking means finding molecules that fit in proteins
[9:53] Doolin Chemistry: One of the things I'm interested in is how these open collaborative efforts can help with the drug discovery problem
[9:53] Digital Despres is Offline
[9:54] Doolin Chemistry: J-s's group, like a lot of academics have only a vageue idea of what it takes to find a drug.
[9:54] Doolin Chemistry: On the other hand, noone really knows very well how to find a drug.
[9:55] Doolin Chemistry: Industry is concerned about their "pipeline" and what it will mean for profits. and yet about 9 out of 10 compounds that make ito clinical trials fail.
[9:56] Doolin Chemistry: Increasingly they fail not because of unexpected toxcitites, but do to lack of positive effect.
[9:57] Doolin Chemistry: When the baisc problem is not well understood, I htink a strong case can be made that the way to approach it is through the baisc standards of science: that is free and open communication and even agrumentation
[9:58] Doolin Chemistry: The project wih J-C's group is a start to explore what might happen if the proces was open to a much wider range of thoughts and input, rather than one group trying to do it all.
[9:58] yucca Gemini is Online
[9:59] Doolin Chemistry: One of the things I hope to take advantage of, is learning how best to transfer our (NCI) knowledge and experience of testing > 100,000 compounds into a synthetic academic group.
[9:59] Tenaya Tomsen is Online
[9:59] You: we're fortunate to have Dan collaborating with us
[10:00] You: he has tested our compounds
[10:00] Doolin Chemistry: I think that is about all I can get out at the moment, but would be happy to try to discuss.
[10:00] You: it also looks like we are at the end of the session
[10:00] You: maybe we can continue on another week
[10:00] You: next week tuesday is on
[10:00] Emile Pintens: Same time?
[10:00] You: Definitions in Open Science
[10:00] You: yes 16:00 GMT
[10:00] Berci Dryke: not Monday?
[10:01] You: no Monday is a holiday here
[10:01] Berci Dryke: o
[10:01] Troy McLuhan: 16:00 GMT is 9:00 AM PDT (SL time)
[10:01] Berci Dryke: oh
[10:01] You: any suggestions for future sessions?
[10:01] Berci Dryke: Thank you all for coming!
[10:01] Morrhys Graysmark: Thank you for the presentations.
[10:01] Berci Dryke: if you have any kind of questions, I think some of us will stay here now
[10:01] Morrhys Graysmark: They were most informative!
[10:01] DoctorAnn Buchanan: Thank you.
[10:01] You: thanks everybody
[10:01] Emile Pintens: SciVee I think should be included...
[10:02] Berci Dryke: Deepak couldn't make it
[10:02] You: good idea emile
[10:02] Berci Dryke: he stucked in a meeting
[10:02] You: I think we can build a session around scivee and video science
[10:02] Berci Dryke: Deepak will be so glad :)
[10:02] You: JOVE and such
[10:02] Berci Dryke: and Bioscreencast
[10:02] You: absolutely
[10:02] Vidal Loon: I've got a bunch of posts on the video/science bubble that's formed
[10:02] Emile Pintens: sounds good
[10:02] Troy McLuhan: If anyone here knows someone at SciVee, please tell them to clarify the license. They are ambiguous about whether it is CC-by or CC-by-nc-sa
[10:02] Rakerman Yellowjacket: science video sounds interesting
[10:03] You: on the wall to my left is the list of upcoming confs
[10:03] You: I'll update
[10:03] Rakerman Yellowjacket: maybe someone from Scientific American can come and clarify what they're doing?
[10:03] Vidal Loon: Yes, indeed. I bet Deepak would be interested in talking about that.
[10:03] Berci Dryke: absolutely
[10:03] Berci Dryke: any questions about web 2.0 and medicine?
[10:03] You: we'll leave these posters up
[10:04] You: feel free to show your friends :)

Sunday, August 26, 2007

Medicine and Web 2.0 Session Tomorrow

Here's a reminder for our second SciFoo Lives On session in Second Life tomorrow Monday August 27, 2007 16:00 GMT/12:00 ET. Berci and I will be the moderators.

I've put up a one page poster to briefly discuss our drug development efforts with our collaborators using Web 2.0 tools.

Everyone is welcome to attend. There is still time to put up a poster - just contact me or Berci to do that.

Like last time, it will be held on Nature Island (SLURL)

Thursday, August 23, 2007

Cameron Neylon on Open Notebook Science

There has been a lot of discussion lately about the philosophy of Open Science in general terms.

This is certainly worthwhile but I think it is even more interesting to discuss the mechanics of its implementation. That is what I was trying to push a little more by setting up the "Tools of Open Science" session on SciFoo Lives On.

That's why I've been very impressed by Cameron Neylon's recent posts in his blog "Science in the Open".

He has been discussing details of the brand of Open Science that interests me most: Open Notebook Science, where a researcher's laboratory notebook is completely public.

Cameron has been looking at how our UsefulChem experiments could be mapped onto his system and this has sparked off some interesting discussion. I am becoming more convinced than ever that the differences between how scientific fields and individual researchers operate are much deeper than we usually assume.

By focussing almost entirely on the sausage (traditional articles), we tend to forget just how bloody it actually is to make it and we probably assume that everybody makes their sausage the same way.

The basic paradigm of generating a hypothesis then attempting to prove it false is certainly a cornerstone of the scientific process but it is certainly not the whole story. However, after reading a lot of papers and proposals, one gets the impression that science is done as an orderly repetition of that process.

