Tom Keays :: Blog

Rest in Peace, Dave Stryker

Tom — 2007-06-06T12:01:24-05:00

Edit: If you have pictures of Dave that you would like to share, there is a Flickr pool for Friends of Dave My song is done, I must be gone I can no longer stay God bless you all, both great and small And send you a joyful May. -->...

Vanity, thy name is Science

Tom — 2007-06-01T12:56:29-05:00

Every so often I come across articles that have an absurd number of authors. Science magazine is often the source of these. OK. I get it. This may be an author's only chance to publish in this journal, but it just seems so... petty. Here's my latest example. Replication of Genome-Wide Association Signals in UK Samples Reveals Risk Loci for Type 2 Diabetes Science 316 (5829): 1336-1341 (1 June 2007) DOI: 10.1126/science.1142364 270 authors (see below) 2124 words (a very rough count, not including table captions or the last third of the paper that summarized committee members and contact information) 7.867 words/author Eleftheria Zeggini, Michael N. Weedon, Cecilia M. Lindgren, Timothy M. Frayling, Katherine S. Elliott, Hana Lango, Nicholas J. Timpson, John R. B. Perry, Nigel W. Rayner, Rachel M. Freathy, Jeffrey C. Barrett, Beverley Shields, Andrew P. Morris, Sian Ellard, Christopher J. Groves, Lorna W. Harries, Jonathan L. Marchini, Katharine R. Owen, Beatrice Knight, Lon R. Cardon, Mark Walker, Graham A. Hitman, Andrew D. Morris, Alex S. F. Doney, The Wellcome Trust Case Control Consortium (WTCCC), Paul R. Burton, David G. Clayton, Nick Craddock, Panos Deloukas, Audrey Duncanson, Dominic P. Kwiatkowski, Willem H. Ouwehand, Nilesh J. Samani, John A. Todd, Peter Donnelly, Dan Davison, Doug Easton, David Evans, Hin-Tak Leung, Chris C. A. Spencer, Martin D. Tobin, Antony P. Attwood, James P. Boorman, Barbara Cant, Ursula Everson, Judith M. Hussey, Jennifer D. Jolley, Alexandra S. Knight, Kerstin Koch, Elizabeth Meech, Sarah Nutland, Christopher V. Prowse, Helen E. Stevens, Niall C. Ta ylor, Graham R. Walters, Neil M. Walker, Nicholas A. Watkins, Thilo Winzer, Richard W. Jones, Wendy L. McArdle, Susan M. Ring, David P. Strachan, Marcus Pembrey, Gerome Breen, David St. Clair, Sian Caesar, Katherine Gordon-Smith, Lisa Jones, Christine Fraser, Elaine K. Green, Detelina Grozeva, Marian L. Hamshere, Peter A. Holmans, Ian R. Jones, George Kirov, Valentina Moskvina, Ivan Nikolov, Michael C. O'Donovan, Michael J. Owen, David A. Collier, Amanda Elkin, Anne Farmer, Richard Williamson, Peter McGuffin, Allan H. Young, I. Nicol Ferrier, Stephen G. Ball, Anthony J. Balmforth, Jennifer H. Barrett, D. Timothy Bishop, Mark M. Iles, Azhar Maqbool, Nadira Yuldasheva, Alistair S. Hall, Peter S. Braund, Richard J. Dixon, Massimo Mangino, Suzanne Stevens, John R. Thompson, Francesca Bredin, Mark Tremelling, Miles Parkes, Hazel Drummond, Charles W. Lees, Elaine R. Nimmo, Jack Satsangi, Sheila A. Fisher, Alastair Forbes, Cathryn M. Lewis, Clive M. Onnie, Natalie J. Prescott, Jeremy Sanderson, Christopher G. Mathew, Jamie Barbour, M. Khalid Mohiuddin, Catherine E. Todhunter, John C. Mansfield, Tariq Ahmad, Fraser R. Cummings, Derek P. Jewell, John Webster, Morris J. Brown, G. Mark Lathrop, John Connell, Anna Dominiczak, Carolina A. Braga Marcano, Beverley Burke, Richard Dobson, Johannie Gungadoo, Kate L. Lee, Patricia B. Munroe, Stephen J. Newhouse, Abiodun Onipinla, Chris Wallace, Mingzhan Xue, Mark Caulfield, Martin Farrall, Anne Barton, Ian N. Bruce, Hannah Donovan, Steve Eyre, Paul D. Gilbert, Samantha L. Hider, Anne M. Hinks, Sally L. John, Catherine Potter, Alan J. Silman, Deborah P. M. Symmons, Wendy Thomson, Jane Worthington, David B....

