March 13, 2006

Knowledgespeak Updates

.: One of the consequences of working two jobs at the same time is that my inbox is growing faster than I can hit the delete button. Here are a few recent items from the Knowledgespeak news archive, which I have been meaning to post for some time:

  • BioMed Central unveils new online open access journal - "Open access publisher BioMed Central, UK, has announced the launch of Biology Direct, a new online open access journal with a new peer review system. Led by Editors-in-Chief David J Lipman, Director of the National Center Biotechnology Information (NCBI); Eugene V Koonin, Senior Investigator at NCBI; and Laura Landweber, Associate Professor at Princeton University, the journal seeks to provide authors and readers with a unique system of peer review.

    The journal will cover original research articles, hypotheses and reviews, and is available online at The journal includes publications in the fields of Systems Biology, Computational Biology and Evolutionary Biology, to be soon followed by an Immunology section..."

Continue reading "Knowledgespeak Updates" »

February 12, 2006

UniProt - The Universal Protein Resource

.: The following is of interest to those working in molecular biology and requiring access to protein sequence daabases. The UniProt Consortium is comprised of the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). Until recently, EBI and SIB together produced Swiss-Prot and TrEMBL, while PIR produced the Protein Sequence Database (PIR-PSD). The UniProt databases (UniPARC, UniProtKB, UniREF) are built upon the pooled overlapping and complementary resources, efforts and expertise of these pioneereing efforts; UniProt FAQ

July 26, 2005

Reproducible Research: A Bioinformatics Case Study

:: Via the Faculty of 1000, an article that may be of interest to readers. Reproducible Research: A Bioinformatics Case Study1, by Robert Gentleman, of Harvard University, suggests a new approach to scholarly publishing as follows:

While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2003), suggests a methodology and basic infrastructure that can be used to publish documents in a substantially different way. Their approach is suitable for the publication of papers whose message relies on computation. Stated quite simply, Gentleman and Temple Lang (2003) propose a paradigm where documents are mixtures of code and text. Such documents may be self-contained or they may be a component of a compendium which provides the infrastructure needed to provide access to data and supporting software. These documents, or compendiums, can be processed in a number of different ways. One transformation will be to replace the code with its output -- thereby providing the familiar, but limited, static document.

In this paper we apply these concepts to a seminal paper in bioinformatics, namely The Molecular Classification of Cancer, Golub et al (1999). The authors of that paper have generously provided data and other information that have allowed us to largely reproduce their results. Rather than reproduce this paper exactly we demonstrate that such a reproduction is possible and instead concentrate on demonstrating the usefulness of the compendium concept itself.

Continue reading "Reproducible Research: A Bioinformatics Case Study" »

April 20, 2005

Headless, Remote Controlled Flies

:: Be afraid. Be very afraid. Via: Clive Thompson.

April 14, 2005

JSTOR Collection Announcement: Biological Sciences Collection

:: As announced by JSTOR on 13 April 2005:

JSTOR is very pleased to introduce the Biological Sciences Collection. The Biological Sciences Collection will include at least 100 titles when it is completed by the end of 2007. This collection will bring together the twenty-nine journals available in our existing Ecology & Botany Collection with more than seventy titles new to JSTOR. The journals in this collection offer greater depth in fields such as biodiversity, conservation, paleontology, and plant science, in addition to introducing new areas such as cell biology and zoology.

In developing the Biological Sciences Collection, JSTOR has partnered with two leading organizations in biological sciences publishing: the Ecological Society of America (ESA) and BioOne. Similar to the assistance they provided with the development of Ecology & Botany, the ESA assembled a committee of scholars to review and recommend journals to us, in addition to taking the lead in securing a grant from the Andrew W. Mellon Foundation to digitize a portion of the collection. BioOne has joined this collaboration by facilitating the inclusion of many BioOne participating publications in the collection. In the future we hope to develop cross-site searching and article-level links between BioOne and JSTOR.

