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SciBarCamp

SciBarCamp

This room is a general meeting place for everything related to SciBarCamp.
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Andrew Lang
ORU Science and Science Fiction Conference. April 12-13, 2012 http://sciencefiction.oru.edu Plenary Speakers: Paul Davies and Joan Slonczewski
Richard G. Lanzara
Silent Springs: Why Are All the Frogs “Croaking”? - http://www.plosbiology.org/article...
Richard G. Lanzara
Scientific wandering about receptor function and activation - http://www.bio-balance.com/Ref...
Kubke
Shirley Wu
Building Something SciFoo Style - REALscience - http://www.realscience.us/2009...
Kubke
Spinning Science: The good and the bad of media sensationalism - Kiki and Naomy
Provocative hypothesis: sensationalism is the way to report science. - Martin Fenner
"Our best plan is probably to try to crowd out falsehood by truth and to present scientific information in a way that will be at least as attractive as the misinformation that now holds the field." Edwin Slosson 1921 - Martin Fenner
How do we find stories that grab people's attention. - Martin Fenner
Kiki @drkiki - Naomi @nthmost - Kubke
People have a very tribal basis for what they believe. - Martin Fenner
Scientists try to appeal to the people in the world, sometimes not aware there is this whole other set of people for whom science is a luxury that happens in another world - Kubke
Many Americans (50%?) think that science is irrelevant for their lives. - Martin Fenner
Not 'teach people science" instead, give them the relevant information that makes them gain 'appreciation" - Kubke
We need primary, secondary (e.g. science blogs) and tertiary sources for science communication. Tertiary sources (such as local papers, radio) are not used enough. - Martin Fenner
Science Entertainment Exchange: http://www.scienceandentertain... - Martin Fenner
We need more translators of science, rather than more people doing science. We are already overwhelmed with the massive amount of science created today. - Martin Fenner
There are different realms of science communication: a) science for scientists b) science for scientists working in different fields c) science for the educated public, d) science for students. - Martin Fenner
Scientists could do more to publicize their work themselves - Kubke
Discussion of misunderstandings between scientists and their institution's PR people. - Martin Fenner
What is the role of PR: start the buzz about the institution/scientist/product... - Martin Fenner
Science in general has an image problem - Martin Fenner
What's a rock star scientist? - Andrew Lang
Why do kids look up more to basketball players rather than scientists? They are taller. - Martin Fenner
Should scientists care about what they PR people publicize? - Martin Fenner
Part of the problem: scientists are not automatically good communicators. Should they all become good communicators? Probably not possible and not required. - Martin Fenner
Degenerated into a discussion on how to argue with ID proponents. - Andrew Lang
Questions to go home with: who are the people you want to reach? Why do you want to talk to them? What do you want to tell them? - Martin Fenner
I think it's time to start a relationship counseling service for scientists and their PR departments. - Naomi Most
the first 50 minutes of this talk were captured here: http://bit.ly/2G0DE - Naomi Most
Helping people appreciate science is also a teaching step, because understanding the value motivates learning. - Mike Chelen
Jim Hardy
Subversive Science on Pirate Cat Radio: SciBarCamp Palo Alto coverage - http://subversivescience.blogspot.com/2009...
Bosco Ho
My vote for best dressed at #sbcpa is Jason Hoyt wearing the tight v-neck white t-shirt and a black tie.
I dug Naomi Most's key necklace as well - Shirley Wu
+1 to Naomi for her necklace and ninja shoes - Mackenzie Cowell
We should also do best T-shirts. Todd's "Science: It works, bitches!"; Duncan's "Alright my luvver". Others? - Chris Patil
Duncan's shirt was making me LOL - Mr. Gunn
w00t! yeah i dug Jason Hoyt's hipster geek look as well. - Naomi Most
I'm liking my new 23andMe and PLoS Hamster ball T shirts! Thanks guys! - Jim Hardy
In all fairness, Jason's shirt was collared, so technically "not" a T-shirt http://is.gd/1uNMQ - Jim Hardy
Kirsten Sanford
I want to help you introduce your research to the world. Let's talk!
Although I didn't actually get to sit down and talk to you at any point! :-( - Cameron Neylon
Not having been to SciBarCamp, why do you want this? But, with great pleasure. ;-) - Heather
You know where to find us! I think you need a "Opt Out" option instead :-) - Jim Hardy
Jim Hardy
#sbcPA WTF Psychedelics? http://psychedelicresearch.org/ Matt Baggott
Ayahuasca Churches becoming more accepted and holding up to Supreme Court scrutiny http://www.ayahuasca.com/ - Jim Hardy
MDMA quantitatively increases feelings of "Closeness to Others" in controlled clinical trials - Jim Hardy
MDMA exhibits non-linear kinetics, increasing risks of toxicity - Jim Hardy
however, neurotoxicity has been "grossly exaggerated" - Jim Hardy
Synethesia: http://en.wikipedia.org/wiki... Kewl new word. - Jim Hardy
Almost no studies of pharmacological synesthesia, although it was discovered over a century ago - Jim Hardy
Best theory is that hallucinogens/antidepressants work through type of increased neuroplasticity - Jim Hardy
Here's at least 95% of this talk caught on ustream: http://bit.ly/2G0DE - Naomi Most
Mackenzie Cowell
How much does an annual library subscription to the top 20 closed-access journals cost? Lets start a virtual library for non-scientists.
