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Posts from the ‘Scifoo Lives On’ Category

Scifoo lives on: Vote!

Scifoo lives on is a conferences series launched by Jean-Claude Bradley. After several successful events, we keep on organizing new ones but now would like you to weigh in. Which topic we should dedicate the next sessions to in 2009?

Further reading:

23andMe in Second Life: LIVE

23andMe, one of the (if not the) most famous companies focusing on personalized genetics, presented a slideshow today in Second Life in the latest session of the Scifoo Lives On series. The speakers were Erin Davis (science writer) and Joyce Tung (human geneticist). The title was 23andMe and 23andWe. Details here.


Live coverage starts (Pacific Time):

  • 9:30: The poster is up, everything seems to be ready. The first speaker, Erin, just arrived. The other residents are having a rest…

  • 9:40: The audience is slowly bigger and bigger. You can also follow us on Twitter. Our speaker, Joyce, just arrived. Here are both speakers:

  • 9:55: A few more people and some weird creatures arrived.

  • 9:58: Here is the crowd. We are really thankful to Second Nature for the place.

  • 10:05: I launched the session.

Welcome on Second Nature island!

Today’s Scifoo lives on session will feature 23andMe, a privately held biotech company focusing on personalized genetics. Two members of their editorial board will present a slideshow about their service, research and the future plans. Please welcome Erin Cline Davis, Ph.D. (SL: Luttibelle Eames ) who received her Ph.D. in Molecular and Cellular Physiology at the Stanford University School of Medicine.

and Joyce Tung, Ph.D., Human Geneticist (SL: Joyce Footman ) who pursued a Ph.D. in Genetics at the University of California, San Francisco. Please feel free to ask them questions after the presentation. Thank you!

  • 10:10: They started the presentation (excerpts):

  • 10:11: The SNP chip analyzes about 600,000 specific points in the genome that are known to vary. It’s important to understand that this is NOT sequencing, which would look at every single point in the genome.
  • 10:13: Samples are analyzed using an Illumina HumanHap550+ BeadChip plus a SNP chip custom designed by 23andMe scientists. The 23andMe custom SNP chip allows us to analyze the Y chromosome and mitochondrial genome (for paternal and maternal ancestry purposes) in much greater depth than conventional SNP chips.

  • 10:16: While they’re talking about Gene Journal, the audience is growing hugely…

  • 10:18: Your DNA tells you more than just what your genetics say about certain physical traits (such as ear wax type or lactose tolerance) or what conditions you might be at risk for — it can also tell you about where your ancestors came from.
  • 10:21: Sharing your genome is really as simple as sending an invitation. Because we understand that people may have different comfort levels when it comes to sharing their genetic information, we offer two levels of sharing to choose from.
  • 10:24: Here are our two speakers, Joyce and Erin:

  • 10:27: We now turn to 23andWe: 23andWe is consumer enabled research or as we like to call it, Research 2.0.
  • 10:31: It’s important to remember that a version of a SNP that is associated with a condition is not necessarily causing the condition. It may just be a marker that is linked to the truly causative DNA variation.
  • 10:32: Genome wide association studies are in the focus as you can see:

  • 10:35: 23andWe is a new way of doing research that will bring researchers and individuals together in a dynamic, web-based environment. By removing the obstacles of geography and the cost of maintaining multiple study sites, 23andWe hopes to enable large studies that would otherwise be infeasible. 23andWe is a serious research enterprise.
  • 10:38: The process: research proposal, data collection, data analysis, publication…

  • 10:41: We’re very excited about the potential for this project to show how the multimedia capabilities of the web can really enhance health research… We think 23andMe is a first step towards the concept of personalized medicine. We are now able to give customers access to technology that was not that long ago restricted to specialized laboratories. People can actually see what the latest research might mean for them.
  • 10:43: It’s time for questions: How will you get Informed Consents from every person for every study? Who actually owns the DNA results and samples…..?
  • 10:45: That’s a hard one… are you excited/concerned that you are providing the tools for any group of people to get together and self-test on “snake oil” compounds ?
  • 10:48: More and more hard questions… Erin must type fast: we are as concerned as you guys are about privacy. we really have no interest in violating your trust. our business only works if we can maintain your privacy.