What I have observed in my own career, after working and collaborating with several chemists, most of the experiments we do are done for the purpose of writing papers! The reasoning is that if it is not published in a journal, it never happened. This often leads to the syndrome of sunk costs, similar to a gambler throwing good money after bad, trying to win back his initial loss.

After a usually brief discovery phase, the logical scientist will try to conceive of the fewest number of experiments (preferably of lowest cost and difficulty) to obtain a paper. In this system, like in a courtroom, an unambiguous story and conclusion is the prefered outcome. Reality rarely cooperates that easily and that is why the selection of experiments to perform is truly an artform.

We're currently going through that process. We have an interesting result observed for a few compounds and a working hypothesis. That's not enough for a paper in my field. We cannot prove the hypothesis without doing an infinite number of experiments but we are expected to make a decent attempt at trying to falsify it. I know from experience roughly the number of experiments we need with clear cut outcomes to write a traditional paper.

So how much more value to the scientific community is that paper relative to the single experiment where this effect was first disclosed on our wiki then summarized on our blog?

Is this really the most efficient system for doing science or is this the tail wagging the dog?

When the scientific process becomes more automated, I predict that the single experiments will be of more value than standard articles created for human consumption and career validation.

Sometimes the pieces just don't fit in the sausage maker. Does that mean we shouldn't eat them (making sure to cook them first, of course)?

One of the most useful outcomes of Open Notebook Science (and why I'm highlighting Cameron's work) might be the insight it will bring to the science of how science actually gets done. (Researchers like Heather Piwowar should appreciate that)

Monday, August 20, 2007

JSpecView problem with Java Update

Under Windows XP, updating to JAVA 1.6.02 will break JSpecView.

This is a major problem for UsefulChem users who depend on viewing NMRs with the software.

Don't update until a fix is in place. If you have updated already, you'll need to switch back to version 1.6.01 - thanks to Robert Lancashire for the tip.

First SciFoo Lives On Session

We had our first SciFoo Lives On session today on Nature Island (Second Nature) in Second Life. We had about a dozen people participate.

The topic was "Tools for Open Science". I wanted to explore more fully the actual technology that people are starting to use towards doing more open science. I started off by showing screenshots of UsefulChem wiki and blogs from my poster. The other posters there (and still there) included MyExperiment, Nature Precedings, Bill Hooker's Thoughts, Knowble and Connotea.

Overall it went very well I think. Initially I was disappointed that most people did not have voice working but it turned out to be a good thing because I was able to capture the entire chat transcript (see below).

Based on Berci's suggestion, we'll do "Medicine and Web 2.0" next week on Monday Aug 27, 2007 ET noon. So bring your posters and join us!