My guess would be on the order of $25-50,000 per year. The UC OSC maintains a curated list of price info for about 3000 of the "top scholarly journals" (http://osc.universityofcalifornia.edu/journal...). The average list price is about $1250/title (http://www.sennoma.net/main...), but I would expect the "top 20" to be more expensive than average. - Bill Hooker
Two potential problems: first, 20 journals doesn't get you very far -- there are more than 20,000 to choose from; and second, how do you determine the "top 20"? We have had many, many conversations around here on this topic... - Bill Hooker
I was niavely thinking we could pick based on eigenfactor ranking. Maybe we could afford many more than 20 - it all depends on how much the licenses could be negotiated for and the tension between number of subscribers and subscription cost. How much do alumni organization (that include access to the Uni library) subscriptions typically cost? - Mackenzie Cowell from iPhone
Why do scientists keep playing hostage to the copyright bandits that pistol-whipped their publicly-funded intellectual property from them to begin with? Let's consider the grey option, not too seriously, just as a fun literary idea: One could use existing hashes (pubmed ID, DOI, etc.) and paper databases (pubmed) to build a "swedish-hosted" bittorrent database of every article ever... more... - Anselm Levskaya
Anselm, good idea. We should focus from the beginning on empowering researchers from the BRIC. A successful international sci-pirate bay will be helpful in demonstrating the size and desire of this otherwise hidden market. Like how napster and bittorent forced the music industry to develop iTunes and Amazon MP3. - Mackenzie Cowell from iPhone
Anselm -- by "patchwork of charitable proxies" I assume you mean HINARI/OARE/AGORA, recently rebranded "research4life (http://www.research4life.org). They provide access to almost 9,000 journals to researchers in qualifying countries (http://www.research4life.org/Pages...). If someone were to try to put Mackenzie's idea into practice, that is a reasonable benchmark. - Bill Hooker
Bill -- HINARI/OARE/AGORA is charming, but the fact is that they provide access to third world scientists in countries so third world they don't have any science to speak of. Most of my experience with developing science is in Chile, a country that does -not- qualify for these free access points and in truth has very little general access to journals that is not provided by individuals... more... - Anselm Levskaya
I don't really disagree, Anselm; I was just using R4L as a benchmark for Mackenzie's idea. (Although I would add that even if a country doesn't have much research infrastructure it surely has some kind of health service, or at least some struggling doctors and nurses, for whom access to the primary health literature could mean a great deal.) - Bill Hooker
The bittorent idea is interesting, though blatantly illegal -- I could see a role for civil disobedience... Just some thinking out loud: you'd need more greyhats -- there are 19 million documents in PubMed alone. You would also need to withstand the full legal and technological might of a $5 billion/year industry, since what you propose would, if successful, destroy traditional... more... - Bill Hooker
I like the pirate bay idea. A lot of people have a lot of PDFs stored for themselves already. I've been thinking along these lines for quite some time now, essentially since I started entering metadata into my Mendeley library. Now if one could get the PTP technology from PB and write an interface such that one could post your Mendeley library with metadata to the PTP network, one would have quite a sizable db to start with... - Björn Brembs
Bill does have a good point about shooting ourselves in the foot with back-catalog digitization efforts. Unless your army of disobediant first-world grad students is ready to spend some time with a scanner, this isn't a no-harm process. - Mr. Gunn
Can't we just rely on google for the back cataloging? I like the PDFbay Idea, although it's blatantly illegal, and I have no problem accessing every journal I could possibly want to read from my current university. There's also that pesky issue of PDF watermarking... - Brian Krueger - LabSpaces
Google can't index a book existing only in paper form. They do have a digitization program, but I don't know how much support is has. - Mr. Gunn
getarticles@googlegroups.com, run by http://contentliberation.com/, already demonstrates that at some scale, on-demand liberation of protected content works. We should think about how to build PDFbay on a foundation of on-demand liberation requests mediated by groups like getarticles. (I hear there is a similar friendfeed room?) - Mackenzie Cowell
Content Liberation seem to want to describe what they do as civil disobedience, but it isn't. Quite apart from the issues of unintended harm that MrG and I have pointed out, I am not down with simple lawbreaking. If you break a law because you think it's unjust, you should be willing to accept the unjust consequences, using the whole process as a means to challenge and change the law.... more... - Bill Hooker
The Refs Wanted room (http://friendfeed.com/referen...) operates deliberately and openly in the grey area between Fair Use and PR Nightmare for publishers who might want to prevent such activities. It's not clear that the room's activity is illegal, largely because it would be very difficult to demonstrate that it causes measurable harm to subscriptions. This grey status depends... more... - Bill Hooker
I gather that 2nd/3rd world distribution of article sets is already happening through the distribution of hard drives filled with indexed articles. 1.9E6*~5MB = 9.5TB. So it's not that big for modern storage media. A single drive would soon be able to hold it. I'd never recommend anyone in america or europe to post themselves up for legal annihilation by playing at revolutionary. But... more... - Anselm Levskaya
Cameron Neylon
SciBarCamp Palo Alto - Photos from Alex Pang - http://www.flickr.com/photos...
Mackenzie Cowell
Hey SciBarPeeps, my girlfriend and I are taking short hike up Stanford's The Dish "park" (http://en.wikipedia.org/wiki...) at 3pm this afternoon - want to join us? We might go GeoCaching. Twitter DM me if interested #sbcpa
Kirsten Sanford
OMG! This barcamp was so AWESOME! (I know that was very valleygirl, but I can't help it when I'm excited.)
