by Walter Jessen on Sunday, May 16, 2010 | No comments
Graham Steel (FriendFeed: McDawg) has started a contact list for people who are directly or indirectly affiliated and/or associated with Open Science. He discussed the reason for an Open Science Contact List yesterday on his blog. Although his focus in on the Life Sciences, people from other disciplines are also welcome. If you’re such an individual, add you name to the list.
Tags:
blog,
contact list,
disciplines,
FriendFeed,
life sciences,
open science
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by Walter Jessen on Friday, May 14, 2010 | 4 comments
I first discovered Biostar, a StackExchange for bioinformatics, computational genomics and systems biology, via a post of Deepak’s (FriendFeed: mndoci) back in March: BioStar – A bioinformatics stackexchange. I’ve been meaning to use it, but with the job change and move, I just haven’t had time. It’s similar to the Life Scientists room on FriendFeed, although obviously more focused on Q & A.
Part Digg, part forum, part blog and part wiki, StackExchange is a place to get expert answers to your questions. Today, I stumbled across Meta StackExchange, a forum to ask questions about StackExchange itself. Scanning down the page, I saw the question “Proposal for Physical Computing StackExchange” and thought to myself, “Oh, that’s interesting, you can create smaller, more focused groups.”
Little did I know … those focused groups are called “Stacks” and there’s a number of them, several of which revolve around science.
Just yesterday, Andrew Perry (FriendFeed: pansapiens) wrote about StackExchange Sites for Science. He briefly reviewed a couple of them and linked to a list of science-related StackExchanges. I was interested in the Neuroknowledge stack until I saw all the spam. Hopefully, Stack Exchange 2.0 with it’s new site creation process and Creative Commons licensing will address the problem.
Scientific research today no longer happens in a vacuum. Networking technologies and online resources such as StackExchange are helping to increase the pace of scientific communication, scholarship and progress in the digital age. It’s truly an exciting time for networked science.
Tags:
andrew perry,
bioinformatics,
communication scholarship,
computational genomics,
life scientists,
networked science,
networking technologies,
physical computing,
science,
StackExchange,
systems biology
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by Walter Jessen on Sunday, January 31, 2010 | 20 comments
There has been a number of posts written about the ScienceOnline2010 conference. Rather than write another one simply about my personal experiences, I thought it would be interesting to have a discussion about the conference with a number of people that both attended in person or via the Internet. Since discussion is often challenging on blogs, I posted four questions about the conference on FriendFeed. I also cross-posted the questions to my personal Twitter account. I loved the idea of using Web 2.0 technologies (social media, blogs) to discuss a conference about science communications. Below is an amalgamation of the discussion that followed.
What did you think about the Friday food tours/workshops/lab tours?
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Walter Jessen: I didn’t go to any of the food or lab tours, but I heard some of the lab tours were fun (the DiVE into Alcohol and RTI International tours looked cool). Instead, I went to the Blogging 102 and Podcasting 101 workshops. Both were informative; I found out about a few tools/resources I didn’t know about at the Blogging 102 workshop. In retrospect, I should have attended the workshop Repositories for Fun and Profit as many of the Tweets coming from attendees looked interesting.
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Bora Zivkovic: Hard to sift through all the blog coverage but there were a number of posts that mentioned their experiences at Lab/Museum Tours and they were all very positive. Nancy Shepherd, who organized the tours, has collected posts about each tour and sent the links to the hosts. I wish more people blogged about the tours as we wish to have them again next year (they kinda expect that if they host a bunch of bloggers, they’ll get some coverage in return).
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Graham Steel: ScienceOnline2010 – I wish I was there (my post-conference analysis in the comments section of a recent post by Martin Fenner).
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Dorothea Salo: The transportation arrangements failed me, so I didn’t get to the Friday tour I’d signed up for. It looked like a really good one, too! Walter, thank you, I’m flattered.
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Walter: I wish the tours didn’t have to overlap with the workshops; it makes for a difficult choice. Dorothea, you’re welcome (and disappointed we didn’t get a chance to meet).
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Graham: Interview with Moshe Pritsker (JoVE) #scio09
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Bora: The tours did not overlap. Workshops ended at 12noon. Tours started at 2pm. (only coffee overlapped)
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Walter: Yes, I was thinking of the Food Tours (coffee). Unfortunately, the two lab tours I was interested in were full by the time I checked them out. I won’t make that mistake next year.