Here is the transcript:
[9:00] You: I think many of you were at scifoo
[9:00] You: one of the problems is ther was not enough time to cover everything
[9:01] You: this is a continuation on that
[9:01] You: on Tools for Open Science
[9:01] You: this really should be a discussion
[9:01] You: so we'll just take a few minutes each to explain
[9:01] You: I'll start on the Open Notebook Science poster
[9:02] You: then we'll go to the right and around the corner
[9:02] You: please stop me if you have a comment or question
[9:02] You: I was hoping to do this by voice but not enough people have it
[9:03] Max Chatnoir: good to have the chat record.
[9:03] Berci Dryke: sure
[9:03] You: what I would like for my 5 mins is to show screenshots of our Open Notebook Science
[9:03] You: so we have one component that is a blog
[9:04] You: the idea is to record everything from ongoing research in my lab
[9:04] You: I'm skipping over stuff because I don't want to take 1 hour :)
[9:04] You: we started tracking molecules in my lab using a blog like this
[9:05] You: but now we are moving this to Chemspider
[9:05] Stew Alito: Um.... can Phoenix move to the side a bit? It's the wings... can't see!
[9:05] Berci Dryke: lol
[9:05] You: we started tracking experimnents using a blog
[9:05] You: but there were too many edits
[9:05] Troy McLuhan: To adjust your camera position, hold down ALT and then click-drag with your mouse
[9:05] You: so we moved to a wiki
[9:06] You: the wiki has all the lab notebook pages and organization pages
[9:06] You: the wiki tracks nicely the contribution of everybody over time
[9:06] You: and we can prove who-knew-what-when
[9:06] You: with each version
[9:07] You: we use Wikispaces because it is free and offers thridparty time stamps
[9:07] Max Chatnoir: These are suggestions for the synthesis?
[9:07] You: which one max?
[9:07] You: there were comments from others yes
[9:08] You: but it turns out our collaborators prefer to use our mailing list to share
[9:08] You: so the wiki is mainly my students in the lab
[9:08] You: I will leave the rest here - tha's it for me
[9:08] You: any comments/questions?
[9:08] Berci Dryke: What about competition?
[9:09] You: you mean fear of being scooped berci?
[9:09] Berci Dryke: yes
[9:09] You: I think that this is safer than many other things scientists do
[9:09] You: like proposals
[9:09] You: because all this is indexed quickly in google
[9:10] You: it would be very embarrasing to get caught stealing text
[9:10] Max Chatnoir: So this is a sort of ongoing multicontributor proposal presentation?
[9:10] Max Chatnoir: But very publicly documented!
[9:10] Stew Alito: Have you ever been scooped, to your knowledge?
[9:10] You: max this simply our standard lab notebook on a public wiki
[9:10] You: no I don't know of anyone having "stolen" anything
[9:11] Max Chatnoir: So the contributors are mostly your own students?
[9:11] You: max - yes the wiki is mainly my students
[9:11] Berci Dryke: your wiki can be edited by anyone (or just those who have access to it?)
[9:11] You: on the mailing list we have great collaborators like
[9:11] Max Chatnoir: Do you get external contributions as well?
[9:11] You: Rajarshi Guha that does docking for us
[9:11] You: max - you have to register
[9:12] Troy McLuhan: Which mailing list service/software do you use?
[9:12] You: simply because otherwise my students forget to login!
[9:12] Max Chatnoir: But the registration is open?
[9:12] You: we use Google groups
[9:12] suhky Rezillo: now I am here
[9:12] You: we are ALL google - blog, wiki, lists
[9:12] Berci Dryke: why is better than creating an own wiki (I mean used in an internal network)
[9:12] Max Chatnoir: Like WebCT?
[9:12] You: Google has been a huge gift to open science
[9:12] You: what is like webct maX?
[9:13] Max Chatnoir: Internal network.
[9:13] Stew Alito: Do you share references with Zotero or Connotea etc.?
[9:13] Max Chatnoir: I was adding to Berci's question.
[9:13] You: I have used Connotea with my class students
[9:13] You: but not systematically
[9:13] Rakerman Yellowjacket: I wonder about the amount of information - do you think there's any difference between someone getting a protocol from your notebook, or a "refined" version from myExperiment or Nature Protocols?
[9:14] You: good point raker
[9:14] Corwin Carillon is Offline
[9:14] You: Nature protocols is great for established protocols
[9:14] You: but it takes time to get the info in there
[9:14] You: UsefulChem is real time so by necessity messy
[9:14] You: BUT - the question is can scientist use the info
[9:15] You: and based on the types of searches we observe - I say yes
[9:15] You: we can always collect and publish these as full papers later
[9:15] Rakerman Yellowjacket: I am wondering - if everyone published their lab notebooks online, what would google search results look like - how would be be able to find the most relevant results? Would online notebooks s scale?
[9:15] You: well we have to add metadata
[9:15] Adastar Galsworthy: how do people feel about citing online resources?
[9:15] Max Chatnoir: So this is one way to get "tried this, didn't work" into a publicly accessib le space.
[9:16] You: for example in chemistry we tag with inchis
[9:16] Adastar Galsworthy: particularly informal resources
[9:16] You: each field will have to add metadata
[9:16] You: do we have our myexperiment guy here?
[9:17] You: ok, someone want to say a few words about Precedings?
[9:17] You: we can move to that poster
[9:17] Max Chatnoir: Can people not in your class register for the wiki?
[9:17] You: max - yes they can
[9:18] You: suhky?
[9:18] suhky Rezillo: yes?
[9:18] Max Chatnoir: So, Berci, that would be why it is in a public forum rather than an internet network like WebCT or Blackboard.
[9:18] You: would you like to say a few words about precedings
[9:18] Berci Dryke: understood, Max :)
[9:19] Joanna Wombat: Hilary's just coming now
[9:19] You: I've use precedings myself
[9:19] Joanna Wombat: I think she can say something about precedings
[9:19] suhky Rezillo: one moment Hilary will talk about Nature Precedings as she co-developed the site...
[9:19] You: and I think it is a fantastic addition to tools for open science
[9:19] You: oh good
[9:19] Max Chatnoir: Indeed!
[9:19] Hilary Serevi: hi everyone
[9:19] Troy McLuhan: Would it make sense to publish the transcript of this discussion on Nature Preceedings?
[9:19] Joanna Wombat: Hi Hilary
[9:19] You: hilary you have the floor
[9:19] suhky Rezillo: Everyone, let me well you to Hilary Serevi
[9:20] Berci Dryke: nice to meet you!
[9:20] Hilary Serevi: thanks--I haven't spent too much time in second life
[9:20] Hilary Serevi: but hopefully I can answer some questions about Precedings
[9:21] You: hilary what was your role in precedings
[9:21] You have offered friendship to Krystine Qinan
[9:21] Hilary Serevi: I'm the Product Development Manager
[9:21] Krystine Qinan is Online
[9:21] You: did you make this poster?
[9:22] suhky Rezillo: Yes she did, with Timo Hannay
[9:22] Hilary Serevi: yes
[9:22] You: anyone else here use precedigns?
[9:22] Troy McLuhan: Can you summarize what it is?
[9:22] You: basically you can publish in any format
[9:22] You: the submissions are editorially reviewed
[9:22] You: but not peer reviewed
[9:23] Hilary Serevi: that's correct, Horace
[9:23] You: but it does not have to be an article format
[9:23] You: I have published blog posts there
[9:23] You: well the poster will stay there after this session
[9:23] Berci Dryke: can I have a personal question about it?
[9:23] yucca Gemini is Online
[9:23] You: yes berci
[9:23] Berci Dryke: I'm a medical student and have a presentation about web 2.0 and medicine (Medicine 2.0). Why would it be good for me to publish it on Precedings? And could I publish it?