and thanks to the organizers :) - Pedro Beltrao
Definitely worth the pacific ocean crossing. Thanks to all session leaders, organisers and great crowd! - Kubke
The attendees make these conferences work :-) - Jamie McQuay
Cameron Neylon
Efficiency and incentives in research - How to bend the internet to scientists - Cameron Neylon, Jason Hoyt, Duncan Hull
http://livestream.com/cameron... - hopefully with sounds this time. OPr search fo @nthmost scibarcamp - she seems mjch better set up than I am - Cameron Neylon
What do we do as scientists, why do we do it, should we be allowed and funded to do it? - Kubke
Cameron starts with a few introductory slides he also showed at a recent NESTA workshop on "Science in Society": http://www.slideshare.net/Cameron... - Martin Fenner
Cameron: What do we do as researchers? - Chris Patil
Science in society? for society? with society? - Chris Patil
Science in society, vs. science *for* society, science *with* society - Kubke
We want to do great things, but what are the risks if we all try to change the world at the same time? - Chris Patil
Do we want to put more money into scientific research? Or should we rather spend that money to build hospitals or pay teachers? - Martin Fenner
The money that goes towards science (including the naturally expected failure of it) could go into hospitals, secondary teacher salaries, etc. - Kubke
...and government expects a return on the investment. - Martin Fenner
Trying to watch the stream but sound is rather low and image pointing towards the ceiling. - Ricardo Vidal
How do you maximise efficiency in generating impact for your research? - Martin Fenner
Thanks!!! :) - Ricardo Vidal
Hi Ricardo. - Martin Fenner
Now over to Jason and Duncan... - Martin Fenner
We aim to please. - Chris Patil
Hi guys. Now this is power. Interfering with a presentation from across the Atlantic via FriendFeed. Carry on, Cameron. LOL - Ricardo Vidal
Jason Hoyt: Bending the Internet to Scientists or maximizing efficiency. - Martin Fenner
Most social networks for scientists are a failure. - Martin Fenner
The problem: research is inherently social, but the tools we are using are not. - Martin Fenner
If you build it, they will not come... build projects for communities that already exist (Sean Mooney from yesterday) - Kirsten Sanford
Many social tools need a critical mass, maybe that is not the right way to go. - Martin Fenner
Tools should work with a userbase of 1. - Martin Fenner
The internet needs to bend over for scientists. - Bosco Ho from iPhone
Seems like a good place to plug an article I wrote recently about the barriers that prevent scientists from adopting social tools: http://dx.doi.org/10... - Chris Patil
Jason talks about last.fm. - Martin Fenner
interesting that the musician scientist is making comparisons between music and science... - Kirsten Sanford
Could papers as social objects work? - Martin Fenner
Jason needs to move from between cameron and the screen - Mr. Gunn
I hear a familiar point being made here - networking is an emergent property of good tools. - Mr. Gunn
Peter Binfield asks about the analogy between last.fm and Mendeley. - Martin Fenner
The Mendeley approach to articles could also apply to other "habits" of scientists. - Martin Fenner
There might be a million people with Micheal Jackson on last.fm, but how many scientist for an article in medeley? - Bosco Ho from iPhone
Bosco - can't hear audio(just questions, speaker OK), but did you mean articles/scientist? - Mr. Gunn
Now over to Duncan... - Martin Fenner
Shared annotated documents collection - will people use this feature? - Bosco Ho from iPhone
Duncan Hull: Digital Identity on the Web - Martin Fenner
annotation of documents will increase interaction and usability of information contained within papers. I totally see people using that feature... - Kirsten Sanford
I love the idea of having an embed code for a collection. I can share bib-lets. - Mr. Gunn
Duncan Hull - who am I, digitally speakin? - Bosco Ho from iPhone
All the social tools for sharing data on the web rely on some kind of digital identity. - Martin Fenner
Traditional way to gain identity as scientists: publish a journal article. - Martin Fenner
Julian Gough is digitally schizophrenic. - Bosco Ho from iPhone
scientist identity has changed. Much more complicated than traditional list of publications. Now includes, social alignments (research groups), work (research projects), friends (social web)... - Kirsten Sanford
Many papers by "forgotten password", "already registered", etc. in Google Scholar. - Martin Fenner
A popular user on google scholar: Mr F. Password. - Bosco Ho from iPhone
machines are too stupid to tell the difference between real authors and random words... is this something that could be solved by better AI? artificial learning algorithms> - Kirsten Sanford
Author disambugation in article is hard comp sci problem. - Bosco Ho from iPhone
this paper talks about "page rank for people" not nec. a new idea, but could be important for research reputation / attribution - Kirsten Sanford
MyExperiment allows OpenID, but only 16% of users use it. - Martin Fenner
OpenID is prohibitively complicated to start using... anti-intuitive... barrier to entry. - Kirsten Sanford
Openid seems to be pretty hard to use for most scientists. - Bosco Ho from iPhone
OpenID is probably not secure enough for some scientific applications. - Martin Fenner
Some universities are requiring ResearcherID for admin. - Bosco Ho from iPhone
Researcher identifiers would make life for journal publishers such as PLoS easier. - Martin Fenner
Will there be a tipping point from NIH or NSF or PLoS in the use of a unique identifier? - Bosco Ho from iPhone
What will change if we had the perfect researcher identifier? - Martin Fenner
Unique researcher ID would level the publication playing field between men and women. Women often struggle with name changes and loss of recognizability due to name changes at marriage. - Kirsten Sanford
Long discussion about potential benefits of researcher identifiers. - Martin Fenner
I do wonder about the pitfall of the identifier in non-democratic states... could make scientists easier government targets? - Kirsten Sanford
Thank you all for the comments. This plus Cameron's video stream was as is if I were there. - Ricardo Vidal
Awesome awesome awesome! - Bill Hooker
16% is actually pretty good for such a new technology. there are also some user interface designs which would help such as http://drupal.org/project... - Mike Chelen
Andrew Lang
I'm following 18 peeps on FF and 5 were at #sbcPA
Brilliant people all - Ariel Waldman, Cameron Neylon, Duncan Hull, Martin Fenner, and Sirley Wu - first time to meet all of them in person. I also got to meet two SL friends in RL for the first time - Joanna Scott & Melanie Swan. It felt like a family reunion. :) - Andrew Lang
like a kid in a candy store, right? :) - Jean-Claude Bradley