We invite you to view the complete details for this new collection on JSTOR’s web site. For collection descriptions, fee information, journal lists, and participation instructions, please see:

We are very happy to facilitate the growth and diversification of the JSTOR archive holdings with this new collection. The multidisciplinary JSTOR Arts & Sciences and Biological Sciences collections and the existing discipline-specific collections (e.g. Business, Ecology & Botany) have been designed to offer participation flexibility for libraries and institutions. With several options available, participants are able to choose both the collections and growth paths that are most appropriate for their needs.

This is great news, especially for campuses with large biological sciences departments like our own.

March 14, 2005

Infotrieve to Launch Life Science Research Center

:: Paula Hane reports the following on InfoToday:

March 14, 2005 — Infotrieve, Inc. (, a company that has specialized in document delivery for information professionals in the STM (scientific, technical, and medical) markets, has announced the upcoming launch of a new Web-based “search and discovery” research environment for scientific researchers in biotechnology, pharmaceutical, and other life science-related industries. The new Life Science Research Center (LSRC), which is scheduled to launch on March 25, will let bench scientists and lab workers search the full text of diverse types of content (both core literature—like journals, book chapters, and patents—plus scientific content, such as gene data) and then discover common themes and relationships among the results.

“Infotrieve’s LSRC will have an immediate positive impact by simplifying the search process for pharmaceutical, biotechnology, and other life science-related researchers,” said Wes Crews, Infotrieve president and CEO. “Scientists shared with us that they are overloaded with information and that information is in too many places, making the discovery process inefficient and time-consuming. The LSRC streamlines the search process, facilitating faster and more relevant results.

December 2, 2004

Journal of the Academy of Natural Sciences of Philadelphia, First Series

:: Reading through the December issue of Choice, I stumbled upon a rare gem of early American scientific publishing. Using an IMLS grant, the Ewell Sale Stewart Library of the Academy of Natural Sciences has digitized the entire first series of Journal of the Academy of Natural Sciences of Philadelphia.

Journal of the Academy of Natural Sciences of Philadelphia
Fulltext First Series v1-8 (1817-1842)
ISSN: 0885-3479

The website provides details on the techniques used in the digitization in addition to the historical and scientific bounty of the journal proper. Whether one's research interests run to ornithology, entomology, ichthyology, or botany, American scientific luminaries of the first half of the 19th century wrote major pieces in this early giant of American scholarly communication. The article which caught my eye initially is John James Audubon's prospectus for his monumental Birds of North America. - George Porter

October 28, 2004

BioMed Central Provides MARC Records

:: George Porter sent an e-mail about the following:

BioMed Central provides MARC records to facilitate the cataloging of their large collection of Open Access journals. A delimited spreadsheet containing titles, URLs, ISSNs, journal abbreviation and date of initial publication is also available. Very few publishers have proven so supportive of the library community. BioOne, a SPARC Scientific Community, is deserving of special mention in this regard for being a pioneer in providing application-neutral spreadsheets to facilitate cataloging.

September 20, 2004

News Items of Interest from Information Today

Amazon Launches Search Site, Inc., a subsidiary of, Inc., has launched to make searching the Internet more effective. The new site builds on a beta test version the company introduced in April 2004 that offered Google searching of the Web combined with searches of Amazon's books and site information from Amazon's subsidiary, Alexa Internet. The official launch of adds several information sources and new search and organizational features. The company says the new site is more of an information management tool.

Continue reading "News Items of Interest from Information Today" »

August 19, 2004

Cell Press Announces Free Access to Recent Online Archive

:: From the Cell web site:

Cell Press is pleased to announce that access to the recent online archive of Cell and the other premier journals of the Cell Press collection will become freely available beginning in January 2005. The recent archive of these journals includes content that is 12 months old or older and dating back to content from 1995. Each month as new issues are published, the year old issues will be added to the freely accessible recent archive. Free access to the recent archive will be available on both ScienceDirect ( and on the Cell Press journal sites (

Continue reading "Cell Press Announces Free Access to Recent Online Archive" »

May 6, 2004

Annals of Botany Backfiles Now Available

:: George advises that the Annals of Botany, published by Oxford University Press, on behalf of the Annals of Botany Company, a non-profit educational charity established to promote plant science worldwide, has opened their fulltext for free access, following a 1 year period of exclusive use by subscribers.

