Tuesday, January 27, 2009

WFUBMC Burn Center Tour

Seven people from Coy C. Carpenter Library had the pleasure of touring Wake Forest University Baptist Medical Center's Burn Center on Tuesday, January 27, 2009. We have all worked here for awhile but did not know much about the eight-bed Burn Unit and the sixteen-bed/step-down Burn and Plastics Unit.

According to our tour guide, Jim Johnson, PA, WFUBMC's Burn Unit was the first one in the state of North Carolina. It was founded in 1979. We "experienced first-hand," the hydrotherapy room, complete with the ambient heat lights. The hydrotherapy room is the first stop on the floor for the burn patient. The patient is cleaned with regular soap and water and the room is kept very warm, hence the heat lights, to keep the patient as comfortable as possible.

While we learned a lot about burn and skin disease care, we also learned how the Burn Center does business. For example, in the three years that Burn Center Director Dr. James Holmes has been here, he has developed a relationship with hospitals in the western part of NC as well as other states. Now, the Burn Unit accepts patients from Tennessee, North Carolina, South Carolina, Virginia, West Virginia and Georgia. Another example is as of February 1, 2009, the Burn Center here will treat all worker's compensation patients from South Carolina. South Carolina does not have a Burn Center so people who get burned on their jobs will be coming to North Carolina for care.

Dr. Holmes and two physician assistants have reached out to the community at large to educate people about how to handle burn patients in the field, i.e. before they are transported to WFUBMC's Emergency Department. There is a local Burn Survivors Support Group that reaches out to the community as well but members spend a lot of their time counseling recent burn patients.

As WFUBMC employees, it is good to know what our "coworkers" do on a daily basis.

Wednesday, January 21, 2009

ScienceOnline'09: Social Networks for Scientists

The final session of the day I attended was on social networks for scientists. As someone who has not embraced most social networks (exceptions being LibraryThing and LinkedIn), and recalling David's intro of BiomedExperts during a reference meeting last year, I was interested to see if the general audience felt that networks specifically for scientists were beneficial or redundant, and how/if they might be useful to our faculty, students and librarians. Cameron Neylon and Deepak Singh did a great job framing the discussion.
  • Facebook helps people find people
  • scientists need to find people therefore it obviously follows that scientists need Facebook
  • so...people want to build a "Facebook for scientists"
  • quick room survey exposes that some people use science-specific social networks but almost entirely Nature Network
  • two issues in usefulness for any social network: critical mass and features
  • Facebook was built around a pre-existing community (Harvard undergrads) but people tend to forget
  • Twitter is standout network that launched on the world without a pre-existing community
  • myExperiment paid people to put stuff on site
  • FriendFeed is relevant for filtering; if people like/comment that item keeps coming to top
  • also useful for finding people with expertise
  • FriendFeed pulls in *everything* friends do online, so recipe for disaster: blog, Flickr, YouTube, Digg, Twitter, etc.
  • Nature Network more like a group of scientists socializing than a social network for scientists
  • fatal flaws I: social networks rely on network effects; no members means no network; if I arrive and no one else is there why come back?; must provide up front value - solve a problem I know I have
  • only a few of the current offerings do this
  • social networks have histories going back to usenet days
  • serendipitous discovery on Google extremely useful
  • do we need social networks for scientists or just use existing such as LinkedIn?
  • CiteULike, Connotea do something better for scientists than Delicious
  • several people use FriendFeed to find others' CiteULike
  • branding as MySpace-like or Facebook-like for scientists backfired
  • may not need to know you have a problem but still needs to solve; barrier for most people is need to do something
  • fatal flaws II: scientists not very social; looking for solutions, not people; data finds data, people find people
  • five guidelines for online services:
    1. tool must solve problem and solution must fit what you're doing
    2. tool must outperform existing tools
    3. must be near 100% reliability
    4. provide at least one killer feature
    5. prepopulate
  • need to be able to take data out when you want to leave or network shuts down
  • site also can't claim copyright on your data/input/contributions
  • BiomedExperts did a good job of prepopulating using existing connections via literature citations
  • Ravelry for knitters, crocheters
  • very much like science in that people connect via materials (yarns) and how they are used
  • not necessarily connecting around people, but yarns, patterns, etc.
  • large number of people, small number of items and agreed upon way of talking about - but this is not true for science/scientists