Nice to meet you too Andrew, and all the others not mentioned. One and a half days is really short. So a little bit like the candy store 30 min before closing. - Martin Fenner
Some interesting talks today but really it is the people that made the event. Many thanks to the organizers. - Andrew Lang
Martin Fenner
SciBar Camp: Keynote by Sean Mooney; Biomedical Research in the Age of Cyberinfrastructure
Keynote at an unconference is difficult, an untalk? Will take about why he thinks scientists don't use the internet. - Martin Fenner
hi martin :) - Pedro Beltrao
Is all the discussion on Twitter? - Martin Fenner
seems to be quite a lot over there at #scbPA but we know where the quality is... - Cameron Neylon
Scientists are certainly all connected: email, manuscripts and news on the internet - Martin Fenner
but integration a problem, dissemination of data is a challenge - Cameron Neylon
Most of the tools that his group builds are web-based - Martin Fenner
For the majority of scientists, there is no interest in using tools like Twitter or Facebook. - Martin Fenner
streaming video at http://bit.ly/uTeV4 - not from me at the moment - Cameron Neylon
His groups built a biorepository inventory management software, community portal software, bioinformatic analysis tools (often web-based). - Martin Fenner
need to get lots of citations of tools to keep getting funding - Cameron Neylon
Individual tools are not in a vacuum, they should be connected together as cyperinfrastructure. - Martin Fenner
lots of web based tools but individual tools are not in a vacuum. The collection of resources is key and how to combine them together - Cameron Neylon
nasa space programme as an analogy for building an integrated cyberinfrastructure - Cameron Neylon
each part can be tightly specificed for e.g. shuttle but harder to push that kind of integration specification for funded research projects - Cameron Neylon
Difference in space program: NASA clearly says what they want, different in bioinformatic tools. - Martin Fenner
Examples of integration (cyberinfrastructure) tools, CaBIG, NCBI, BIRN, homw-grown... - Martin Fenner
talking about different big programs like https://cabig.nci.nih.gov/ and http://www.nbirn.net/ - Pedro Beltrao
Administrattors always want "big picture", e.g. asset management, researchers want data analysis. This leads to two kinds of projects. - Martin Fenner
researchers totally focussed on specific problems. Administrators have other concerns, want "asset management" - Cameron Neylon
administrators often misjudge their needs for scientist's needs. Scientists often mistake today's need for tomorrow's needs - Cameron Neylon
NIH has 27 institutes, they all have their own approach to informatics. - Martin Fenner
Traditional approach: domain specific coordination - Martin Fenner
traditional approach is to build a specific system or portal for a consortium of researchers - Cameron Neylon
Data sharing was key to PGRN's value - but not the last place the data might go - Cameron Neylon
horribly complicated workflow with lots of different research foci - Cameron Neylon
i guess this approach creates isolated domain knowledge that is hard to integrate with other domain specific projects - Pedro Beltrao
Need to collect disparate data to pull everything together and then push on to the mandated site - Cameron Neylon
Management needs: secure platform, database eneabled - Martin Fenner
Question: are researchers actually using the web-based tools to collect data? - Martin Fenner
and every lab is probably doing something different to the workflow they say they are using... - Cameron Neylon
but if you designed better to start with (but need heavy resourcing to do this) then it might be - Cameron Neylon
CaTissue is great tool for tissue sampling, was built from the beginning to work for many different situations. - Martin Fenner
Current challenges: connect to bigger projects, next generatin suequencing, etc. - Martin Fenner
pedro asks a good question - is there any mandate for annotation or tagging? Answer from Sean: No, there is money available to support but no compulsion - Cameron Neylon
Big mover in the next 10 years: funding for translational research centers (CTSA). - Martin Fenner
mandates for CTSAs to work together but no idea how that is going to happen in practice - Cameron Neylon
Ask for a laundry list of informatics functionality. Sean "do you know how much this is going to cost" Admin: "No, how much do you need" Sean: "Well all of the money available..." - Cameron Neylon
ability to embed applications in a virtual machine in the web portal. - Cameron Neylon
hub doesn't directly integrate scientific data or handle group collaboration - Cameron Neylon
personal information actually put into their hub implementation by administrative assistants - Cameron Neylon
integration across CTSA informatics projects is not happening, everyone is trying to do everything themselves - Cameron Neylon
And now, the Web2 bit! - Cameron Neylon
popular with adminstrators and funders I think - possibly developers, less so with scientists... - Cameron Neylon
NIH has started to put more grant money into social networking tools, e.g. with the CTSAs mentioned above. - Martin Fenner
but sharepoint very popular in government - never really understood why I have to admit - Cameron Neylon
Challenges faced in Mooney lab: Creation of collaborative documents: manuscripts, proposals, management of datasets, discussion. - Martin Fenner
Laboratre solves problems in Mooney lab. - Martin Fenner
Applications can be embedded in Laboratree using OpenSocial. - Martin Fenner
Web portals for science suffer from under-use. - Martin Fenner
Successful tools are simple. - Martin Fenner
Start with an existing community. - Martin Fenner
Discussion: Open Science is important, but is a long way to go (publishing as example). - Martin Fenner
Discussion: will HTML be used instead of .pdf or .doc? Is a paradigm shift, particular difficult in clinical medicine. - Martin Fenner
One reason to use OpenSocial for Laboratree is the hope that people would build applications that can easily be reused. - Martin Fenner
Discussion: a lot of our data from a years ago is probably no longer relevant to what we do today. - Martin Fenner
Darn, would have loved to be at this session. Some day I will actually make it to one of these - Deepak Singh
I posted the keynote as a video in three parts on my blog: http://bit.ly/2G0DE - Naomi Most
Thanks Martin, Pedro, Cameron, Duncan, and Naomi! With so many notes and videos, it is almost like being there :) - Mike Chelen
Chris Patil
Aaron Rowe & Rick Henrikson: The future of medical technology
"ASSURED" Solution: Affordable, Sensitive, Specific, User-friendly, Rapid, Equipment-free, Delivered to those who need it. Important for the third world. - Chris Patil