Ten Simple Rules for a Successful Collaboration

Tom — 2007-03-30T14:19:30-05:00

Quentin Vicens, Philip E. Bourne PLoS Comput Biol 3(3): e44 (2007) Abstract Scientific research has always been a collaborative undertaking, and this is particularly true today. For example, between 1981 and 2001, the average number of coauthors on a paper for the Proceedings of the National Academy of Sciences rose from 3.9 to 8.4. Why the increase? Biology has always been considered the study of living systems; many of us now think of it as the study of complex systems. Understanding this complexity requires experts in many different domains. In short, these days success in being a biologist depends more on one's ability to collaborate than ever before. Interesting and not limited to science research collaborations. Rule 1: Do Not Be Lured into Just Any Collaboration Rule 2: Decide at the Beginning Who Will Work on What Tasks Rule 3: Stick to Your Tasks Rule 4: Be Open and Honest Rule 5: Feel Respect, Get Respect Rule 6: Communicate, Communicate, and Communicate Rule 7: Protect Yourself from a Collaboration That Turns Sour Rule 8: Always Acknowledge and Cite Your Collaborators Rule 9: Seek Advice from Experienced Scientists Rule 10: If Your Collaboration Satisfies You, Keep It Going...

Sign the Petition

Tom — 2007-03-16T11:12:16-05:00

Dorothea Salo at Caveat Lector writes about the Petition for Public Access to Publicly Funded Research in the United States. I couldn't say it better. Finally, the United States has a signable electronic petition urging public access to publicly-funded research. I would consider it a personal favor if every single States-based reader of Caveat Lector would at least go read this petition. If it appeals to you, sign it. If you are an academic librarian, please bring this to the attention of your library's and/or your institution's administration. Open access to taxpayer-funded research is the wedge issue that brings us closer to a solid resolution for the serials crisis. Without your support, and your institutions' support, we'll be stuck in the same old stalemate we've endured for three decades. Please. It's time, and past time. Read, and consider signing. Thank you. I signed. Did you?...

O'Reilly Radar notes WorldCat Identities

Tom — 2007-02-20T09:15:21-05:00

Tim O'Reilly, in his Radar blog, has written about OCLC's WorldCat Identities. A lot of people think that there's a single big identity play out there, and focus on technology solutions, but it seems to me that in true bottom-up internet style, we may eventually build our online identities out of a mashup of all the tracks we already leave in cyberspace. ... One more small step in this direction was released by the OCLC (Online Computer Library Center) last week. It's a prototype of an author identity system that shows holdings of books by any author in all of the libraries tracked by OCLC in its worldcat system. Nice to see that the library world occasionally catches some attention outside our own community....

WorldCat Improvements

Tom — 2007-02-06T11:05:02-05:00

Some nice additions to OCLC's WorldCat.org service were announced yesterday. The features I found most useful are these: Automatic geographic location code by IP address. The WorldCat.org service will determine a geographic location for each user based on IP address, even when the user has never before entered a postal code to view a list of local libraries. The automatic display of library lists should connect searchers to the library nearest them. Faceted browse now allows user to expand search category options. The faceted browse feature of WorldCat.org search results now allows a user to expand the abbreviated results within each facet via a "Show More" link. Faceted browse allows a user to filter search results by categories, or facets, using the left-hand Refine Your Search panel. This dynamic navigation further leverages WorldCat's structured metadata and helps users who may have difficulty narrowing a large result set understand the refinement options available to them. More visibility for evaluative content and Web resource links. Individual item records reached from WorldCat.org search results now include links to supplemental Web content on the top-level page. Previously displayed beneath the "Details" tab, these links can include publisher-provided item descriptions, author biographies and Web sites, tables of contents and content excerpts. Additional links may be provided with the heading "Web Resources," which may give a user access to content related to the displayed item. If the displayed item is a digital object -- such as an electronic book, or a digitally preserved photo, document or artifact -- the link may provide direct viewing or retrieval of the object. I noticed that they now have library-specific "Library Information" and "Ask a Librarian" links, as appropriate, in the Libraries view at the work level. I don't recall seeing that there before....