Annals of Botany
Fulltext v71+ (1993+) 1 year moving wall
Print ISSN: 0305-7364; Online ISSN: 1095-8290

A complete list of titles to which Highwire provides free online access to full-text articles, either upon publication, or after a certain time period, is available here.

April 27, 2004

Arabidopsis Book

George posted the following biology resource to STS-L. Note that the Arabidopsis Book is open access.

The Arabidopsis Book is an Open Access project bringing together an encyclopedic description of one of the most heavily studied plant species. Quoting from the American Society of Plant Biologist's (ASPB) website:

This electronic book, The Arabidopsis Book (TAB), ISSN: 1543-8120, is an attempt at a new mode of communication between researchers and a new model for scientific publishing. TAB in its initial stage is a compilation of over 100 invited chapters, each reviewing in detail an important and interesting aspect of the plant Arabidopsis thaliana, with reference to what is known in other plants and in other kingdoms.

Arabidopsis Book
Fulltext v1+ (2002+)
ISSN: 1543-8120

The ASPB version is organized into sections, then access is at the individual chapter level, in PDF only. BioOne provides both HTML and PDF versions of each chapter. In addition, BioOne has implemented a search interface.

Although BioOne's materials are primarily subscription-based, The Arabidopsis Book is one of a few BioOne collections which are Open Access. In addition:

Florida Entomologist
Fulltext v85+ (2002+)
Fulltext v1+ (1917+)
ISSN: 0015-4040

April 5, 2004

New ClusterMed Organizes PubMed Results

New ClusterMed Organizes PubMed Results

Vivísimo, Inc. (, a provider of clustering and meta-search software for organizing search results, has announced the release of ClusterMed, a new research tool that allows biomedical and life sciences researchers to search the MEDLINE database far more productively and efficiently. Vivísimo has had a version of PubMed (MEDLINE) searching available on its site to showcase the capabilities of its metasearch engine, but the new ClusterMed is a software solution that is licensed to companies on a yearly subscription for local server installation. A demonstration site is now available at Unregistered users can cluster up to 100 results for a search; register for a free 30-day demo and cluster up to 500 results per query. ClusterMed organizes the long list of results returned by PubMed into hierarchical folders with meaningful categories, allowing researchers to hone in on the most relevant results quickly. ClusterMed does this on-the-fly without requiring any pre-processing, using terms taken from the brief descriptions in the search results. With the folders, users can discover themes, view related articles, and drill down from the topic hierarchy or drill up (show-in-clusters) from a specific article. Vivísimo calls ClusterMed a breakthrough improvement in search productivity and efficiency. Users will call it an answer to information overload.

March 9, 2004

BioMed Central goes RSS friendly

Today's BioMed Central update mentions their new move to RSS!

RSS headline feeds

You may have noticed that the home pages and most-viewed articles pages of all BioMed Central journals now include a small XML button. This indicates that there is an RSS (Really Simple Syndication) feed available for the articles on that page.

An RSS feed is a list of articles in a standard XML format that can automatically be processed by newsreading software. Since RSS feeds can be read by robots, these feeds can also be used by webmasters to incorporate BioMed Central content automatically into their own sites.

For more information about how to use BioMed Central's RSS feeds, see our RSS information page.

March 8, 2004

European Cells & Materials now available open access

:: George Porter reports the following on STS-L:

February 23, 2004

Genetics Back-file Freely Available

As posted to STS-L by George Porter...