  • 10:52: Strange creatures, sometimes strange questions: These tools allow for the other extreme, that is a group of people getting together on their own without medical assistance to self test and analyze. Will this be a problem ?

  • 10:57: Joyce: In the future, we hope to use some of the data from our chip to provide information about copy number variation.
  • 10:59: The question of the day award goes to… and as also Google is involved (is that right?) how long will it take until my search habits will be matched up with my genome? ;-)
  • 11:01: Wow, that sounds great: We will be encouraging our users to submit ideas for research studies that we can conduct.
  • 11:04: It’s over! The presentation was fantastic, Erin and Joyce answered all the questions. Thank you, 23andMe for the presentation and Second Nature for the island and place. See you next time!

Live coverage ends…

Nature’s role in e-Science: Second Life conference LIVE

Another day with live blogging, but this time from the Scifoo lives on Second Life conference session, where we’ll talk about‘s role in e-Science. Enjoy and join us here!

Live Coverage starts (Second Life time):

  • 8:25: Everything seems to be ready! We’ll start exactly at 9:00 (or 17:00 GMT). Here is a funny welcome image with Adastar Galsworthy:


  • 8:40: You may remember our first Scifoo lives on session that took place on the 20th of August. Emile Petrone talked about, a knowledge community for researchers to connect, communicate and collaborate. Now Emile told us they closed the site and started a new project. It’s good to be informed.
  • 8:45: Joanna Scott, the owner of the Second Nature island is with us as well. More and more people are coming…


  • 8:58: About a dozen attendees are here. We should start the session in some minutes. Come and join!
  • 9:02: Kick-off! Matt Brown will be the first speaker and he focuses on Nature Network. He has a weird avatar:


  • 9:07: I’ve always wanted to know why Nature Network is better (if it is) than WordPress or Blogger. “They’re getting about 1000 new scientists a month signing up on NN, but tens of thousands more regularly browse it.”
  • 9:09: Emile Pintens: Are you looking to move into other disciplines? Outside of the life sciences? … Matt: Really, we’re trying to cover the whole of science from physics to maths to biology.
  • 9:10: Richard Akerman asked a great question: say a research organisation … a research council wanted to subscribe all of it’s members – any cost? something to discuss offline?
  • 9:11: The answer is they’re working on it…
  • 9:14: The next speaker is Ian Mulvany from


  • 9:20: Connotea “is is somewhere between being an online social bookmark manager and an online social reference manager. The goal is to create a tool that allows the researcher to stay on top of the literature.”
  • 9:24: Connotea is going to be integrated into Nature Network. Wow! As Emile pointed out we all have to follow the guideline 1 site to rule them all.
  • 9:26: They have “a little over 60,000 people request an account, but less than that use it regularly”. What a number!
  • 9:28: According to Ian Mulvany, they have something in the region of 300,000 bookmarks with citation data, and more if you roll in non citation bookmarks… + 1.2 million tags!
  • 9:30: I asked him what he thinks about the recently launched 2collab. And the answer of the day is: i don’t think any one service is going to capture the market, and as a result i think it’s important for all of these services to find a way to share data and api calls, otherwise we will do a disservice to our useres
  • 9:32: Here is the page for Medicine 2.0 tag on Connotea.

A panorama image of us:


  • 9:36: We move on to Hilary Spencer from Nature Precedings. She talked about her project back in August, in the first sesison. Nature Precedings is a site for “Pre-publication research and preliminary findings”.
  • 9:40: I remember that last time we tried to find out where is the border between review and peer-review.