Participatory Networks : The Library as Conversation

Tom — 2007-02-01T12:11:07-05:00

The whole of this report is available on the IIS website. Worthwhile reading. Participatory Networks : The Library as Conversation http://iis.syr.edu/projects/PNOpen/ R. David Lankes, Joanne Silverstein, Scott Nicholson Executive Summary Goal The goal of the technology brief is to familiarize library decision makers with the opportunities and challenges of participatory networks. In order to accomplish this goal the brief is divided into four sections (excluding an overview and a detailed statement of goal): A conceptual framework for understanding and evaluating participatory networks (see "2. Library as a Facilitator of Conversation" in the full brief) A discussion of key concepts and technologies in participatory networks drawn primarily from Web 2.0 and Library 2.0 (see "3. Participatory Networking, Social Networks and Web 2.0" in the full brief) A merging of the conceptual framework with the technological discussion to present a roadmap for library systems development (see "4. Libraries as Participatory Conversations" in the full brief) A set of recommendations to foster greater discussion and action on the topic of participatory networks and, more broadly, participatory librarianship (see "5. Recommendations" in the full brief). This summary will highlight the discussions in each of these four topics. For consistency, the section numbers and titles from the full brief are used. 1. Library as a Facilitator of Conversation This section describes a participatory model that is later applied to modern web services as participatory networking, and a broader new approach to libraries, participatory librarianship. The theoretical foundation of this model, Conversation Theory, posits that individuals, organizations, and even societies build knowledge through conversation; specifically, by interacting and building commonly held agreements. Since libraries are in the knowledge business, they are also in the conversation business. The library community implicitly adds a corollary to this theory: The best knowledge comes from an optimal information environment, one in which the most diverse and complete information is available to the conversant(s). Conversation Theory is very much in line with current and past library practice, and shows a clear trajectory for the future. The value of this viewpoint is not just theoretical. It has real consequences and uses. For example, much of library evaluation has been based in numeric counts of tangible outputs: books circulated, collection size, reference transactions, and so on. Yet this quantitative approach has been frustrating to many who feel they are counting outcomes, but not getting at true impact of library service. Librarians may ask themselves, "Which numbers are important...and why?" If libraries focused on conversations, however, there might be some clarity and cohesion between statistics and other outcomes. Suddenly, the number of reference questions can be linked to items cataloged, or to circulation numbers...they are all markers of the scope and scale of conversations within the library context. This approach might enable the library community to better identify its most important conversations and demonstrate direct contributions to these conversations across functions. 2. Participatory Networking, Social Networks and Web 2.0 The brief then turns to the operational and technological underpinnings of participatory networking. Core concepts...

Nature's Expose on Publisher's Tactics to Rout Open Access

Tom — 2007-01-24T21:06:00-05:00

Jim Giles, writing in a column in Nature 445 (7126): 347 (January 25, 2007) reveals that a major group of sci-tech publishers (reportedly Elsevier, Wiley and the American Chemical Society) has hired a pit-bull PR firm to advise them on how to best combat the Open Access movement, particularly PubMed Central. Reportedly the publishers are spending up to a half-million dollars for the advice of Dezenhall Resources, a group that has had as clients in the past such illustrious folks as Jeffrey Skilling, the former Enron chief. According to the Nature article, Denzenhall is advising the publishers to give out the message that "Public access equals government censorship". He hinted that the publishers should attempt to equate traditional publishing models with peer review, and "paint a picture of what the world would look like without peer-reviewed articles". (Via Issues in Scholarly Communication)...

True Lies

Tom — 2007-01-24T20:18:37-05:00

The Onion reports (so you know it's true): SYRACUSE, NY -- In a rare instance of icy-cold January weather, much of the Northeast awoke Tuesday morning to find itself buried under nearly 1.5 inches of snowfall....

Dealing with huge bookmark files in Firefox

Tom — 2007-01-24T12:14:04-05:00

I noticed today that my Firefox bookmark file had bloated up from 259KB on November 28 to 477KB -- almost a half megabyte. The November size itself seemed much larger than I would have expected, but the size of the file today was of great concern to me. I knew that I hadn't been adding new bookmarks in Firefox at a rate that could account for this tremendous bloating in size. Furthermore, I shuddered to remember that about a year ago, my bookmarks has similarly bloated in size to such an extent that Firefox ceased to open. At that time, the only remedy offered by the Library systems guy was to delete the bookmark file and start over. I knew I had to take some action before it became critical. I made a copy of my bookmark file and took a look at the code in a text editor. Immediately, I noticed that there were instances of lines that were much longer than others. A visit to the archives of the mozilla.support.firefox newsgroup revealed a solution. It turns out that Firefox stores icons for pages that you visit and bookmark as text-encoded binary data. Look in your bookmark file for 'ICON="data:image/x-icon;base64' and you will probably see many examples of what I'm talking about. You will note that all bookmarks start with "

" and are one continuous line (I've wrapped it in my example for better display). Below is an example of a single (polluted) bookmark from bookmarks.html. The line is a total of 2042 characters long, most of which is the "ICON" attribute.