Genetics, published by the Genetics Society of America, has finished retrospective conversion of the journal. Distributed via Highwire Press, the entire back-file conversion project has been gifted to the scientific community. Current material becomes freely available after 3 months.

Fulltext v1+ (1916+)

February 9, 2004

News from IOP

The information below regardings developments to the Institute of Physics' (IOP) Electronic Journals service was received in an e-mail from the IoP.

    *Electronic Journals Quick Guide*
    A new step-by-step guide to our Electronic Journals service is now available online. A good introduction for new users and a useful refresher for existing ones, the Quick Guide runs through all of the key features of the service including searching, clustering, e-mail alerting and reference linking (forwards and backwards).

    The Quick Guide has been prepared in Microsoft PowerPoint so it can be used in a number of ways: you and your library users can work through it onscreen (in 'slide show' mode); the slides can be used for presentations or training sessions and/or they can be printed out and distributed as handouts.

Continue reading "News from IOP" »

February 2, 2004

Suber, SPARC Open Access Newsletter, 2/4/04

New issue: SPARC Open Access Newsletter, issue #70February 2, 2004 is available now. Of note: an interesting report back on PLoS's first month of publication.

January 27, 2004

Directory of Open Access Journals

Further to my last posting, for a listing of open access journals in biological sciences, or for that matter, other subject areas of interest, be sure to visit the Directory of Open Access Journals (under the direction of a new project coordinator).

January 26, 2004

Quantitative Biology at

The following email re: open access materials was posted to STS-L on Friday.

I just noticed a new eprint archive at arXiv (formerly -- Quantitative Biology. Subject groupings include:

# BM - Biomolecules
# CB - Cell Behavior
# GN - Genomics
# MN - Molecular Networks
# NC - Neurons and Cognition
# OT - Other
# PE - Populations and Evolution
# QM - Quantitative Methods
# SC - Subcellular Processes
# TO - Tissues and Organs

The q-bio announcement indicates the archive was established in mid-September 2003. This development is especially noteworthy in that biology, as a discipline, has not had the same preprint sociology which nurtured the development of for the mathematics and physics communities.

George S. Porter
Sherman Fairchild Library of Engineering & Applied Science
California Institute of Technology

Two other big(ger) open access models covering Biological Sciences are of course those of BioMed Central and BioOne*.
*(BioOne is actually not open access, but rather yet another model of publishing involving "innovative collaboration between scientific societies, libraries, academe and the private sector." Journals via BioOne are low cost, but not open access.)

January 16, 2004


And the number continues to shrink...

Thomson Corp. said yesterday that it had acquired the publishing assets of Philadelphia-based Biological Abstracts Inc. and Biosis, a life-sciences indexing service. Financial terms of the deal, which closed Friday, were not disclosed. The nonprofit Biosis' 125 employees, at 20th and Market Streets, and 40 other employees in York, England, now work for Thomson ISI, a business unit of Thomson Scientific & Healthcare, based in Philadelphia. Biosis' employees, now in leased space at Two Commerce Square, will move eventually to Thomson offices at 35th and Market Streets, said Michael Tansey, president and chief executive officer of Thomson Scientific. "Nobody lost their jobs," he said. Because the transaction involved a for-profit company buying a nonprofit, proceeds from the sale of Biosis' publishing assets will go to a new foundation, the J.R.S. Foundation, run by Biosis' former board of trustees to "further the work of biological scientists," said Joel Baron, an adviser to the former Biosis board. "The foundation money could be used for funding life-science research, supporting the work of researchers in Third World countries, or to support other foundations," Baron said. "A final determination has not been made." Biosis, which was founded in 1926, produces databases and services for life-sciences research, including Biological Abstracts, Biosis Previews and Zoological Record, which is published jointly with the Zoological Society of London. Thomson said Biosis was the world's largest abstracting and indexing service. Toronto-based Thomson, with $7.8 billion in revenue in 2002, is a publisher of specialized information for businesses, with more than 20 million users in the fields of law, tax, accounting, financial services, higher education, reference information, corporate training, scientific research, and health care. Thomson's products range from Westlaw legal databases and the Physicians' Desk Reference to university textbooks. Thomson ISI, which was founded in Philadelphia in 1958 as the Institute for Scientific Information, provides Web-based information to researchers, students and businesses worldwide. Biosis announced in May that it was seeking a partner to ensure that researchers, educators, students and others would have continued affordable access to biological research. In October, Biosis said it was in final negotiations with Thomson. [Source:]