  • 9:46: Hilary: Nature Precedings is a place to store pieces of scientific communication in a way that allows them to be easily shared, referenced, and found by other researchers. We accept submissions in biology, medicine, chemistry and the earth sciences (except for clinical medicine).
  • 9:49: They also include collaborative “web 2.0”-like features. Like commenting directly on papers; a feature called “vote to promote” (kind of like the voting on Digg); tag-based classification; RSS feeds and e-mail alerts.
  • 9:53: Ricardo Vidal always has a great question: By using nature precedings does it bind the documents in any way to Nature? The answer is No, papers in Precedings receive a Creative Commons 3.0 license.
  • 9:56: I just subscribed to the Genetics channel of Precedings. It’s going to be useful to follow.
  • 9:58: I’m a bit surprised. They “only” have about 240 documents on the site. I thought they had many more.
  • 10:03: It’s not peer-reviewed, but moderated to keep things within guidelines.
  • 10:06: Helen Jaques is here on behalf of Nature Clinical Practice. Helen King couldn’t make it. She talks about Dissect Medicine.


  • 10:11: 642 users in total in 2006. I asked her how Dissect Medicine is different from Biowizard.
  • 10:14: Now some words about Nature Clinical Practice. As it seems to be involved in medical education, I’m curious whether they’d be interested in organizing medical educational exercises in Second Life.
  • 10:23: That’s all folks! It’s been great to hear the thoughts of the guys at I hope we got closer to understand Nature’s role in e-Science.

See you next time! Check out the transcript at the official page.

Live Coverage Ends

Read more!

Famous Scientific Bloggers in Second Life: LIVE

We’re back again with a live coverage of this week’s SciFoo Lives on session in Second Life. Famous scientific bloggers will talk about blogging.

Live Coverage Starts

  • 8:23: I’m setting up the presentation of Bora Zivkovic.
  • 8:34: I’m still uploading the slides of Bora. We expect to see Bora, Sandra Porter, Jean-Claude Bradley and some presenters from Nature Publishing Group today.


  • 8:42: Greg Petersen, a reader of Sandra’s blog is with me now. The poster of Bora is nearly ready.


  • 8:45: Sandra Porter is with us now as well.
  • 8:49: More and more people are coming. The poster of Bora is finally up! Jean-Claude Bradley arrived as well.


  • 8:53: Bora Zivkovic and some more guests are here. Bora has something in his hand:


  • 9:00: Kick-off! The first speaker is Sandra Porter from Discovering Biology in a Digital World.
  • 9:04: Sandra said: ” I started doing this [blogging] because it complemented my teaching activities. I’ve found that it’s addicting.”


  • 9:05: She contrasts her experience with blogging with her experience with two of the papers that she published this year.
  • 9:06: Extremely valid points: As a molecular biologist, I am not always patient and so I enjoy the immediate gratification of blogging. And I enjoy knowing that people actually read what I write.
  • 9:09: How do bloggers become respectable? It’s getting very interesting:


  • 9:11: Sandra expressed a very important opinion: I think it’s really good for scientists to have an opportunity to share what they do with the public. And show the public that science isn’t an entirely abstract activity.
  • 9:14: Sandra: I don’t always think it’s worthwhile for me to spend years publishing peer-reviewed research anymore.
  • 9:17: You should check out the last few slides of Sandra’s slideshow. Perfect!! How can a blogger present a peer-reviewed article to the blogreaders…
  • 9:20: Some questions about what experiment she would not blog abou and whether she plans to use blogging in her course this Spring.
  • 9:23: The next presenter is Bora Zivkovic who fights with his computer. He’s in panic, as he said. :)


  • 9:28: What is a science blog? A blog written by a sientist or a blog that cover science, or both, with some exceptions?
  • 9:30: The number of participants is still growing…


  • 9:33: How true it is!! Bora: There are others who translate from Scientese to English – professional journalists. Journalists usually do not have PhDs on science. Bloggers often do. So bloggers often compare the papers to media reporting and find the media lacking.
  • 9:38: Bora is talking about the role of science bloggers in combating pseudoscience and educating people.
  • 9:42: There is a lot of humor and fun on science blogs. Of course, check out LOLDiabetes:)
  • 9:47: Bora is presenting science blogs writing about different fields of science and from different aspects. It’s so good to see how many blogs we have out there…
  • 9:51: Bora just disappeared… So Jean-Claude presents his slide.