ScienceOnline'09: Anonymity, Pseudonymity

Abel Pharmboy and PalMD moderated this session, which touched upon the pros and cons of anonymous or pseudonymous blogging, including the added challenges faced by female bloggers. Great group discussion on various angles of anonymous/pseudonymous blogging, including the ability to remain anonymous/pseudonymous, the reasons various people choose to blog openly or not, and how to balance visible and less visible online selves.
  • Abel Pharmboy started blogging when working for a non-profit research organization and would've jumped through too many hoops to blog under real name
  • pseudonym acknowledges his field (pharmacology) and one of his field's pioneers (John J. Abel)
  • when going back to academe Abel was able to "come out" as himself
  • after his name was revealed, Abel asked readers if they'd trust him more if he wrote under his real name; majority said no, they didn't care
  • PalMD's pseudonym consists of his initials and his career
  • it's an illusion that writing anonymously/pseudonymously allows more freedom
  • anonymity will often get blown, or at the least people with figure out who they *think* you are
  • if using anonymity as a level of protection in medical blogging to protect patients, think through implications of cover being blown because it hits patient privacy too
  • female bloggers have an added issue of being cyberstalked
  • protection of anonymity/pseudonymity also extends to family
  • avoiding Google is desire for some to blog anonymously/pseudonymously
  • desire to be evaluated on merit of CV and person, not blogging
  • need for support for personal life [or personal aspect of professional life]
  • people get more "press" when writing letter to editor than on blog, but concept of owning one's opinions in these mediums different
  • what about bloggers' First Amendment rights? First Amendment doesn't protect what others say on your blog
  • is masking of identity intrinsically antithetical to society?
  • times when pseudonymity can come back to bite you: when story hits wider audience, given less credence/legitimacy/credibility
  • when part of an inward-looking network, sense of peer-review forms and will get blasted, regardless of persona so no protection there
  • when blogging under real name people feel they know you even though you only share one side of yourself
  • if trying to put genie back in the bottle (either after outing or adopting pseudonym after blogging under real name), go over to a different blog and try to write in a different voice; use UK spellings/grammar if in US and vice versa; readers are smart and will put 2+2 together to continue following you
  • would think if Nature supports blogging then researchers would embrace but they don't
  • if you want to maintain a pseudonymous blog alongside real name blog best if subjects don't overlap
  • blogging pseudonymously allows for greater integration of different parts of life for some
  • can blog pseudonymously but not anonymously to allow some to have different persona than in real life
  • shouldn't blog pseudonymously to attack people
  • threat and fear of outings can put damper on community and willingness to share even more than actual outing incidents

ScienceOnline'09: Web and the History of Science

My one fun-just-for-me-with-little-direct-applicability-to-my-job session of the day was the history of science on the web session that immediately followed a yummy lunch from Saladelia Cafe. (Wait, I should clarify: all the sessions were fun, but most I chose because there was a strong professional correlation; this one was just for the fun!) Moderated by GG, Brian Switek and Scicurious, this session appealed to me, someone who loves history and is fascinated by science (even when she doesn't always understand it), and got me thinking that this might be an angle to plug with grad students who express interest in blogging but don't know where to start...hey, look at that, potential job applicability!
  • The Giant's Shoulders: monthly blog carnival about classic science papers
  • so...why is the history of science important?
  • interesting to dig up "lost" bits of science history
  • one of the earliest researchers on cocaine was Freud; first to propose drug replacement therapy (although is plans wouldn't have worked...); many researchers in this field don't know this
  • as some fields get older/more involved, forget people who started it all because core facts become gospel so well known it is no longer necessary to cite
  • people cite review rather than citing original article
  • good way to show how science actually works and doesn't work
  • fun way of showing "humanity" of scientists
  • great way for scientists to develop research/writing skills
  • rewriting of history to mythologize history and bring into current aspect of field to frame paper occurs
  • scientists in 1700s and 1800s had day jobs and did science in their basements because it was cool; granted, they were often independently wealthy...
  • doing/explaining/highlighting history of science helps people understand modern science; however there is a risk of showing science as something that is constantly marching forward to the truth
  • get mistaken impression that science publications have to be complete packages
  • JSTOR is a good source for historical papers
  • public really involved in science when it was changing a lot (1870s-1930s) [need to reclaim!]
  • lots of pop sci books coming out are focused on history of science
  • by telling people how science is weird can also explain how it works
  • reporters are reading blogs and blog stories do get picked up by traditional media
  • if beginning blogger, will help build your reputation if you blog about the history of your niche
  • older papers are going into PubMed, PMC because being republished
  • scientists ideally writing for clarity which helps when translating