December 23, 2003

OUP and continuous online publication model

:: Back in August we posted about OUP's move towards experimenting with new online publishing model. A few more details have been released.

Oxford University Press is pleased to announce that Nucleic Acids Research (NAR) is adopting a continuous online publication model. The key aim of this new model is to ensure the fastest possible online publication time for accepted papers. The online version of the journal will be the definitive and final version, but a print version will continue to be available to print subscribers.

If your institution subscribes to NAR, you may be interested to know about the various implications for users of the journal. If so, please visit for details. [via OUP Journals Library E-Mail Lis]

Yours faithfully

Claire Saxby
Journals Editorial Department
Oxford University Press

PLoS Biology -- December Issue Now Out

:: Vol 1(3) is here! Please let your friends and colleagues know that a new issue of PLoS Biology is up and running, and invite them to read it for free at

PLoS has just announced [last week] that individuals can become members of our organization. For a small donation (tax deductible in the US), you can be part of PLoS! For more information or to donate online, visit and click beneath "Become an Individual Member."

December 5, 2003

Max Planck Research Awards 2003 Presented

:: "As part of the efforts to promote international cooperation in science, the Max Planck Society and the Alexander von Humboldt Foundation presented the Max Planck Research Award for 2003 on November 26, 2003 at 5:30 PM to 12 scientists and researchers in an award ceremony at Harnack-Haus in Berlin-Dahlem. Each award is endowed with EUR 125,000 and gives highly qualified German and foreign scientists and researchers the opportunity to initiate, deepen, or expand mutual projects with the goal of achieving maximum scientific performance on the international scene."

December 3, 2003


The latest issue of Open Access Now is now available online. From the very interesting article Fingerprinting the Literature...

Grivell likes to think of E-BioSci as a discovery tool, and he emphasizes the differences between E-BioSci and more conventional bibliographic service such as Entrez-PubMed ( "PubMed simply indexes everything. When you do a search you are actually looking up an entry in the index and that points you to a number of abstracts," explains Grivell. Of course, one can do more advanced searches using several keywords and Boolean terms (such as 'AND' and 'NOT'). "But every term is equally weighted and it's black and white - it's there or it's not there," says Grivell. "We deliberately took a different approach. Here, the concepts are derived from the article itself. We take out the words and use them to generate the fingerprint that forms the basis of the search. The search process itself is very interactive. The user can look at the fingerprint and modify the weight given to each concept. In that way you can change the focus or sharpen a search. You may end up with something that is similar to that which conventional searches produce, but there are always the additional unexpected results in there, which people may have missed."

October 21, 2003

U Alberta Mech Engineers Make Important Energy Breakthrough, More on PLoS Biology

:: University of Alberta mechanical engineering professors Dr Daniel Kwok and Dr Larry Kostiuk (additional information here), working with two graduate students, Fuzhi Lu (L) and Jun Wang (R), have discovered a new way to produce electricity, the first such discovery in 160 years.

Their research was the front page story in today's Edmonton Journal, and received coverage elsewhere on the Internet.

More information is available on the University of Alberta Express News site. The news of this discovery was also of personal interest to me, as I am the librarian responsible for mechanical engineering here at the U of Alberta.