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Bora: Here’s [blog posts] on the Duke DiVE, the Raleigh museum, lemurs (here, here and here). There are also lots of images on Flickr from the tours. And Dorthea – next time stay in the hotel with everyone as we had organized transport and hired extra shuttles and made sure nobody was left behind.
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Dorothea: I was *at* the hotel. None of the shuttles for the Durham Museum of Life and Science seems to have left from there. Also, I saved you guys $$$ by staying with my parents, so .
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Bora: Really – our problem with the Durham museum tour was that the (expensive) shuttle we got for this specific tour was sitting there empty (after the shuttles for other tours already left) while many of the participants organized (without telling us) carpooling among themselves and went directly. Need to check on what happened …
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Dorothea: Sounds like ordinary miscommunication. Don’t beat yourself up over it; it happens.
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Bora: Thank you for your understanding, Dorothea.
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Dorothea: No worries; I wasn’t aiming to make you feel bad. It was a great conference, and those can’t happen without a bobble here and there.
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Bora: Here’s another [blog post] on Duke DiVE.
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Stephanie Willen Brown: The Museum of LIfe & Science tour was AWESOME – Larry the tour guide was quite knowledgeable and the behind-the-scenes look at the animals was a lot of fun. I am going to be join the museum based on that tour and will be taking my husband along with me next time. Images from the @lifeandscience tour are on flickr, thanks to Karyn Traphagen.
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Bora: Larry is on Twitter @larryboles
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Bill Hooker: I went to Dorothea’s IR workshop in the morning and the Duke Lemur Center in the afternoon, and loved every minute of both! I wish there had been more scientists in the IR session — as per all the recent discussion about librarians and scientists. In re: shuttles, there always seemed to be one just leaving for wherever I wanted to be; I thought they were great.
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Steve Koch: Dorothea’s IR workshop was very informative … If it has been longer than 1 hour, the time would have been used productively. Duke DiVE tour was good, but the format (6 people in the room at once) wasn’t so hot. I would much rather have had 10 minutes to myself, and I would have wanted to look at a 3-D crystal structure, not the alcohol tour. Though it was interesting to see how they’re using it for education.
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What did you think about the sessions (scope and presentation)?
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Walter: The scope of the sessions spanned everything from applications in scientific research, such as Science in the Cloud, to science communications, such as “Science Online Talks Between Generations, to science in society, such as the Science on Radio, TV and Video. From my perspective as a scientist, the conference was dominated by people in science journalism/communication/policy. I thought the Science in the Cloud session was really interesting, especially from a professional point of view. Unfortunately, there were too many interesting sessions that overlapped; I regret not being able to attend the Broader Impact Done Right or Government 2.0.
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Bora: For context (and behind-the-scenes insight) see my own summary.
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Walter: I really enjoyed the unconference format. Several sessions I attended were mostly a presentation and not nearly as engaging. For the Medical Journalism session that I co-moderated with Karl Bates, we pulled up chairs and invited everyone to sit in the front part of the room. The discussion was great!
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Graham: As per the last two years, I followed events virtually. I thought the scope was very diverse and quite a change from a couple of years ago. I think that’s a good thing. The way that the sessions were divided meant that you could very much tailor the weekend to best suit what the attendee was particularly interested in whilst also getting a chance to learn about subject matters that one didn’t know much about. I’m sure I’m not the only one who is looking forward to watching the official #scio10 video footage once it has been edited and uploaded .
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Martin Fenner: Some sessions had a fairly broad topic. Difficult to cover in 60 minutes.
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Steve: Agree that unconference-style worked the best. The audience discussion in the Science in the Cloud was very informative. I think John Hogenesch did a great job initiating that with the brief example in the beginning followed by opening it up. Walter, your session (Medicine 2.0/Science 2.0) also had a lot of good audience participation, though you had slides throughout. Clearly both worked in terms of engaging the audience, so maybe format isn’t so important as a good moderator and a good collection of people in the audience. I liked the diverse scope of topics. I too had to miss many I’d wanted to attend, but I suppose that’s much better than having a bunch of lousy sessions. Wanted more time between sessions for talking in the hallways!