ScienceOnline'09: Semantic Web

The last session before lunch happened to be the one where I felt the most overwhelmed by the breadth of information that I simply cannot seem to grasp in any cogent fashion: John Wilbanks's session on the semantic web in science. I've heard and read about the semantic web, but have yet to be able to fully understand what it might look like. Although I still have lots of questions, this session thankfully illuminated some of the goals/aims of the semantic web. You can view the slides here. As with all my posts, but especially this one, any incoherency is my fault alone...
  • open innovation (as understood under traditional collaboration model) aimed to expand the capacity of the external market, and inflows and outflows of knowledge, to aid internal knowledge/advantage
  • Joy's law: the smartest people work elsewhere
  • user innovation: only people who have problems can solve problems
  • new innovation/collaboration enables people to design their own shoes, t-shirts, etc., but doesn't exist for science
  • why not?: intellectual property rights - scientists don't share well; funding models; inertia; incentive structures; no web for data
  • Google search won't give you genes but papers about genes
  • the "semantic web" isn't great but all we can come up with
  • computers need to understand relationship between websites
  • coffee ontology explains relationship between aspects of coffee needs/uses/properties
  • semantic web is lots of specifications: RDF at heart, GRDDL, RDFa, OWL, SPARQL
  • need domain name system for concepts; lack has been reason for failure
  • use web to integrate
  • RDF: Resource Description Framework
  • every arc has direction
  • "literals": facts, instances about things
  • "reification": categories
  • RDF simply and ugly; meant for machines not humans
  • GRDDL gleans resource dialects out of existing
  • RDFa: RDF in HTML
  • OWL: Web Ontology Language; structured relationships
  • essentially wants to query 1000 web pages as 1 same way 1000 papers are queried as 1
  • SPARQL is SQL for semantic web
  • RDF allows data [to be] remixable that is contextually accurate
  • is it legal? have to reconstruct public domain for licensing angle
  • CC Zero license (CC0) allows contractual reconstruction on public domain in database licenses
  • does conflict with protection instinct; if you don't want your data remixed don't put under RDF
  • just because you put genome data online and claim copyright doesn't mean you have it because facts cannot be copyrighted (at least in US)
  • database law has been killed in US several times
  • doesn't scale across science: some (e.g., earth science) cool with sharing, but others (e.g., biology) would rather share toothbrush than data
  • web isn't going to do this for us
  • get practice answers out of existing databases and resources
  • queries are interface to this [semantic web] world
  • lot of this isn't baked yet
  • got to have problem worth solving to use this; wouldn't use this for your calendar
  • trademark is the only way to protect; if you don't like, fork but don't infringe trademark by using name
  • Swoogle is a semantic web search tool
  • Open Biomedical Ontologies is a compilation of ontologies used for semantic web
  • has always been about machine interoperability on data

ScienceOnline'09: Video in Scientific Research

In the second session I attended Saturday, Moshe Pritsker of JoVE (Journal of Visualized Experiments) and Apryl Bailey of SciVee talked about two options for publishing research videos: journal-like and YouTube-like.
  • why publish research videos? to demonstrate techniques that aren't easily explained
  • essentially pits a scientific article description against a demonstration
  • text does NOT provide adequate description of biological experiments; solution is to visualize description of experimental methods
  • similar to cooking: helps if someone shows you either in real-life or TV show
  • JoVE is a video journal; indexed in PubMed/MEDLINE
  • focuses on three key issues: incentives, tools, format
  • grants and publications are two things scientists care about, so JoVE is a video journal not a video database
  • has an editorial board
  • operates a distributed network of video production to help those who lack the necessary tools [none in NC, closest in GA]
  • videos are divided by chapters
  • although not immediately available on site, embedded code for flash videos available upon request for including in papers
  • brings video and text together
  • are scientists taught not to speak in jargon? as publication intended for other experts in field, jargon may not be a problem, as the video visualizes the jargon; also pointed out that verbal description of experiment methodology often different than written description
  • video production network is competitive advantage for JoVE
  • 70,000 visitors/month; 200,000 downloads; 80% scientific/academic visitors
  • SciVee is a science media repository: a science video website that can be synchronized with other media
  • pubcast = peer-reviewed paper + video
  • people more quickly grasp paper topic
  • offers profiles and communities so people can connect on SciVee; lots of room for growth in this area
  • people wanted to upload videos not connected to papers, so SciVee began accepting
  • postercasts document transient poster session information; gets research to a larger audience
  • from postercasts people developed slidecasts
  • papercasts is a new format about to be rolled out: videos and papers not published in peer-reviewed journals
  • JoVE charges a $1000 production fee if they do the video through network, but if a researcher creates a video there is no charge to publish in JoVE
  • SciVee's poster presentation feature very helpful
  • biology and medicine are the most sensitive fields to visual description but could be expanded to chemistry, applied physics, ecology, etc.
  • SciVee uses share revenue model with conferences by agreeing to host posters
  • in addition to charging for video production, JoVE also sells advertising, had European investments
  • JoVe is for-profit; SciVee is moving from non-profit to for-profit
  • SciVee tries to negotiate OA when working with others not amenable to OA
  • SciVee's software is proprietary, but might eventually move toward open source
  • viewers have to be cognizant of commercial vs. educational video
  • SciVee can be embedded but not duplicated on own website or blog
  • can't say that much in script; bulk of info in written part; layperson wouldn't understand because need to have basic knowledge; benefit to simplifying so mass scientific audience can understand, but not necessarily mass general audience
  • talking through methods while demonstrating uses different language than writing methods
  • might be best to have different language in video than accompanying text so people can view/assess from two different angles
  • just as likely to find appeal among older scientists who have tenure because more willing to experiment than among younger scientists who are more techno hip
  • institutions would be nervous about videos with animals being posted despite videos being peer-reviewed for proper handling; issues include safety for researchers when face is shown; regular publishing at least only gives name