"Africa is like space" : limited resources, harsh environment. The main difference is financial. - Chris Patil
Biosensor kiosks: Swab yourself, drop off the goo in a kiosk (like an ATM), get a prescription automatically sent to you. - Chris Patil
Aaron sees small siRNAs designed against specific diseases as an important future strategy for the "long tail" of diseases (i.e., rare illnesses) - personalized medicine made easier - Chris Patil
DX-box: a home device that would schedule and collect biological samples for diagnostic purposes, based on the user's risk factors. (Under development at Microsoft) - Chris Patil
Rapamycin: effects on aging, immunology - Chris Patil
Chris Lipinski: "god of medicinal chemistry" - ways to repurpose drugs: start with drugs that are already known to be bioavailable and safe, and then test them with clever assays for their effects in other contexts - Chris Patil
Jim Hardy from HemaCell: Rapid PCR machine that works on a small thermal loop. Battery-operated, loaded/sealed loop. Good amplification and selectivity. Problem: How to detect the product? Aaron: use a compact electrochemical DNA detector. - Chris Patil
repurposing drugs example announced yesterday re: immune-suppressor rapamycin used for life extension http://bit.ly/o5usp - LaBlogga
Many drugs that are viable, even efficacious, don't make it into the clinic - these are a potential gold mine for repurposing efforts - Chris Patil
The bioengineering field has become "MacGyver-esque": cool new diagnostics using sometimes mundane starting materials: eggbeaters, CD players, paper microfluidics - Chris Patil
Fast sequencing is useful for infectious disease diagnostics - Chris Patil
There are only two major classes of flu drugs, but already strains immune to both. There are "entry inhibitors" undergoing trials - Chris Patil
Zinc finger nucleases: Engineer an enzyme to find a site in the genome and then clip it out. Currently claimed by Sangamo, but there is an academic consortium that is challenging them -- and making their information public! - Chris Patil
If you want to be a good science reporter, be out of phase with the press release cycle <- Aaron Rowe - Chris Patil
Affordable metagenomic sequencing (~$5 / sample): http://bioweathermap.org - Mackenzie Cowell from iPhone
Martin Fenner
Peter Binfield: Scientific Publishing in 5-10 years
1. Do current publishers exist? 2. Does the journal exist as a package? 3. Does the article exist? 4. What business models dominate? 5. What new technical features do we seriously expect? 6. What new modes of scholarly communication may gain wide acceptance? - Martin Fenner
Over 0-5 years probably much the same as it is now - but 5-10 years a much more itneresting timeframe - Cameron Neylon
Do we need articles when people just want to look at the data? - Kubke
3D in PDFs has become available only recently. - Martin Fenner
who is actually doing the science - is it still professional scientsits or is it much more diverse - Cameron Neylon
Other questions: What money exists in 5-10 years? Who is doing the actual work of publishing? What are the customers? - Martin Fenner
What will happen to society journals in 5-10 years? These journals bring in a substantial amount of revenue to the societies. - Martin Fenner
Average annual price increase of journals: 5-10%. - Martin Fenner
40-45% of revenue currently comes from U.S. academic institutions. - Martin Fenner
Anyone else having trouble getting audio from Cameron's livecast? (Will comment at livestream.com from now on). - Michael Nielsen
Who is paying for the pay-per-article? - Martin Fenner
"Even at 99 cents an article, there will still only be an X number of buyers" translation - lower revenues for publisher to go the route of iTunes - Jason Hoyt
Most people think that the scientific article will be around in 5-10 years. - Martin Fenner
NLM-DTD is mentioned as a technical standard: http://dtd.nlm.nih.gov/ - Martin Fenner
Article-level metrics will accelerate the death of the journal. - Martin Fenner
The role of the librarian will change. More about information, less about journal subscriptions. - Martin Fenner
Is an article the smallest unit of scientific output? - Martin Fenner
Example of a publishing tool that uses NLM-DTD: Lemon XML http://network.nature.com/people... - Martin Fenner
Current cost of article semantic markup: $10000. - Martin Fenner
Problems with permanent record for articles containing multimedia. - Martin Fenner
Extended discussion about problems with archiving of articles in digital form. - Martin Fenner
We will have to discard data, as the carbon footprint of the storage solutions will get too high. - Martin Fenner
Publishers might want to look at Business Week for ideas. Appears to be working as a model to move from print to online. Effective at engaging the community in the content. Research is the original peer review, it shouldn't be that hard to move to a blog and social media model. Why not have all science become collaborative? Just need to define the right rules that fit the community. - Leonard Kish
Medpedia just released functionality to collaborate on documents. Wonder where that's going? - Leonard Kish
Societies are really communities first. I would think they would have an easier transition to online media and extending their communities online. - Leonard Kish
Kubke
Second life: science communication and data visualisation - Andy Lang and Joanna Scott
used for education to teach students about molecular structure/spectra, also through games - Kubke
Jean-Claude Bradley also creates virtual exhibits in second life that the students can visit - Kubke
virtual conferences - Kubke
increasing activity in second life, primarily astronomers and chemists, but seems to be spreading to different areas - Kubke
Education: Invite academics and anyone with something interesting to say to give talks in second life - can live video stream from real life lecture venues. Questions from second life relayed to speaker - increase breadth/size of audience - Kubke
$150/month for educational institutions to maintain an island. The real cost goes into development. - Kubke
For Darwin's anniversary they build the Beagle and people go into it and visit it. - Kubke
Budget to have in mind to do something depends on whether you can use prefab things or whether you need to bring in specialists - Kubke
Second Life science discussion being ustreamed here: http://bit.ly/AI2pV #sbcPA (via @nthmost) - Kubke
can live video stream through the web to increase audience - Kubke
Funny anecdote: someone didn't attend a lecture because there weren't enough chairs :) - Kubke
The difference with webinars is that second life appears to adjust to real life social rules - Kubke
Younger academics steered away from second life etc because of impact in 'credibility'. - Kubke
Martin Fenner
Peter Binfield: Article level metric from the PLoS perspective