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Cameron Neylon: I like the format of SciOnline – the short presentation – often from a group of people who don’t naturally agree with each other, followed by discussion seems to work really well. But the quality is a little bit too dense I think – I would argue for extending the length and reducing the number of concurrent sessions a little. The catch there is you would have more people in the rooms so maybe discussion wouldn’t be so good. But its a little like SciFoo – you spend the day getting stressed about which sessions you’ve missed and then get home to discover that there were a dozen people you wanted to meet who you never even realized were there.
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How was access (livestreaming and social media)?
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Walter: Since I was there and attended sessions that weren’t being livestreamed, I can’t comment. I did see on Twitter that there was problems with the livestreaming in the morning. There was *a lot* of people using Twitter, which is funny since FriendFeed would have been much better for discussion. When I put together summaries of the sessions I moderated, I also found the #scio10 tag to be rather limited. It was great for the conference overall, but didn’t allow for individual sessions to be identified. Next year, there should be session specific tags so that it’s possible to look up online discussion (which I imagine will be used even more than it was this year).
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Dan Hagon: I was following online from the UK. When it was available livestreaming worked well and probably better than twitter as twitter feeds can depend quite a bit on what individual interests are being selected. Although it’s difficult for me to judge if it was being used in this way at this particular event, I’d say that twitter works best as a back channel rather than a relay channel. Having said this twitter did provide a bidirectional link – this is possible with ustream but was not heavily used in the end.
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Graham: I also followed events from the UK. I would say that the bar was set extremely high at the same conference two years ago (I had no internet connection during last year’s event so unable to comment on that one). Almost all of the sessions in 2008 were livestreamed and archived immediately on Ustream, cue this recent blog post. Bora, can you confirm what tech. difficulties were encountered this year? I would appreciate this. Thanks.
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Martin: I wrote a blog post about virtually attending ScienceOnline2010 and Graham’s comment was like a blog post in itself.
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Steve: The conference was the first time I’d found twitter seriously useful. I used it because others were, but I still strongly prefer FriendFeed for discussing things. Overall, wireless access at the conference was great. And live-tweeting/FriendFeeding was quite fun and I definitely think it reinforced ability to take away things from the conference. Wireless at the Radisson and the workshop the first day wasn’t sufficient.
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Cameron: I think it worth pointing out that the wireless actually did do the job which is highly unusual. I was there and didn’t follow the livestream. I used Twitter because that seemed to be what everyone else was using but agree with Steve that FriendFeed is my preference. Without wishing to bang the drum – this kind of coverage is something that Wave is extremely good at – but it currently doesn’t provide the public facing interaction in the way one would like. But it is a specific use case that it works well for – particularly if video or slide images can be incorporated.
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How much technology was on display?
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Walter: None, really. This has already been discussed on FriendFeed. Part of the problem was that demos ran concurrently with conference sessions; I like Christina Pikas’ idea to run the demos separately from the sessions, for example during breaks or lunch. I also think a Friday afternoon tech expo would be cool and would attract more geeks to the conference. What types of technology would be of interest to conference participants? Hardware such as laptops or mobile devices? Software demos that focus on communication (such as Google wave or Google sidewiki)?
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Graham: My chips would be on mobile devices and also software demos (preferably OS ones). Like Walter, I also agree with Christina’s idea. Similarly, I also think a Friday tech expo would attract more tech geeks to the Conference.
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Bora: We are reading all these FF threads and jotting down all these ideas. We’ll keep them on the table when we start planning the next one … keep the ideas coming.
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Martin: There was a lot of technology behind the scenes at #scio10, from SignalShare to all these Web 2.0 tools that we take for granted. I would like to see a few demos of new tools, i.e. those that are almost ready to launch.
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Bill: Love the tech expo idea. As Graham says, I think mobile devices and software demos would be popular. What might be good is a “linux for n00bs” session or demo, and/or “linux for science”. I often feel a pang of guilt over not having switched to an Open Source OS, but I always feel I can’t afford the time to climb the steep learning curve. Andy Farke gave me a quick tour of his Eee PC running (I forget which) Linux, and showed me that it is not as daunting as I had thought. Crazy idea for a demo: could you set up a small research institute’s IT department (intranet, internet access, storage, backup, all the usual personal and scientific software equivalents) for, say, $1000? $500? How low can you go, using Open Source OS and software and various cheap hardware sources? The demo could consist of a server and several client machines, all running various software as though they were sitting in offices and labs throughout the institute.