[9:24] You: they do have a lot of presentations
[9:24] You: I published my ppt as well that we were loking at
[9:24] You: let's move on
[9:24] You: Bill could not make it
[9:24] You: so I'll say a few things
[9:25] Stew Alito is Offline
[9:25] You: Bill Hooker has been reporting on Open Science for a long time
[9:25] Hilary Serevi: since we've moved on, perhaps I can answer your question later, berci
[9:25] You: and he asked me to ask you about what you thought about the def o open science
[9:25] Berci Dryke: ok, Hilary
[9:25] You: sorry hilary
[9:26] You: please answer
[9:26] You: does anyone have thoughts about the definitions?
[9:27] You: the term open science has been used so much we don't know what it means somtimes
[9:27] Samara Barzane is Online
[9:27] Rakerman Yellowjacket: it's more like "publically shared pre-publication science"
[9:28] Adastar Galsworthy: i have a thought about the reasons for the need for open science
[9:28] Troy McLuhan: PLoS is open though, and is for publication
[9:28] Adastar Galsworthy: I think it was in the middle of the 18th century that the last man to have read everythin lived,
[9:28] Emile Pintens: Rakerman, I do not know if that it has to be pre-published. I think the ultimate goal would be for pre-published, and published works to be open.
[9:29] You: so you don't consider precedings to be "published"
[9:29] You: according to patent law that is certainly a publication
[9:29] Hilary Serevi: so precedings doesn't "publish" documents--they'i think that the term "open access" tends to be applied to peer-reviewed publication
[9:29] You: it is not peer-reviewed
[9:29] Troy McLuhan: Sorry, that's what I mean
[9:30] Hilary Serevi: i think the definition of a "publication" is changing with the development of the internet
[9:30] You: so when people say pre-publication they mean pre-peer-reviewed
[9:30] Emile Pintens: Isn't Precedings screened? It isn't peer-reviewed, but it is reviewed
[9:30] Rakerman Yellowjacket: pre-peer-reviewed is maybe a better term
[9:30] Troy McLuhan: I guess what I really mean is, does the tenure review committee consider it "published"?
[9:30] You: definition confusion was big at scifoo i think
[9:30] Hilary Serevi: It's screened, but the screening process is mainly to prevent the posting of obviously commercial documents (e.g. spam)
[9:31] Hilary Serevi: or pseudoscience
[9:31] Hilary Serevi: although pseudoscience is also another term that is difficult to devine
[9:31] Hilary Serevi: define--sorry
[9:31] You: but without defining "peers", it is hard to define peer review
[9:31] Emile Pintens: Ok thank you for the clarification. Is there a time lag between an item being submitted and the time it makes it on the site?
[9:31] Adastar Galsworthy: in peer reviewed journals there is plenty of pseudo-science. that was my experience as an editor for a few smaller physics journals for a while
[9:32] Hilary Serevi: yes--the mean time between submission and posting is less than a day
[9:32] DrDoug Pennell is Offline
[9:32] You: yes precedings made me change my abstract to they did read it!
[9:32] Adastar Galsworthy: I'd like to jump the discussion back a few rungs
[9:32] Max Chatnoir: That's a really fast turnaround.
[9:33] suhky Rezillo: Horace - what or how much do you submit to precedings?
[9:33] Adastar Galsworthy: less about the specifics of what the mechanics of open science are, and discuss the issue of accreditation
[9:33] You: suhky - I only submitted 3 times
[9:33] Troy McLuhan: Preceedings is quite new I think
[9:33] Hilary Serevi: it's because we don't send the submissions out to scientists currently working in the field
[9:33] Emile Pintens: Change the abstract? Thats the first time I've heard of that happening in Preceedings
[9:33] You: Emile - well they had some good points
[9:34] Emile Pintens: Ah gotcha
[9:34] Troy McLuhan: Adastar - What do you mean by accreditation?
[9:34] You: told me to be more explicit
[9:34] Max Chatnoir: The fact that there is some editorial review should carry some weight with things like tenure committees.
[9:34] You: absolutely max
[9:34] Adastar Galsworthy: the point someone raised earlier about the leve of acceptance by tenure committees and so forth.
[9:34] You: we have to explain it to the tenure committees
[9:35] Hilary Serevi: Adastar--is your question about whether accredation is a prerequisite for participation in open science?
[9:35] Emile Pintens: The question is how long with the tenure committees take in accepting Web 2.0 tools like the ones we are talking about
[9:35] Emile Pintens: How long will*
[9:36] You: it is certainly an issue (accreditation) and that is why it is important that we continue to talk
[9:36] You: we will need each other to support what we are doing
[9:36] Max Chatnoir: I would think that this kind of publication would at least have the status that a presentation at a meeting would have.
[9:36] You: to explain, to validate
[9:37] You: max that is true presentations count and are not peer reviewed
[9:37] Adastar Galsworthy: I'm working for Nature, and there is certainly belief within this comapny that such metrics will emerge.
[9:37] Max Chatnoir: Also, you're putting your work out in a very public venue, so there is a very wide potential peer pool for comments.
[9:37] Troy McLuhan: I don't think it's a matter of accepting tools. Scientists are always bringing new tools into use. It's a matter of determining "what counts". For example, the recent proof of the Poincare Conjecture was never published in a Peer Reviewed journal as far as I know, but certainly "counts"
[9:37] You: adastar - we are looking for Nature to take some lead in that
[9:38] Emile Pintens: Adastar, metrics from where?
[9:38] Hilary Serevi: there's an interesting paper by the PLoS medicine editors about how impact factor will change in response to web 2.0 tools
[9:38] Berci Dryke: Hilary: could you please give a link to that?
[9:38] Hilary Serevi: troy's reference is to Perelman's use of ArXiv rather than a math journal to distribute his work
[9:38] You: hilary - yes Heather Piwooar
[9:38] You: piwowar
[9:38] Hilary Serevi: doi: 10.1371/journal.pmed.0030291
[9:39] Berci Dryke: thank you
[9:39] Hilary Serevi: the chronicle of higher education also had an article about that
[9:39] Hilary Serevi: i don't have the link available
[9:39] Rakerman Yellowjacket: I think scientists need to push back against impact factor and move to a concept of "science portfolio" - what work have you done - there are going to be all different types of contributions
[9:39] Adastar Galsworthy: at the moment we are building social tools, but they are mostly in their first generation
[9:40] You: racker very good point - metrics are limited compared to portfolios
[9:40] Adastar Galsworthy: the obvious things to start looking for are the spoead of influence of ideas through social networks
[9:40] Adastar Galsworthy: but there is a bit of a way to go before anything solid is around to this robustly
[9:40] You: but we can still play with metrics - let just not give everything else up
[9:41] Adastar Galsworthy: however, I want to stress that I feel the reason that we need to do this is so that we can support open science, which I happen to think is vital in the presence of too much information to sift through
[9:41] Adastar Galsworthy: open science goes hand in hand with social networking, and this provides a platform for collaborative filtering
[9:42] You: Ada - do you wnat to talk about Connotea/Emile about Knowble
[9:42] suhky Rezillo: Doesn't Connotea acknowledge users' contribution to the site?