Google By removing the "ICON" attribute and its data, I determined that I could reduce the length of this to 132 characters; a 93.5% (1910 characters) reduction in size. Clearly, this is worth doing. Before editing the bookmark file, you first need to stop new icons from being added or this problem is just going to recur. In Firefox's location window, enter "about:config". A long list of file settings will appear. In the "Filter" search box, type the string "icon". Locate and toggle the following two entries from "true" to "false" by double-clicking them. browser.chrome.favicons false browser.chrome.site_icons false Now you need to add the following new entry in "about:config". browser.chrome.load_toolbar_icons 0 You do this by right-clicking in the "about:config" box and selecting "New" > "Integer" as an option. In the "New integer value" > "Enter the preference name" window, type in "browser.chrome.load_toolbar_icons" and click "OK". In the "New integer value" > "browser.chrome.load_toolbar_icons" window, type in the integer "0" and click "OK". When you have done this, no new icons will be added to the bookmark file, but existing icons will not be removed. To reduce the size of your bookmark file, you have to hand...

Open Library Catalog Data

Tom — 2006-12-18T13:02:28-05:00

The Open Libraries blog reported earlier this month that Casey Bisson, information architect at Plymouth State University, was presented with a $50,000 Mellon award for Technology Collaboration by Tim Berners-Lee for his creation of WP-OPAC, a mash-up of a library catalog with the tagging functionality of blogging software. The revolutionary part of the announcement, however, was that Plymouth State University would use the $50,000 to purchase Library of Congress catalog records and redistribute them free under a Creative Commons Share-Alike license or GNU. OCLC has been the source for catalog records for libraries, and its license restrictions do not permit reuse or distribution. However, catalog records have been shared via Z39.50 for several years without incident. "Libraries' online presence is broken. We are more than study halls in the digital age. For too long, libraries have have been coming up with unique solutions for common problems," Bisson said. "Users are looking for an online presence that serves them in the way they expect." He said "The intention is to bring together the free or nearly-free services available to the user." Bisson said Plymouth State University is committed to supporting it, and will be offering it as a free download from its site, likely in the form of sample records plus WordPress with WP-OPAC included. "With nearly 140,000 registered users of Amazon Web Services, it's time to use common solutions for our unique problems," Bisson said. Following the announcement, there was some low-key discussion about it on the Next Generation Catalog listserv and other library discussion forums congratulating Casey Bisson, but the remarkable nature of the proposal for an open data release of the cataloging records went largely unremarked. I find it reassuring, therefore, that last week, Ross Singer, Tim Spalding, Rob Styles, Richard Wallis, and Paul Miller recorded a podcast about this award which did focus on the open data aspects of the announcement. It's worth a listen. Much of the podcast focused on the apparent ambiguity about the legality of Bisson's intention. While LC's data is, at least in the US, free of copyright restrictions, it is not clear that this is true outside the US. Purchase of the data does not in itself change that situation. Certainly, Talis in the UK was mentioned as paying quite a lot (unspecified) to use LC's MARC records. And OCLC, the primary distributor of MARC records to libraries, as mentioned above has a set of restrictions that governs the use and transfer of these records by member libraries. Ultimately, I am left unsure how to sort out the contradictions made apparent by this announcement. Most importantly, LC's MARC cataloging data is already freely accessible, both by Z39.50 and by their cool SRU gateway. There was a passing mention of SRU in the podcast but they didn't dwell on it. Construct a valid query to the SRU gateway and you get back a complete cataloging record in MARCXML. Both the MARCXML schema and the SRW schema are fully documented and available for use...

The OPAC Sucks

Tom — 2006-12-04T14:52:15-05:00

A YouTube video recorded by the anAACRonisms with lyrics by Brian Smith. Via The Laughing Librarian....

Unsuggester: Finding the Book You'll Never Want

Tom — 2006-12-04T12:15:51-05:00

Ooops. LibraryThing got SlashDotted this morning for their new UnSuggester feature. In the meantime, they are redirecting traffic to their blog posting about it. I keep encountering this: SlashDot runs a story and the resulting traffic brings the featured site to its knees....