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Graham: Brilliant idea, Bill.
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Neil Saunders: Liking Bill’s idea. And no, Linux is not as daunting as you may think. At one level, it’s no different to using any OS: there’s a desktop, menus containing applications, folders for files – you can use it entirely in a desktop-y, pointy-clicky fashion, just like anything else. I guess the daunting thing is that its full power come through using a terminal and the myriad scripting/language options that come with command-line use.
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Steve: I went to the first demo session (Google Wave, Trixie Tracker, Fish reporting via sms, analysis of collaboration between scientists) and it was fun and stimulating. As a researcher, I love seeing demos that can help me carry out open science. But things I want to see are possibly very specific and many of the other attendees wouldn’t care.
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Cameron: I went to some of the demos but I was much more motivated to discuss ideas than tech. Ideas around tech would have been worth my while but a very short introduction to something that was probably quite complex seemed to not provide the opportunity to really dig in properly. So I’d argue for longer demos, perhaps even a sort of “trade show” session where people can wander from demo to demo over the course of an hour or so … ?
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Walter: Exactly what I was thinking when I suggested a tech expo. Run it all afternoon on Friday — this would provide ample time for participants to see a number of demos and to really “dig in” to those they were interested in. The extended time slot and trade show feel would also allow time for networking between participants (since I think all of us wish there had been more time to meet and talk with others).
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Are you a Twitter user? Tweet this!
This post was developed from four separate discussions on FriendFeed:
Tags:
communications,
conference,
demo,
food tours,
FriendFeed,
lab tours,
science,
ScienceOnline,
scio10,
sessions,
tech,
tech expo,
Technology,
twitter,
unconference,
workshops
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by Walter Jessen on Saturday, January 16, 2010 | No comments
Twitter hashtag: #scio10
FriendFeed group: ScienceOnline2010
Flickr tag: #scio10
YouTube videos: tagged with scienceonline2010
UStream channels:
All other sessions are being recorded and will be uploaded to the Science in the Triangle YouTube channel.
Update: Livestreaming should be up and running by the 10:15 session (EST).
Tags:
FriendFeed,
room,
science,
sessions,
triangle,
twitter
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by Walter Jessen on Saturday, January 9, 2010 | 10 comments
I’m looking over the ScienceOnline2010 conference schedule tonight and deciding which sessions to attend. To make it easier to read, I copied the wiki and made a PDF (sometimes paper is best). In case anyone is interested in downloading a copy for themselves, you can get it here: ScienceOnline2010 program PDF
I’m hoping to blog throughout the conference next weekend here on NGS. I’ll post links to other resources as I find out about them. Below I’ve listed the sessions I’d like to attend and will thus be writing about — unfortunately, there’s several time slots that have more than one session! I know I can always go back and watch the video later, but I’d really like to be involved in the discussion.
Decisions, decisions …
Saturday, January 16, 9:00 – 10:05am
Saturday, January 16, 10:15 – 11:20am
Saturday, January 16, 11:30 – 12:35pm
Saturday, January 16, 2:00 – 3:05pm
Saturday, January 16, 3:15 – 4:20pm
Saturday, January 16, 4:30 – 5:35pm
Sunday, January 17, 9:00 – 10:05am
Sunday, January 17, 10:15 – 11:20am
Sunday, January 17, 11:30am – 12:35pm
Tags:
PDF,
program,
schedule,
ScienceOnline2010,
scio10,
session
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by Walter Jessen on Wednesday, December 2, 2009 | 25 comments
BioKM is a new way to keep research knowledge organized. An internet-based service, BioKM is designed to meet the everyday needs of researchers in an academic lab environment, allowing them to store, search, share and manage laboratory and research data.
BioKM provides a number of tools that enable users to plan and track research projects, organize materials and maintain a knowledgebase. To promote communication and discussion, users are able to exchange comments in all areas of BioKM. I asked Jonathan Gross, founder of BioKM, if NGS could get a closer look at the service and he was happy to set us up with an account. Read on for the review and a special offer for NGS readers.