[9:42] Rakerman Yellowjacket: ISI algorithms shouldn't be the end-all of evaluating a scientist for tenure and promotion - we already have a system to evaluate grants - tenure committees should recognize the full work of the scientist - SOME of which must pass both the review of peers and hopefully be tested through being reproduced
[9:42] Emile Pintens: I can talk about Knowble anytime
[9:42] Emile Pintens: Am I next?
[9:42] You: sure
[9:43] Emile Pintens: Knowble is a knowledge community for researchers to connect, communicate, and collaborate.
[9:43] You: hold on
[9:43] Emile Pintens: ok
[9:44] You: sorry emile not for you - go on
[9:44] You: brb
[9:44] Emile Pintens: O ok, sorry.
[9:45] Emile Pintens: I came up with the idea while I was an undergrad at UNC, and we received funding from the School of Medicine as a part of UNC's CTSA proposal.
[9:45] Emile Pintens: Right now we are in Beta, but the idea is to provide a common community where researchers, professors, and scientists may connect based upon common research areas or methodologies.
[9:45] Max Chatnoir: Brilliant, Emile.
[9:45] You: I've tried Knoble recently
[9:45] Troy McLuhan: Wow this is a great idea
[9:45] Berci Dryke: is it similar to
[9:46] You: to specify our need for a docking expert
[9:46] Hilary Serevi: Over here!
[9:46] Emile Pintens: We are taking an approach similar to Facebook where we must accept your institution before a person may be able to register.
[9:46] Emile Pintens: I have not seen
[9:46] Emile Pintens: Hilary, you have a question?
[9:46] Max Chatnoir: I just discovered that, Emile!
[9:46] Berci Dryke: that is a medical community site with the same goals
[9:46] Hilary Serevi: sorry - no
[9:47] suhky Rezillo is Offline
[9:48] You have offered friendship to Troy McLuhan
[9:48] Troy McLuhan is Online
[9:48] Emile Pintens: Ah ok. While the School of Medicine provided the initial funding, we are moving to allow researchers from really any discipline to join. Our tools are not at the level of any discipline, but we are working on it. An example, we are linked to PubMed, which some professors at UNC feel it does not include all of their works.
[9:48] Rakerman Yellowjacket: how does knowble compare to pronetos and other scholar community sites?
[9:48] You have offered friendship to Rakerman Yellowjacket
[9:48] Rakerman Yellowjacket is Online
[9:48] You have offered friendship to Xantha Oe
[9:49] You have offered friendship to Joanna Wombat
[9:49] You have offered friendship to Hilary Serevi
[9:49] Emile Pintens: From what we know about Pronetos, they are focused on Publishing. We are focused on connecting people.
[9:49] Hilary Serevi is Online
[9:49] Emile Pintens: But since Pronetos isn't online yet, I do not know for sure, but we wish them luck!
[9:50] Troy McLuhan: I gather that Knowble is mainly for scientists and academics, as opposed to the general public with an interest in science?
[9:51] Joanna Wombat is Online
[9:51] Xantha Oe is Online
[9:51] Emile Pintens: Right now yes. We are trying to ensure a fairly tight user base. In time, I would not count us out in opening up to the general public.
[9:52] Emile Pintens: We are in beta, so user feedback is being gathered and we will be making further changes in the coming weeks.
[9:52] Emile Pintens: Are there any further questions?
[9:52] You: Ada do you want to say something about Connotea
[9:52] Adastar Galsworthy: sure
[9:52] Troy McLuhan: What is the underlying development tools for Knowble? A CMS? A web language?
[9:53] Emile Pintens: Troy, we use LAMP
[9:53] Adastar Galsworthy: first, sorry about the mess
[9:53] Visitor Counter 1.8: Welcome Xantha Oe. You have been counted.
[9:53] Adastar Galsworthy: I just threw these together 1/2 an hour ago.
[9:53] Visitor Counter 1.8: Welcome Berci Dryke. You have been counted.
[9:53] Adastar Galsworthy: am giving a talk on friday and will post the full presentation here in a nice format next week,.
[9:54] You: thanks ada
[9:54] Adastar Galsworthy: as many of you know there are a bunch of tools for bookmarking on hte internet
[9:54] Adastar Galsworthy: the great grand daddy is delicious.
[9:54] Adastar Galsworthy: Nature, and me spcifically, work on a tool for scientists called connotea
[9:55] Adastar Galsworthy: there are about three other specific tools out there for scientists.
[9:55] Adastar Galsworthy: I'd say take em for a test drive and pick the one you like best (as long as it's conotea ;)
[9:56] Adastar Galsworthy: as I was alluding to earlier, one of the things we are trying to do with connotea is make it into a rccomendation engine for scientsits
[9:56] Adastar Galsworthy: to help filter the huge number ot papers out there
[9:56] Adastar Galsworthy: but it is early days yet
[9:56] Adastar Galsworthy: There is an api and some people have bulit some cool apps using conontea as an engine
[9:56] You: what is an example ada
[9:57] Adastar Galsworthy: most of the exentions are greasmonkey extensions.
[9:57] Hilary Serevi: can you use greasemonkey to connect to the api?
[9:57] Adastar Galsworthy: one called Stack it, creates digg like buttons next to doi's on any poge and lets you see if the paper has been bookmarked
[9:58] Adastar Galsworthy: another called the entity describor (which was just provisionally released last week, so give it another week or so)
[9:58] Adastar Galsworthy: connects tags in conntea to a structured ontology, such as the MeSH ontology
[9:59] Adastar Galsworthy: There is another that uses conntoea as a backbone for connecting XML stlysheets for scehmas representing systems biology7
[9:59] Adastar Galsworthy: you can see them at [9:59] You: Ada - do you think you would be able to take Nature Predecings posts in connotea
[9:59] Adastar Galsworthy: yes, we are working on that
[10:00] Adastar Galsworthy: rather than waiting for everything to be perfect our philosophy is torelease and improve
[10:00] You: that would really help push the more open side
[10:00] You: thanks adastar!
[10:00] Adastar Galsworthy: no probs.
[10:00] You: before we go -
[10:00] You: any suggestions for the theme of the next session?
[10:00] Berci Dryke: medicine and web 2.0 :)
[10:01] You: nice berci
[10:01] Max Chatnoir: Horace, it it always in this time block?
[10:01] Hilary Serevi: i'm very intested in the ethical issues associated with putting medical
(theraputic/clinical) infomation on the web
[10:01] You: max I think same time next week
[10:01] Adastar Galsworthy: I gotta go now, thank's guy's
[10:01] Berci Dryke: Hilary: this is a crucial question...
[10:01] Adastar Galsworthy is Offline
[10:01] Hilary Serevi: thanks for organizing horace
[10:01] You: I'll post the transcript also on
[10:01] You: sure my pleasure
[10:02] Berci Dryke: thank you, Horace!
[10:02] Max Chatnoir: Sigh.... I'll have a class then, but will look for the TS!
[10:02] You: thank you all!
[10:02] Berci Dryke: I'll also post about it with many images
[10:02] Max Chatnoir: Excellent, Berci.
[10:02] You: yes please send me you images it you want
[10:02] You: we'll leave these posters up
[10:02] Max Chatnoir: Got a RL faculty meeting. Thanks, Horace!
[10:02] Emile Pintens: I have already made a post in the Knowble blog!
[10:03] Berci Dryke: next week, same time?
[10:03] You: so Berci lets do that then
[10:03] You: yes same time
[10:03] Emile Pintens: Same time next week sounds good
[10:03] You: thanks to joanna too for the space!
[10:03] Hilary Serevi: nice meeting everyone
[10:03] Hilary Serevi: thanks again!
[10:03] Joanna Wombat: thanks!
[10:03] You: bye everyone
[10:04] Berci Dryke: Bye!
[10:04] Emile Pintens: thanks Jean-Claude this was great! Talk to you soon
[10:04] Max Chatnoir is Offline
[10:04] Joanna Wombat is Offline
[10:05] Troy McLuhan: If you're interested in science-related events in SL, feel free to join the Science Center group
[10:05] Emile Pintens: Troy how do we do that?
[10:05] Rakerman Yellowjacket: thanks Jean-Claude