What is the problem: how do you access the worth of impact of journal articles? - Martin Fenner
What is the granularity to measure impact: journal, research institution, individual researcher? - Martin Fenner
So much to read need metrics to winnow things to read a lifetime. - Bosco Ho from iPhone
Usage-based measures are still pretty rare - Martin Fenner
Most people filter based on the impact factor of the journal. - Martin Fenner
Potential metrics: citations, usage, discussions, social bookmarks, etc. - Martin Fenner
Martin made a great point: Why should we even want to assign a number to the quality of a paper? - Chris Patil
Web 2.0 is the solution. - Bosco Ho from iPhone
People are starting to use these, but not very much, so PLoS ONE wants to start the ball rolling. - Chris Patil
PLoS provides article-level metrics for all their articles, e.g. citations, usage, blog posts, etc. - Martin Fenner
there's some good arguments against assigning numbers to students in school, also. I think stats are a good thing, as long as they aren't the only thing. Remember, Mendeley http://www.mendeley.com/stats also is collecting usage stats, in which PLoS figures quite well. - Mr. Gunn
Number of blog posts about an article isn't necessarily a measure of quality - a flawed paper might attract more commentary and blogging than a flawless one. - Chris Patil
Article-level metrics as post-publication peer review. - Martin Fenner
@patil a flawed paper could potentially be more interesting. - Bosco Ho from iPhone
usage numbers going to be available soon at plos - Pedro Beltrao
Use open API data of other web sites to aggregrate stats. - Bosco Ho from iPhone
Citeulike >> connotea - Bosco Ho from iPhone
Plosone is big enough to twist the arms of big sites to provide an open API. The possibilities are endless. - Bosco Ho from iPhone
BUZZWoRD alert: crowdsourcing. - Bosco Ho from iPhone
CrossRef is working on the heuristics of a citation, e.g. good or bad paper. - Martin Fenner
Usage statistics will show trends over time. - Martin Fenner
Otherwise only bmc provides download stats for authors limited data for public. - Bosco Ho from iPhone
Usage statistics is extremely time-consuming, largest EC2 instance is working for 9 days already on PLoS One usage data. - Martin Fenner
Tufte fanatic is critiquing the aesthetics of a beta release graph. - Bosco Ho from iPhone
Still critiquing. - Bosco Ho from iPhone
Currently no open API for PLoS One usage statistics. - Martin Fenner
This man really cares about aesthetics - his apartment must look fabulous. - Bosco Ho from iPhone
Future developments at PLoS: provide open data sets, hope other publishers will follow, hope standards will evolve - Martin Fenner
Article statistics on plos one throws down the gauntlet against elsevier and friends - Bosco Ho from iPhone
Jim Hardy
#sbcPA The World Game, Dewayne Hendricks
a brief summary of psychohistory from Asimov, Freud, and MIT press. Eric Anderson "Young Man Luther" - Jim Hardy
Bucky Fuller: Operating Manual for Spaceship Earth 150 pp and recommended read. - Jim Hardy
Dymaxion (Fuller) Maps: http://www.google.com/search... - Jim Hardy
Don't assume scarcity, assume abundance - Jim Hardy
You cannot predict accurately the future. Must have an infinitely changeable model. - Jim Hardy
40% of the people need to move out of San Diego County NOW! Add Psychohistorical data and there may be an opportunity to improve inevitable outcome. - Jim Hardy
Shirley Wu
Melanie Swan - Personal genomics #sbcPA
First ever consumer genomics conference was Boston 6/9-6/11/09 - Shirley Wu
big question: how many medically actionable genes? Melanie is putting together a catalog of these - Shirley Wu
Technology is moving extremely fast. - Martin Fenner
Carlson curve = price performance cost drop over time for genomics, analogous to Moore's law but much faster - Shirley Wu
some groups having weekly meetings just to keep up with data storage/collection issues - Shirley Wu
1 full human genome = 8 terabytes (because lots of additional annotation included to help search/analysis) - Shirley Wu
Current methods and infrastructure not equipped to handle analysis and transfer of such large files (best solution currently: FedEx) - Shirley Wu
Metagenome also incredibly important for human health. many many times more non-human cells in body than human - Shirley Wu
Martin Fenner - another layer of complexity: genome in one part of body != other parts. e.g. cancer cells, different tissues, etc - Shirley Wu
how then to identify rogue cells when we are limited to sampling what we can sample? - Shirley Wu
Some next-gen technologies can look for methylation/epigenetic mutations - Shirley Wu
Study of cancer shifting to more systemic approach - not just mutations in a gene, but copy num variations, problems with DNA repair machinery - Shirley Wu
Identify actionable genetic changes: e.g. drug metabolism (CYPD6 and others) - Martin Fenner
Diabetes-related gene SLC3OA4 (I think): zinc transport - Shirley Wu
10 genes identified for type II diabetes in NIH-sponsored GWAS for identifying components of disease - Shirley Wu
Also a couple genes implicated for Alzheimer's related to high-cholesterol development in mid-life - Shirley Wu
Knome does full-genome for $100K (DTC), Illumina is not DTC but offers full genome for $50K with doctor's approval (and access to data not guaranteed!?) - Shirley Wu
How do doctors respond to DTC genetic data? Melanie: they say "i don't know what to do with this", then "that information's not medically actionable" - Shirley Wu
Jen McCabe: less than 40% of doctors have training in genetics - Shirley Wu
Mac: right now, onus on individual to find out about their genetic information, and also to interpret, because doctors don't know how to - Shirley Wu
Melanie: genetics is the biggest topic for continuing medical education for physicians now - Shirley Wu
Martin: big difference between "i want to know my risk for a specific condition e.g. warfarin metabolism" vs "i want to know everything related to my potential genetic risks" - Shirley Wu
consumer genomics potentially huge for empowering people to take charge of their health, see doctors as just one of many "consultants" in their overall health picture, medical establishment is going to be broadsided by the availability of this information - Shirley Wu
Many chronic disease conditions are multigenetic, and it's risk assessment rather than yes/no answers. - Martin Fenner
so very hard to predict if someone will/will not get it. Can only say uncertainty, risk assessment, many people not comfortable with this. But in some cases can do something, like better/earlier screening etc - Shirley Wu
Mac: Myriad genetics patented the genetic test for BRCA1/2 - need to regulate this stuff STAT because it's not cool - Shirley Wu
Discussion of patentability of genes, e.g. BRCA1/2. - Martin Fenner
ACLU case going on regarding BRCA patent - Shirley Wu