Their research appears in the November 2003 issue of Journal of Micromechanics and Microengineering:

    Research published today by the Institute of Physics journal, Journal of Micromechanics and Microengineering reveals a new method of generating electric power by harnessing the natural electrokinetic properties of a liquid such as ordinary tap water when it is pumped through tiny microchannels. The research team from the University of Alberta, Edmonton, Canada, have created a new source of clean non-polluting electric power with a variety of possible uses, ranging from powering small electronic devices to contributing to a national power grid.

    The research was led by Professor Daniel Kwok and Professor Larry Kostiuk from the University of Alberta. Professor Kostiuk said: “This discovery has a huge number of possible applications. It’s possible that it could be a new alternative energy source to rival wind and solar power, but this would need huge bodies of water to work on a commercial scale. Hydrocarbon fuels are still the best source of energy but they’re fast running out and so new options like this one could be vital in the future”.

Reference: Yang J, Lu F, Kostiuk LW, Kwok DY J Micromech Microeng 13 (November 2003) 963-970.

:: Expanding coverage of PLoS Biology: articles have appeared in EContent and CNET

October 1, 2003

Interview with Tim Berners-Lee

:: Tim Berners-Lee is credited with inventing the world wide web in 1989. He shares his ideas of a more "intelligent" web in this interview from the BBC.

:: Today's website is from the Life Sciences Libraries at the University of British Columbia. Today's resource guide is "Agriculture: Guide to Library Resources & Information" from Pendergrass Agriculture and Veterinary Medicine Library, U Tennessee.

August 15, 2003

in-Cites, Project Links

:: From in-Cites: The 20 Most-Cited Countries in Geosciences,
January 1993-April 2003
, and Microbiology journals ranked by impact.

:: Project Links: Mathematics and It's Applications in Engineering & Science

    "Integrating the concepts of higher math with their applications in science and engineering lies at the heart of Project Links' mission. Our method relies on interactive web-based modules used in the classroom to engage students in guided learning--providing students with a unique experience unavailable in traditional lecture or textbook lessons.

    One of the primary goals of this project is to more closely integrate mathematics into engineering and science topics in the classroom. As a result, each module must be designed to be used in both a math course and a non-math course."

    Even a cursory look at this website is enough to hint at the exciting content. It is well laid out and well thought out, equally approachable from a mathematics or a science & engineering viewpoint. (From: SciTech Library Newsletter.)

July 10, 2003

Internet Bird Collection (IBC)

The Internet Bird Collection (IBC) is a non-profit endeavour with the ultimate goal of disseminating knowledge about the world's avifauna. It is an on-line audiovisual library of footage of the world's birds that is available to the general public free of charge. While the initial aim is to post at least one video per species, the long-term objective is to eventually include several videos showing a variety of biological aspects (e.g. feeding, breeding, etc.) for every species.

The idea to create the IBC came about through the contact its creators have had with other bird watchers who use video recorders during their trips. It is becoming increasingly apparent that the current trend is for birdwatchers with varying degrees of dedication to videotape the species -both common and rare- that they see during their trips to all corners of the world. This material is obviously not of much use to the global birding community if it is kept at home. Yet, if it is gathered and made accessible to the public via the Internet, it could surely constitute a valuable source of information for birders, ornithologists, conservationists, etc. In short, the essential goal of the IBC is to initiate a collective project that will only be of use if it is truly just that. In other words, the key to the success of the IBC lies in the hands of yourselves, the users.

The advantage of this medium, the Internet, is that it enables the information provided to be accessed from anywhere in the world, thus making it possible for bird lovers across the globe to see species they might not have had the opportunity to observe had the IBC not been created. Those ornithologists who travel extensively will also find this a useful tool, as it will allow them to get a preview of the birds they plan to see before they begin their travels.

Given that the aim is for the website to be as dynamic as possible, the intention is to up-date it with new videos on a daily basis (save weekends). This of course depends on the participation of the IBC users. The quality of one's video should not act as determent from sending in footage; no video is "not good enough" and no species is "not interesting enough" for this website - any and all information is valuable and helps to attain a greater understanding and knowledge of these interesting animals.