Friday, August 17, 2007

Bubblegum and Molecules in Second Life

The American Chemical Society now has a booth in the Chemistry Corner on Drexel Island in Second Life. Finola Graves from ACS will pop in and out to meet people there.

The bubblegum machine featured on Nature Island a few months back is there and has been much improved. You can now just type the name of a molecule (e.g. viagra, caffeine) and it will fetch info from PubChem and create a 3D model on the spot.

To create any molecule (not just in PubChem), Hiro's molecule rezzer is there also and is freely available.


Tuesday, August 14, 2007

Chemistry Corner on Drexel Island

With Eloise's help, we now have a Chemistry Corner on Drexel Island where chemists can put up posters and objects within Second Life.

We have different boards available at the store (multiple image Powerpoint-style, single image url link and single image teleport link) so it is really easy to set up a poster with little experience.
I have seeded the area with a presentation on Open Notebook Science and link to our UsefulChem wiki as well as a link to the Blue Obelisk wiki. The American Chemical Society will have a poster up shortly.

The Chemistry Corner is right next to the Ugi reaction staircase Jessica is building. (slurl)

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Monday, August 13, 2007

C&E News Article on Writing

Rachel Petkewich wrote an article in the August 13, 2007 issue of Chemical and Engineering News about Tips for Writing a Journal Article. Our use of a wiki and Open Notebook Science to track results was mentioned:

A few experimentalists have moved beyond word processing programs like Word and are investigating writing with wikis and other Web innovations. Derived from the Hawaiian word for "quick," a wiki is a collaborative website with content that can be directly edited by people with access. Jean-Claude Bradley, an organic chemist at Drexel University, and Henry S. Rzepa, a computational chemist at Imperial College London, both use wikis.

Bradley explains that his students record their experimental procedures and upload results to the group's public wiki instead of using conventional lab notebooks. Group members post discussion points online, and Bradley writes a manuscript in the wiki. He hopes that journals will accept the open format, citing transparency as a benefit. "Any statements I make can be traced back to the raw experimental data," he says.
Our papers in progress are available off the left sidebar on the wiki: Paper01 and Paper02. The first is on the Anatormy of the Ugi reaction and the second on the mechanism of acid-catalyzed furfuryl group cleavage.