Distinction between data and interpretation. Former maybe shouldn't be patented, but latter maybe should be able to be. But in some cases former is very expensive/difficult to collect. - Shirley Wu
Venter tried to get 6700 patents on human genome, Clinton threw it out and said genome is open source, but apparently now all the genes are patented. - Shirley Wu
How to incentivize development of technologies and analysis for genomics, proteomics, transcriptomics, etc without patents? - Shirley Wu
Do we need patents as incentive for technological advances in personal genomics? There are many alternative models. - Martin Fenner
Joseph Jackson: prize funds, microfinancing... - Shirley Wu
Jen: can you create a market without IP? Will be interesting to see how things develop - Shirley Wu
Dawei: multigenic conditions = multi-drug, systems-level approach to treatment. Draws analogy to drug discovery environment, it's changed a lot recently towards open drug discovery, with many compounds that have proved challenging to develop, Eli Lilly e.g. put one out saying "someone figure out how to use this" - Shirley Wu
Martin: shift towards long tail in drug discovery - less emphasis on single blockbusters, more on specific treatments for boutique conditions - Shirley Wu
Back to consumer genomics.... DNA Direct - test single condition. Navigenics ($2500 inc genetic counseling), Decode ($900), 23andMe ($400) - test multiple variations - Shirley Wu
People who have tried all three find that data is very similar between them, but the interpretation, e.g. assessment of risk for health conditions can vary greatly. Includes even the variations that are used to calculate risk. e.g. breast cancer markers - only 1 marker is shared between the three companies (each uses essentially a different set of markers to determine risk) - Shirley Wu
Many of the most medically relevant SNPs not included in the DTC chips, perhaps bc of patent/cost issues - Shirley Wu
Example for drug development based on science rather than market analysis: Recent approval of Ilaris for a rare autoimmune disease: http://www.businessweek.com/bwdaily... - Martin Fenner
People can open source their genetic data on SNPedia (bout 20 have done it so far) - Shirley Wu
Standard risk assessment multiplies relative risk from all markers used. Not the best way to do it since weights each factor equally, individual risk numbers themselves vary by interpretation, so problem is compounded - Shirley Wu
Social implications of consumer genomics? e.g. Non-paternity issue.. - Shirley Wu
Chronic terminal conditions like Huntington's, patient's right NOT to know - Shirley Wu
What if you get the test, find out you have a condition or are a carrier, your sibling is planning to have kids but didn't get the test, should you tell him/her? - Shirley Wu
Jen is patient 0 for 23andMe's Research Revolution - Shirley Wu
Melanie: "which condition did you sign up for?" Jen: "migraine." Mac: "you should have done testicular cancer!" Jen: "I was going to! I thought about it!" Melanie: "Well we know Jen has a lot more balls than ..." - Shirley Wu
is 23andMe's approach towards consumer-oriented research appropriate? for some, $99 for just a few specific tests and no access to data (just to the report) not worth it.. - Shirley Wu
Cameron Neylon
Sharing Data on the Web - Tantek Celik
Techniques and tools for sharing data on the web to make things easier. Guy is from microformats.org. - Cameron Neylon
recommended the "firefox operator" plug in (just google it) - Cameron Neylon
showing that he has marked up a series of the tags with class attributes - Cameron Neylon
showing that the operator plugin can then pull contact information into other areas after adding class="fn" and class = "url uid external" into e.g. address books - Cameron Neylon
Now proposing key points for making science stuff available on the web - Cameron Neylon
1. Just publish it - whatever format, whatever site, however - Cameron Neylon
2. open robots.txt - make it clear that it can be scraped or whatever - Cameron Neylon
3. Public domain licence - Cameron Neylon
4. Permalinks - make sure the URLs are stable - Cameron Neylon
5. Publish reports and data in html and microformats - mmm but I would say use XML where appropriate and where a vocabulary exists - Cameron Neylon
comment on public domain dedication - that if you put it up it is indexed and archived by google etc. - Cameron Neylon
question - does that mean Tantik is not advocating use of specific data stores - saying first step is to get it up, if you can do more then great but get it up first. - Cameron Neylon
Chris asks - if someone steals a dataset then what are the practical steps to show that you had it up first - argument over exactly how google presents or caches data - Cameron Neylon
Cameron talking about making data up. :) - Andrew Lang
Cameron saves that talk. Yay! - Andrew Lang
getting too involved in the argument to liveblog now :-) - Cameron Neylon
Discussing permalinks - importance of provenance, don't edit in place, create a new version - means everything is archived separately, people can refer to specific versions - Cameron Neylon
Publish in html - question, what is the problem with pdf? What about the costs of both formats? - Cameron Neylon
What about data (as opposed to reports), surely CSV or XML are better? Question from the floor. - Cameron Neylon
talking about the lack of microformats specifically for data, only thing really relevant is hatom - Cameron Neylon
permalinks looks like something to investigate: citability.org - Andrew Lang
Cameron Neylon
Chris Patil - Open Source Textbooks #sbcPA
John Cumbers - what is the size of the market, do people make money out of textbooks. Example of Cell - Alberts etc. - Cameron Neylon
Some people make a lot of money out of textbooks but not very many. Very long tail. - Cameron Neylon
Big text books take a lot of work - how does the textbook look in a web based world. What is a textbook for if the university doesn't exist any more. - Cameron Neylon
chris is pretty god like ... but not christ, i dont think. :) - Kaitlin Thaney
thanks for that - typing not good at this time in the morning - insufficient coffee... - Cameron Neylon
Chris - the lack of return on text book authoring is an opportunity for new types of approach. - Cameron Neylon
There is no shortage of text books, there is a glut - Cameron Neylon
Alicia, "I would pay $20 if I knew it went straight to the author" - Cameron Neylon
discussing the concept of "beta" versions of books. The Pragmatic Programming series. - Cameron Neylon
Alicia - benefits for people who need accessible versions - Cameron Neylon
John - PDF sucks, need something much better than PDF for flexibility. - Cameron Neylon
Martin - but want access to multiple formats - Cameron Neylon
Bosco - print on demand is getting cheap and very high quality - Cameron Neylon