(more…)
Tags:
biocollection,
BioKM,
define,
knowledge management,
knowledgebase,
materials,
papers,
project management,
projects,
protocols,
PubMed,
track
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by Hope Leman on Friday, November 6, 2009 | 5 comments
CureHunter is a web accessible, fully integrated scientific search, data retrieval and analysis engine. Developed by a team of scientists with expertise in medical data mining, artificial intelligence software development, computational linguistics and computational biology, CureHunter “reads” the entire U.S. National Library of Medicine Medline Archive and automatically extract and quantifies the evidence for successful clinical outcomes of all known drugs for all known human diseases.
Hope had an opportunity to talk with Judge Schonfeld, CEO and Chief Scientist of CureHunter. In part II of their interview below, Hope focuses on the users and uses of CureHunter; Judge discusses the differences between CureHunter and Wolfram|Alpha, and compares search results from CureHunter to novo|seek, GoPubMed and PubMed.
(more…)
Tags:
bioinformatics,
computational linguistic model,
CureHunter,
data mining,
discover,
disease,
drugs,
EMR,
evidence-based medicine,
extraction,
graph theoretical ontology,
knowledge engine,
medical informatics,
medical search,
pharma,
semantic search,
semantic web,
Stephen Wolfram,
Wolfram|Alpha
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by Hope Leman on Thursday, November 5, 2009 | 2 comments
CureHunter is a web accessible, fully integrated scientific search, data retrieval and analysis engine. Developed by a team of scientists with expertise in medical data mining, artificial intelligence software development, computational linguistics and computational biology, CureHunter “reads” the entire U.S. National Library of Medicine Medline Archive and automatically extract and quantifies the evidence for successful clinical outcomes of all known drugs for all known human diseases.
Hope had an opportunity to talk with Judge Schonfeld, CEO and Chief Scientist of CureHunter. In part I of their interview below, Judge talks about the development of CureHunter, the definition of “autonomous search” and the difference between CureHunter and other authoritative online reference services.
(more…)
Tags:
analysis engine,
artificial intelligence software developement,
computational biology,
computational linguistics,
CureHunter,
data retrieval,
diseases,
drugs,
expert biomedical system,
medical data mining,
Medline,
ontology,
search,
successful clinical outcomes,
taxonomy
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by Walter Jessen on Thursday, November 5, 2009 | 3 comments
We’ve written previously about DeepDyve, the search engine that searches the deep web, i.e. content that is out of reach of various search engines and other searching algorithms — PDFs, subscription-only archives, databases or other unstructured information located on the “dark web”.
Last week, DeepDyve announced that they are now offering consumers and professionals rental access to more than 30 million articles in their research database. Their new slogan is “Research. Rent. Read.”
(more…)
Tags:
article,
DeepDyve,
journal,
rental,
scientific publishing,
subscription
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by Hope Leman on Wednesday, October 7, 2009 | 2 comments
Before we begin, Dr. Bedlack, I would like to provide a bit of background for our readers to illustrate why your project ALSUntangled is such an innovation in medicine and a contribution to Medicine 2.0, neurology and to the study of amyotrophic lateral sclerosis (ALS) in particular. It really is a fascinating example of how researchers, patients and mainstream scientific publishers (so often maligned by those of us clamoring for open access) can work together and employ Web 2.0 tools such as Twitter and Ning to assist the seriously ill and advance science.
I subscribe to the journal, Amyotrophic Lateral Sclerosis. It is the leading periodical on the subject of ALS (also known as Lou Gehrig’s disease and motor neuron disease). As I was reading through a recent issue I came upon the article, ALSUntangled (ALSU): A Scientific Approach to Off-Label Treatment Options for People with ALS Using Tweets and Twitters and was immediately intrigued. I thought of the seminal article 140 Health Care Uses for Twitter and was very curious to learn more about how you are using Twitter in your work on ALS.
Your project is important not only to the world of neurology but to medicine in general given the explosion in the use of Twitter and in social media in medicine and healthcare vis-a-vis a range of issues from clinical trial recruitment to patient education to the e-patient/digital patient movement.
(more…)
Tags:
ALS,
ALSUntangled,
Amyotrophic Lateral Sclerosis,
group treatments,
healthcare,
interview,
Lou Gehrig's Disease,
Medicine 2.0,
motor neuron disease,
nervous system,
neurology,
Ning,
treatment,
twitter,
web 2.0
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