Tuesday, January 20, 2009

ScienceOnline'09: Open Access Publishing

After a fantastic Friday afternoon behind-the-scenes tour of the NC Museum of Natural Sciences in downtown Raleigh, ScienceOnline'09 kicked off to a great start Saturday morning with a session on the present and future state of Open Access (OA) publishing, led by Bill Hooker and Bjoern Brembs. Although I (obviously) didn't live blog this year's conference, I took copious notes and will share them as is (well, with erroneous spellings corrected...).

  • Peter Suber gave up tenure to promote OA full-time; defines OA literature as "digital, online, free of charge, and free of most copyright and licensing restrictions"
  • online makes OA possible
  • fewer than half of OA journals charge fees but because of BMC and PLoS, that is the model most people know
  • OA archives can be searched as one virtual archive using OAIster
  • ROAR (Registry of Open Access Repositories) is a list of the green road to OA; place to go to find repository to put your work in
  • benefits [of repositories? OA? notes unclear - sorry]: maximizes research efficiency; assessment, monitoring & management; scalability; return on (public) investment
  • OA citation advantage is a little controversial, but evidence is mounting
  • part of the overlooked argument is scalability: untapped potential of text mining
  • iHOP (Information Hyperlinked Over Proteins): pulls sentences out of literature and builds long paragraph of disconnected statements to reorder into brief summary of field; only has PubMed abstracts to mine, not full text
  • we have an overwhelming amount of information available
  • you can't read 35,000+ papers or even 3800+ reviews but your computer can; it is possible for it to pull out info and aggregate
  • GenBank is a great example of what public, open data can do; there now exists a community-wide expectation of openness around gene sequencing
  • librarian salaries are keeping pace with CPI but not journal prices
  • median annual serials expenditures in 2006: $3m-$12m
  • earliest name for OA was Free Online Scholarship
  • Bjoern couldn't get access to his own article because his institution's library didn't subscribe to the journal
  • food for thought: if overnight the journal publishing industry collapsed, how would you restructure? if you were king for the day, how would you redo the system?
  • if the system is faulty, why are so many TA journals (traditional, subscription-based) being created by existing publishers? PROFIT
  • societies are also proliferating TA journals; want to serve members, but TA journals rob members of work and money; must acknowledge that while some membership dues include journal subscription, libraries are still required to purchase
  • journal quality (i.e., impact factor) proxy for article quality simply does not work [I was amazed at how many people in the room did not seem to realize this; quite worrisome]
  • two problems researchers face: 1) how to get research out and used?, and 2) how to assess quality of research?
  • right now we are trying to do this together, but ideally in the future needs to be separate
  • everybody wants to publish and everybody has to find a place to publish even when it's bad because it is necessary to placate university/institutional demands
  • PLoS Biology was never designed to make money but to promote OA and prove that OA journals can be competitive; PLoS One is beginning to make money and subsidizes the other PLoS titles; standard publishing also relies on making money on some "work horse" journals to subsidize the costs of others
  • if Einstein can be wrong about quantum physics, we can certainly be wrong in our assessment of individual papers
  • people want to read their fields' top-level publications not others
  • scholarly enterprise of science doesn't make profit; someone else - often publishers - make profit
  • could pay peer-reviewers and archive publications in own libraries' archives/repositories, which makes them accessible to all
  • majority of Nobel-winning work rejected from top-tier journals (anecdotal)
  • when cost comparisons are made, which is the most efficient way to subsidize publishing: libraries paying subscriptions, or scientists paying OA costs...?
  • if a researcher has an annual grant of $250,000, likely not going to balk at paying $1600 to publish in BMC because his/her research would then be open and accessible
  • if there is a wash between subscription costs vs. OA charges, then why not shift to OA?
  • would shift to OA only force more grant-subsidized research and marginalize non-grant funded researchers? not necessarily because fees may be waived
  • what happens if OA publications go under; how is content accessed?; issue of OA publication going under no different than any other e-journal going under, as libraries don't own electronic content anyway; libraries have plans in place to prevent complete loss of access: LOCKSS, CLOCKSS, Portico; many OA journals/articles also archived in PubMed Central and other repositories