Sean - open access text books is not a technical problem but a social problem - how do you fund the content - Cameron Neylon
Project at stanford to support making course material creative commons - Cameron Neylon
Problems - how do you create new content (resource). If use legacy content then there are problems with copyright infringing content - Cameron Neylon
Me - what about using Wikipedia? - Cameron Neylon
Chris - Wikipedia a reference, not a teaching tool. These things are different. Need to provide a route through the content for the average student. - Cameron Neylon
Needs to be seen from the perspective of the teacher. - Cameron Neylon
Good question - what do teachers use a textbook for? How do you leverage the needs of the teacher to support the creation of better objects that could replace textbooks. - Cameron Neylon
Bosco - major contribution of publishers is the editor - collabortive authoring is a challenge for long documents - Cameron Neylon
debate over the value of a well integrated long work - clearly works well when you actually work through the whole book - does anyone ever really do that? - Cameron Neylon
John - would like guidance through the process of using a "text" - where you've been and where you're going - quizes, checkups etc.. - Cameron Neylon
comment from boston: what to do about the various flavors of CC licenses on OCW content? most have BY-NC, some materials with SA - a design decision made without the forethought of interoperability, reuse (in the context of virtual textbooks) and remix. how/ what to do? - Kaitlin Thaney
How much does it cost to fly in eight people for four weeks to get a draft together. Suggesting around $50k, so 500 people at $100 each. Bosco points out many people who are setting up courses for the first time could have an interest in putting the work in. - Cameron Neylon
Kaitlin - I'll try and feed that in. I think people here are relatively unaware that these already exist. Do you know what the best current examples are? - Cameron Neylon
Question: Is this something Google.org might fund? (that's a reminder to myself) - Cameron Neylon
Chris - in the world where we have $50k to support one of these could put out a call for proposals - Cameron Neylon
would have to check OCW policies, but i know that they're not all consistent across the board for various universities across the world, and most definitely not CC-BY ... lemme look :) thanks cameron. just something to noodle on. - Kaitlin Thaney
Need to identify a good area where a current text doesn't exist - Cameron Neylon
Martin - is the two week retreat model a good one or a wider online collaboration - Cameron Neylon
Me: need the "retreat" or a focussed effort to get the seed content in palce - Cameron Neylon
Martin is a retreat per se great or does it need to be cheaper? What is the right number of people. - Cameron Neylon
Chris - what field is small enough and needs a textbook- me thinking Small Angle Scattering but not sure this is of interest to this group really - Cameron Neylon
K, so to be part of the OCW consortium, the content needs to be subject to a CC license, it seems, or at least is strongly recommended. MIT is CC-BY-NC-SA. but other institutes, such as Michigan State doesn't cite a CC license and provides some content only read-only. So short answer ... it varies. Ugh. - Kaitlin Thaney
Sean discussing status of Stanford efforts on open curriculum content - currently in a holding pattern - Cameron Neylon
Asking the question - why is there no secondary market for teaching materials given the popularrity of blackboad and moodle - Cameron Neylon
Fabbiano talking about NZ universities purchasing Springer textbooks "like journals" on a chapter by chapter basis - Cameron Neylon
The books are purchased as electronic versions by libraries, as far as I know as whole, not chapter per chapter, but can download only chapter of interest - Kubke
Hey I'm in this meeting. - Bosco Ho from iPhone
I was too busy following the discussion, forgot to comment here. - Martin Fenner
Thanks for the input from afar, KT, esp, your first comment - rumors of my divinity are greatly exaggerated. :-) - Chris Patil
Sorry, coming in late. Before O'Reilly programming, etc books weren't exactly what we've become used to. I wonder, even in a non open-textbook world, what would happen if a publisher that enabled people perhaps not that well known to just write stuff. - Deepak Singh
Complete Yale course on iTunes University: http://www.tuaw.com/2009... - Martin Fenner
Just came across wikibook (http://en.wikibooks.org/wiki...) through this article (http://mashable.com/2009...) (via @edNZ). I also read (where?) a suggetsion to have students 'edit' wikipedia pages instead of handing in papers in their courses. Maybe a collaborative effort having the students contribute to wikibook content as part of their course requirements might be a good place to start? - Kubke
OH well, I came across this page in wikibook: http://en.wikibooks.org/wiki... I guess any project will have to have better editorial control? - Kubke
Wiki Educator has a 'book Manager' http://wikieducator.org/Help:Bo... - Kubke
Jim Hardy
#sbcPA CureTogether.com: audio stream http://www.ustream.tv/broadca... Video not working :(
80% of patients are doing google searches for health - Jim Hardy
web 1.0: web general search 2.0 content plus community (sharing) http://www.quantifiedself.com/ - Jim Hardy
Web 3.0 Content plus commerce plus community - Jim Hardy
Patientslikeme own your data. - Jim Hardy
web 4.0 What's missing? n=1 my personal contextuaol support, my personal data. track observations of daily living on twitter - Jim Hardy
datum.org in beta for personal health data tracking - Jim Hardy
Core data/behaviors: wake time, hours of sleep, calories consumed.... - Jim Hardy
Harvard: Gar King Institute of Social sciences. n=1 matters more than aggregated statistics - Jim Hardy
dailyburn.com to track daily excersize - Jim Hardy
HIPPA makes patient data the asset of the hospital testing facility etc, not the patient. - Jim Hardy
PHI = personal health information. new HIPPA regulations forthcoming. Incetivizing docs to create electronic medical systems for more "meaningful use" but not to patients benefit - Jim Hardy
We don't think of our personal health data as an asset, but sure as hell Google and Microsoft do - Jim Hardy
100% of the people in the room agree we should all own our own personal health data - Jim Hardy
http://www.cchit.org/ CCHIT sounds like it is, Chitty :-) - Jim Hardy
Jim Hardy
#sbcPA CureTogether.com want to grow, pharma's disinterested
Jim Hardy
Session 1 #sbcPA CureTogether.com looking at data/symptoms through different disease states
michaelshiloh
Sadly I won't be able to attend, and thus my ticket is available. Please someone enjoy it.
Juhan Sonin
Any open slots/tickets for this afternoon?
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