The Economics of Ecology Journals

Tom — 2006-11-19T20:33:18-05:00

Carl T Bergstrom and Theodore C Bergstrom Frontiers in Ecology and the Environment 4(9): 488-495. eprint Over the past decade, scientific publishing has shifted from a paper-based distribution system to one largely built upon electronic access to journal articles. Despite this shift, the basic patterns of journal pricing have remained largely unchanged. The large commercial publishers charge dramatically higher prices to institutions than do professional societies and university presses. These price differences do not reflect differences in quality as measured by citation rate. We discuss the effect of price and citation rate of a journal on library subscriptions and offer an explanation for why competition has not been able to erode the price differences between commercial and non-profit journals. Katie Newman in UIUC's Scholarly Communication blog quotes several pages from the article lamenting the probable fate of one scholarly journal. In 1844, 15 years before the publication of The Origin of Species, Charles Darwin published a pair of articles (Darwin 1844a,b) in a fledgling natural history journal, The Annals and Magazine of Natural History. This journal had been founded by publisher Richard Taylor and his son William Francis in 1840, who merged several British natural history titles dating back to 1828. The journal published five of Darwin's papers in total. Darwin's contributions to The Annals focused on the specifics of natural history rather than on the theory of evolution. However, the journal earned a prominent place in the history of evolutionary biology, as the venue for Alfred Russell Wallace's 1855 manuscript "On the Law which has regulated the Introduction of New Species" (Wallace 1855). In that paper, published 3 years before the famous Darwin-Wallace outline of natural selection (Darwin and Wallace 1858), Wallace drew upon his own phylogeographic observations to conclude that new species must arise from pre-existing species, giving rise to a tree-like relationship among taxa. One hundred and fifty years later, The Annals and Magazine of Natural History continues to be published, still under the name of Taylor and Francis, which has morphed into an international publishing conglomerate that publishes 800 periodicals. The journal is now titled The Journal of Natural History. Perhaps due to shifts of scientific fashion, the journal's prestige is not what one might expect given its history: its impact factor was an unimpressive 0.611 at the time of our first survey in 2001. While the 2001 price per page, $0.77, was modest for a for-profit publisher, the price per citation, $19.21 was among the highest in the field of ecology. Taylor and Francis responded to the low impact factor in two surprising ways. First, they increased the size of the journal, from 2323 pages in 2000 to 3347 pages in 2004. Second, they dramatically increased the price, from $1784 for print in 2001 to $6735 for the print plus online combination in 2005. Even accounting for the increased number of pages, this represents a near-doubling of the price per page. By 2004, the impact factor had dropped to 0.514 and price per recent citation...

A Solution to Wikipedia Vandalism

Tom — 2006-11-16T19:43:48-05:00

On November 8, Dinosaur Comics featured a compelling argument about how to eliminate all the vandalism that occurs on Wikipedia. They even spun off a companion web site, Every Topic In The Universe Except Chickens dot com, dedicated to the project. The problem was stated as follows. Wikipedia is an encyclopedia that everyone can edit. That's rad! It's a good place to learn a lot about the internet, sex, explosions, Ravenna, Ohio, and Captain Picard. ... The problem is that dudes and ladies like to vandalize it with misinformation, falsehoods, stories about their cats, and sometimes even pictures of wieners in articles that aren't even about wieners. I saw that once. THAT IS NOT COOL because what if you are using the internet for serious research and you ended up thinking that Jodie Foster was History's Greatest Villain? THIS GRIM VISION IS POSSIBLE WITH WIKIPEDIA. You would end up getting a D+. And the solution. I give you a new Wikipedia. A Wikipedia evolved, a Wikipedia that lives in the here in the real world. A Wikipedia that makes just one tiny concession to vandals, a concession for the greater good. I give you Wikipedia 2.0, otherwise known as Wikipedia: Every Topic In The Universe, Except Chickens (Dot Com). HOW IT WORKS: Simple! I just said. Instead of vandalizing Wikipedia in general, we all just vandalize the chicken article. How does it work? Dudes already know about chickens. Ladies also already know about chickens. Does an encyclopedia really need an article about nature's tastiest birds? You know the answer is "no it most certainly does not". Wikipedia simply GIVES UP that article to vandals, and in return the other articles, like the one about octopods (Humanity's Underwater ChumsTM), do not get vandalized. Instead of a quantum encyclopedia, with vandalism and falsehoods peppered throughout at various locations AND at various times, Wikipedia becomes a consistently RELIABLE encyclopedia that covers every topic in the universe, except chickens. Lastly, they asked the question that had to be asked. WON'T WIKIPEDIA GET MAD? No, Wikipedia cannot get mad because despite what some Wikipedia editors claim, Wikipedia is not actually alive. No nation on Earth recognizes Wikipedia as life. The rationalization of how Wikipedia will embrace this proposal goes on in more detail and concludes with Jimbo Wales (fictional) firmly endorsing it. Except... It looks like Wikipedia did get mad. They locked the article to all edits for over a week. So much for the perfect solution. They recently have relaxed the restriction a bit. Now the chicken page says, "Editing of this article by unregistered or new users is currently disabled." A slight improvement, then....