  • 9:54: He is talking about Open Notebook Science. A unique project of him.
  • 9:56: You should also check out UsefulChem wiki!
  • 9:58: Bora is back in action now! The next slide is about Open Notebook Science. What a perfect segue!
  • 10:06: Bora is just finishing his interesting slideshow. He said: So, what is the next step – integration between different modes of communication, including blogs?
  • 10:08: One of the conclusions of today’s session is that Bora needs a better computer. :)
  • 10:12: Questions’ time! Actually, we’re talking about the scientific articles of Wikipedia… As an administrator, I can’t be objective.
  • 10:17: I said: You shouldn’t use Wikipedia as your last source, but a starting point… It’s an old rule.
  • 10:24: The discussion is still going on, but that’s all for today, folks! See you next time! I hope you enjoyed it!

Live Coverage Ends

Further reading:

Live Coverage: SciFoo lives on session about videos in science

The new SciFoo lives on session in Second Life is about videos in Science. We’ll have participants, speakers from Bioscreencast, and many more. For those, who don’t have access to Second Life, I’m going to blog live about what’s happening inside now (PDT time):

Live Coverage starts:

  • 8:42: I’m setting up the poster for It’s Apryl from SciVee on the left.


  • 8:52: We have more and more participants. A lot of people from Nature!


  • 8:55: It seems Videojug and JoVe couldn’t make it…
  • 9:00: Sharp start again! The first speaker is Deepak Singh from Bioscreencast.
  • 9:04: So many interesting sites: SciVee, JoVe, Nature Podcast, Google Tech Talks…


  • 9:08: Deepak convinced me totally: 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.
  • 9:11: We’re watching the poster of Bioscreencast. I should give it a try, first for my Hungarian medical web geekery blog


  • 9:15: If I would like to create screencasts (I would!), then it would cost as much as nothing, as I have a microphone and there are plenty of free screencast softwares (I should write a whole post about it).
  • 9:20: No funding! They are working from their own pockets!
  • 9:24: We had to move on to the next poster of Jean-Claude Bradley (time is running fast). Youtube and UsefulChem…
  • 9:26: Jean-Claude: …in my lab we have been using YouTube to record experiments. Often the students don’t realize what is important to note in their notebook so I encourage them to link from our lab wiki to youtube.


  • 9:32: One of the scientific videos of Jean-Claude has over 5000 views in the past year on Youtube!
  • 9:35: We all had to agree: WikiSpaces – it rules!
  • 9:40: We moved on to see SciVee’s poster. I’m very interested in that!
  • 9:42: SciVee is operated in partnership with the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC). It can be great to work in such a partnership. :)
  • 9:44: 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. (Are we all the same?)


  • 9:46: Nice presentation! We have so many questions about SciVee!
  • 9:49: They accept video content that is relevant to a published peer reviewed paper. But they enable the upload of videos unrealated to a scientific paper. It’s like Youtube, but just for science.
  • 9:52: Licensing issues (CC 3.0) – nice catch from Troy McLuhan. They will contact a lawyer.
  • 9:58: The session is over, we had great presentations and posters. See you next week!

Live Coverage ends.