With our move towards combinatorial libraries, we have not done as much mechanistic work with the Ugi reaction as I thought we would have by now. The challenge now is to rework and expand these preliminary manuscript drafts into complete stories. Of course, while all of this is going on, the "storyless experiments" stand on their own and are available for use by anyone for their own purposes.

Wednesday, August 08, 2007

Falcipain Collaboration

Thanks to Barry Bunin of Collaborative Drug Discovery, we now have a collaborator who will run assays on the compounds from our CombiUgi project. We'll be using our account on CDD to manage the activity results.

Phil Rosenthal from UCSF has agreed to run assays on the inhibition of falcipain-2, an enzyme used by the malaria parasite to digest hemoglobin. As described in UCSF magazine, the Rosenthal group discovered the enzyme and have developed an assay.

That means we'll have to do docking of our 500K library on falcipain-2. The PDB file is available here. Rajarshi and Tsu-Soo, are you up for another round?

Here is an email from Phil to clarify some more details:
We have been involved with docking studies before. Of course, Tack Kuntz at UCSF is a Dock pioneer. In general, Dock studies have identified some low uM inhibitors of falcipains, but it has been hard to move beyond this. However, these studies were based on models of FP structures, based on other papain-family enzyme structures. Now we have structures determined for the two key targets, falcipain-2 (the link that you sent) and falcipain-3 (not yet published, I am not sure if coordinates are yet available). These structures are from a structure group at UCSF. The key question is whether you will be offering a new approach compared to that used previously. It appears that the answer is yes, as you will have access to solved structures, and also to new chemistry methods. From our part, we’ll be happy to do the small number of screens that you envision. 5-10 compounds is quite trivial.

I mention to all collaborators that we have many collaborations with chemists interested in protease inhibitors as antimalarial drugs. Our major collaboration is with a group at GSK, and this project is well advanced using a traditional big pharma approach. We have academic collaborations with chemists in the US, Germany, Portugal, Venezuela, Cameroon, India, and South Africa (not only regarding protease inhibitors). I make it a point to be very open regarding the different collaborations but, of course, to respect each group’s confidentiality concerning results.

For a small set of compounds, we can do screening at any time. For larger projects, we can talk about the path forward. I’ll be in touch, and please let me know any time when you have compounds that you would like to screen or if you have any questions

Tuesday, August 07, 2007

Heather's Report Open Notebook Science at ISMB

Heather Piwowar has done a great job of summarizing the points of her Birds of a Feather meeting on Open Notebook Science at ISMB.

They look awfully similar to those that popped up at SciFoo.

SciFoo Lives On in Second Life

After complaining that there was not enough time to cover everything at the Science Foo Camp, and after getting some very positive feedback from our chemical reaction mechanism representation in Second Life, it occurred to me that it would make sense to attempt to continue the conversation in a virtual medium.

I have previously presented a poster in Second Life and I was thoroughly impressed with how well it worked. People would walk around, look at my poster, ask me for more information and share their experience. And just like in real life, when there was a lull in the traffic, I would chat with my poster neighbor. One big difference was that I didn't have a draining and expensive trip to deal with.

Yes, I know that there is no replacement for face to face interactions during lunch and breaks. But it is surprising just how much one can get out of the experience, given the minimal effort it takes.

So I have set up an area on one of Nature's islands called SciFoo Lives On. I have put up my poster on Open Notebook Science. Clicking on the images flips to the next one in the presentation. Clicking on a side panel opens a browser to a screencast recording of my presentation. I have also included a headshot of myself - clicking on that takes you to my UsefulChem research wiki.

But Second Life allows not only images but also 3D objects. As examples, I included a molecule and an obelisk that generates an organic chemistry quiz upon clicking. Later on I'll copy the reaction mechanism that is currently on display on Drexel Island.

I invite any other SciFoo participants to put up a poster. If you have a Powerpoint presentation it is fairly easy to put it up. Just let me know if you need help. Powerpoint style panels are available for free at the Drexel Island store but you will need to be invited to Nature's island by either by a member like me or the owner Joanna Wombat (Joanna Scott in real life) to build there.

Although we can create a nice place to visit and view posters anytime, it would be very interesting to see how un-conference sessions would work. Keep in mind that Second Life now has voice in addition to chat.

I propose to moderate a session on "Tools for Open Science" at noon EDT (9:00 PDT, 16:00 GMT) on August 20, 2007 for the convenience of our European and US West coast participants. In the spirit of SciFoo, this will be a discussion, not be a presentation, although we should feel free to use pages from our posters to facilitate communication.

I will also set up a thread on the Second Life section of Nature Networks for people to propose sessions.

SciFoo Lives On slurl.

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Sunday, August 05, 2007

SciFoo07 Ends

The past few days have been quite stimulating.

The SciFoo conference started right after I got off the plane in San Francisco on Friday evening around 18:00 and lasted till midnight. With the jetlag from the east coast I was exhausted but the energy of the meeting definitely kept my interest.

Friday night was the only part of the conference deliberately set up with the traditional format of speakers. The most impressive talk was on the big picture of planetary energy input and consumption. It was refreshing because the speakers seemed genuinely concerned with reporting on the actual state of things, instead of building up evidence to support their pet eco-solution. Lets just say things look grim for maintaining current energy consumption with existing renewable and non-renewable energy sources. (However, since we haven't been good at predicting scientific discoveries in the past my guess is this model will become irrelevant in 100 years). If the slides are released I'll link to them in an update.