Live Coverage Now: SciFoo lives on session about the definition of Open Science

We’re back again! Here is a new SciFoo lives on session in Second Life, this time about the definition of open science. For those, who don’t have access to Second Life, I’m going to blog live about what’s happening inside SL now (time in Second Life or Pacific time):

Live Coverage starts:

  • 8:55: More and more participants are coming. Here is the first image of us:


  • 9:01: Jean-Claude Bradley is launching this session with his poster on Open Notebook Science.
  • 9:03: We’re also going to have Bill Hooker and Richard Akerman speaking today.
  • 9:05: There are plenty of definitions for open science.. Could you give us a good definition?
  • 9:06: Jean-Claude defines Open Notebook Science (ONS): it is where the reseracher’s actual lab notebook is made public in real time. You use wikis, blogs, etc. to make your scientific work more public. “By doing ONS, people can also study how science actually gets done, messiness and all…”
  • 9:10: Jean-Claude’s students have a wiki where they can list and mention their experiments and Jean-Claude can leave questions, notes for them. It’s an easy way to track, correct and discuss.


  • 9:11: Bill said: “I think science will (soon?) be reported experiment-by-experiment.”
  • 9:15: Usefulchem wiki is the perfect example for open notebook science. See all those experiments!
  • 9:20: Richard Akerman: it’s about making better *science* through collaboration and open sharing!
  • 9:22: Richard Akerman: often today data and failed experiments are lost from the record, even if they had some original digital format. He says the key is open scientific communication.
  • 9:24: The example for this is the eSciDoc project.


  • 9:25: Richard Akerman: 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.
  • 9:28: That was all about Open Notebook Science. Now we’re moving to Bill Hooker‘s poster.
  • 9:30: First question: do we need/want to define Open Science?
  • 9:33: Ok, Ok open science. But in what format?
  • 9:37: We get back again and again to wikis. Scientists should use wikis to track the experiments, to communicate more easily with other researchers.
  • 9:38: Next question, what is the role that journals such as nature have or should have with open science? (Nature is the leader in this field. Just an example: who does organize this session? Of course, Nature Publishing Group.)
  • 9:40: Nature Precedings again. They accept nearly any kind of format of pre-print publications/works.
  • 9:41: Here is a professional wiki! We seem to be more interested in tools than definitions.
  • 9:42: Please welcome both Bill Hooker :)


  • 9:49: It seems Bill was the last speaker today. Next time (next Monday at 16:00 GMT), we’re going to talk about sites providing scientific videos (JoVe, SciVee, Videojug, Bioscreencast and more. See you then!
  • 9:53: Thank you Jean-Claude for making this happen!


Live Coverage ends!

Thank you for watching! See you next Monday at 16:00 GMT to learn more about science videos.

SciFoo lives on in Second Life: Web 2.0 and Medicine

An other fascinating experience today in Second Life! I enjoyed so much to be a co-organizer with Jean-Claude Bradley of today’s session on the Second Nature island. With about 30-35 participants and 5 posters, I really believe we had some interesting and mind-blowing discussions. According to the feedback, people liked my presentation (Web 2.0 and Medicine).


  • First, I talked about web 2.0’s impact on medicine: medical blogs (code of ethics, rankings); medical wikis (Ask Dr Wiki, Radiopaedia); medical podcasts, videocasts, search engines, and our Second Life project, the Ann Myers Medical Center where we had our first medical training 2 weeks ago.
  • Then Max Sanel from introduced their unique medical community (with more than 2600 members from 70! countries). They’re totally open for any kind of feedback. If you’re a medical professional (or just working to become one), consider joining them!
  • Lauren Possiel accepted my invitation as well and presented PhD students founded the site to create a free, web-based community for life scientists and physicians, aimed at making the world’s biomedical research information universally accessible and useful. So if you would like to use a more interactive Pubmed, then try Biowizard! You can get a Biowizard T-shirt on the SL island. E-marketing, isn’t? :)
  • In the end, Jean-Claude and Dan Zaharevitz told us about Drug Design and web 2.0. It seemed to me that  complicated processes like drug designing become easier by these web 2.0 tools (blogs, wikis, mailing lists, Second Life).

Deepak from bbgm couldn’t make it (How do I know that? Via Twitter!), but he will definitely love the next session about science videos (JOVE, Bioscreencast, SciVee, etc.). So if you’re interested, see you next Tuesday at 16:00 GMT on the Second Nature island.

Further reading:


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