On Friday night people suggested sessions for Saturday and Sunday and I tried to attend as many of them related to Open Science and scientific publication. The idea of this "un-conference" was to create brainstorming and discussion sessions. A few sessions really were like that but most ended up with significant presentation portions, some taking up the whole slot.

There was just enough time during the hour long sessions for people to state their opinions but not enough to innovate and make progress. That will have to wait for discussions and collaborations following the meeting. Anyone following the discussions in the blogosphere on Open Science and scientific publication will be familiar with the debates: peer review, academic credit, fear of getting scooped, etc.

The discussion was much like the blogosphere, except that the more introverted individuals probably did not contribute as much as they would have liked. I'll find out what they were thinking when they get to update their blogs and post comments.

Sometimes it felt like the Googleplex was the tower of Babel. It is apparent that there are enormous differences in the way science is done in various fields. Terms like raw data, peer review, experiment, reproducibility, citation, publication, workflow, etc. can have very different meanings.

This was probably the source of some heated discussions at times. As an organic chemist, if I find a report of a synthesis on the web with full characterization of the product, I can inspect the raw data from the spectra fairly quickly and determine if it makes any sense. I can then use that information to make that product or similar compounds with confidence. In that case, the presence or absence of peer review does nothing to affect my ability to use the information. For a cosmologist, analyzing raw data is so time consuming that the analogous situation does not apply. The only way to remove these misunderstandings is to continue to have conversations. This may be one of the most important functions of science blogs.

I met several scientists who expressed their intent to move at least part of their research to a more open format, beyond the framework of the traditional journal article. I also discussed collaboration on our drug-discovery efforts with a few people. As these materialize, I will be sure to blog about them.

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Thursday, August 02, 2007

CombiUgi on MyExperiment

I've been lurking for a while on the MyExperiment mailing list and noticed that they just opened beta testing. I still don't know exactly how it can useful to help us do science beyond what we are doing but there's just one way to find out.

Of all of our activities I think that the CombiUgi project fits the workflow concept described by MyExperiment. It involves heavy systematic processing of information from the generation of the libraries to the docking evaluation then synthesis and testing.

Since Rajarshi Guha built the CombiUgi webservice to generate the virtual libraries I think we really need his input to see if this can make things easier.

I've created a project called CombiUgi but no workflows yet. You'll probably need to create an account on the beta site to view it.

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UsefulChem on CDD

Barry Bunin from Collaborative Drug Discovery (CDD) has just given me word that UsefulChem now has an account on their database free of charge. Their current business model involves charging data contributors so I appreciate the invitation.

Our account can be accessed at (user: usefulchemistry, password: cdd). There is currently a set of compounds from our molecules blog. One of the features that I think will be useful for us is a way to record assay results. This comes in at a good time, since we just received the first results from the National Cancer Institute on the screening of one our compounds against tumor cell lines.

It will be interesting to compare CDD with other services like ChemSpider, as they evolve. One current limitation with CDD is that it is not possible to create links to molecules or assays that are truly public and indexable.

However, they are making some data pseudo-public by providing a public username and password (UsefulChem is not yet part of this beta): (login as demo, password cdd)

More on this from their recent press release:

Collaborative Drug Discovery (CDD, Inc) is pleased to announce the introduction of its next generation database technology. Collaborative Drug Discovery's Web-based database enables scientists to collaborate in novel, global efforts to more effectively develop new drug candidates for commercial and humanitarian markets. The technology enables novel community-based research efforts that become more and more useful as additional participants contribute data. Publicly available data sets currently in the system include the FDA orphan and approved drugs and small molecule drug discovery data dating back over half a century. These data sets pertain to a diverse group of neglected diseases, including malaria, tuberculosis, African Sleeping Sickness, Chagas Disease and Leishmania.

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First NCI Results

We just got the first results from the National Cancer Institute's testing of one of our Ugi products (UC0204) for activity again tumor cell lines. It looks like there was no significant activity, which is not unexpected since these molecules were not selected based on any tumor related criteria.

In the future, we will be sending over compounds from the CombiUgi project that score higher on Rajarshi's algorithm to predict anti-tumor activity and things should get more interesting.

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Wednesday, August 01, 2007

Chemical Reactions in Second Life

I have previously commented on how organic chemistry can be incorporated into Second Life.

Andrew Lang has created a script to generate 3D structures of molecules and shown how to represent the docking of a molecule in the receptor site of a protein (this is important for demonstrating how drugs can interfere with infectious agents like the parasite that causes malaria).

I have also described how these molecules can be indexed by common search engines, like Google, so that people can discover locations in Second Life where chemistry is displayed.

Now, with the help of Andrew and my students Jessica and Khalid, we can demonstrate a chemical reaction. Andrew came up with an elegant solution for controlling animation in Second Life. Simply by saying "back" or "next" in regular chat next to the molecules, the reaction will proceed to the next step. (see video below)

Jessica minimized the conformation of each intermediate in ChemSketch so that its 3D structure is probably fairly close to what it actually looks like. This should provide an additional perspective to use in the teaching of organic chemistry reaction mechanisms. Walking around a giant molecule with a student is certainly a contrast to looking at a 2D representation in a textbook, especially with the control of animation.

This is actually just the first step in the Ugi reaction that Jessica and Khalid are performing in my lab for the synthesis of anti-malarial compounds. This example starts with the reaction of benzaldehyde with 5-methylfurfurylamine to form an imine. (Note: we generally form the imine without adding an acid catalyst and so the mechanism under basic conditions is displayed).

For the full Ugi reaction keep climbing the staircase on Drexel Island that starts with imine formation here: slurl.

(These reactions are also going to be indexed on the SL molecule wiki)

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