Monday, December 17, 2007

Happy Holidays

Season's Greetings and
a Happy New Year!

Like the rest of the college, the library is closing down until January 2. I will be out until January 14 because I will be going to Dallas, Texas, in the beginning of January for an NCBI course on Molecular Biology Information Sources. The blog will be on hiatus until then (unless I get some incredible news that has to be spread immediately). Have a safe and festive break!

Wednesday, December 12, 2007

New Book Profile: The Periodic Table

New Book Profile

Title: The Periodic Table: Its Story and Significance QD467.S345 2007 (New Book shelf)
Author: Eric R. Scerri
Publisher: Oxford University Press
Year: 2007
249 pages

Dr. Eric Scerri, lecturer in the Department of Chemistry and Biochemistry at UCLA, has written a book that explores the development, both historical and philosophical, of the periodic table of elements. In addition, the book examines the relationship between chemistry and physics. Scerri states in his introduction

One can still consider the more modern question of whether chemistry reduces to its sister science of physics...It is this question that forms the underlying theme for this entire book, and it is a question that is addressed more and more explicitly in later chapters as the story reaches the impact of modern physical theories on our understanding of the periodic system. (p. xviii)

Ten chapters begin with the historical origins of the table, including the concept of an element and its changing meaning throughout early scientific thought, continue through Mendeleev's predictions, to the impact of the nucleus and atomic number, and finally to modern quantum mechanics and astrophysics. Written in a manner accessible to students with some knowledge of chemistry, this book will provide a fascinating basis for students about to embark on more serious study of chemistry and/or physics, whether one agrees or disagrees with Scerri's premise.

A Nature (Q1.N2) magazine review of the book

Bensaude-Vincent, B. (18 January 2007). Display elements. Nature 445, 263-4.

discusses Scerri's argument that chemistry cannot be simply reduced to physics. Although the reviewer finds the introductory historical overview somewhat cliched, she approves of later arguments, especially those surrounding the discovery of isotopes and Niels Bohr's atomic model.

This may be an interesting book to take home for the holidays. Remember the library's holiday hours
Wednesday until 1 am
Thursday until 1 am
Friday until 5 pm
December 15-16 CLOSED Semester End
December 17-18 8:30 a.m. - 5:00 p.m. Semester End

Monday, December 10, 2007

Science Debate 2008

A group of concerned scientists, who saw a lack of scientific questions posed to the presidential hopefuls, formed a coalition calling for a debate on issues related to

  • environment
  • health and medicine
  • science and technology policy
Dr. Lawrence Krauss, professor of physics and astronomy at Case Western Reserve University and chair of the Physics Section of the American Association for the Advancement of Science, published an explanatory Op-Ed piece in the Wall Street Journal, regarding the need for presidential debate on these topics.

Considering the impact the presidency can have policy in science (just a few examples), it seems prudent to learn presidential candidates knowledge and opinions on science:
Vergano, D. (2007.) Science vs. politics gets down and dirty. USA Today
Howden, D. (2007). No Blair! America's Parting Gift to Britain's PM. The Independent.
Rosenberg, D. (2002). The Battle over Abstinence. Newsweek.

Awards for the best lab site

The Scientist, an online magazine for the life sciences, held a contest to find the best laboratory sites. After 60 nominations, the judges chose the top ten sites for life science research labs--based on design, usability, content, and community. The judges were scientists, art/creative directors, and professors. The Scientist's finalist site links to the top sites, and provides individual judge comments for each site. The sites highlight some great research with unique and clever Web designs that include images, diagrams, and multimedia presentations. The purpose of the contest was to focus on the important work of disseminating research information in a vital and approachable manner.

Thursday, December 6, 2007

Global Climate Change talks

I wish I could have reported this to you sooner because some of the talks have already passed. Nature is hosting a Global Climate Change Series in Second Life, the online world being used for just about everything from art exhibits to scholarly lectures, and a whole lot more (there is even a library island staffed with real reference librarians in Second Life). Nature's space in Second Life, aptly called Second Nature, has two more speakers coming in this series:

  • Tues 11th Dec, 6pm GMT, 10am PST, SLT
    Dr Simon Buckle, Director of Policy at the Grantham Institute for Climate Change
  • Thur 13th Dec, 5pm GMT, 9am PST, SLT
    George Monbiot, Guardian columnist and author of Heat: How we can stop the planet burning.
Fly your avatar out there for what I expect will be fascinating lectures.

Tuesday, December 4, 2007

ILL into your e-mail

Because this is the NAS Collegium blog, I usually limit my posts to items of interest for those in the Natural Sciences. Today, however, as the Interlibrary Loan Librarian as well, I want to let you know about an exciting, new feature from Interlibrary Loan. We now have the capability to send documents electronically. Therefore, if a lending library sends us the document electronically (which many do), we can now convert the file to a PDF and send it straight to your e-mail. You will no longer have to wait for delivery via campus mail. The article will arrive immediately. Hurray! Let me know if you have any concerns over this new method of delivery. Otherwise, the e-mails will start arriving in your inboxes. Keep an eye out for them!

Update January 31, 2008: The new process has been successful so far. However, one problem with the new system is that we receive no verification that patrons receive their article. Therefore, if you have not received an email from us updating you on the status of your article or the article itself within 10 days, please contact myself or my assistant Liz Bodie: bodieea at eckerd dot edu

Friday, November 30, 2007

Endnote Web Training

In a previous blog post, I notified you of the availability of Endnote Web. I have said it before, and I will say it again...using a bibliographic citation manager can simplify your writing process dramatically. With Endnote Web, you can take the same group of citations and output them using a variety of specific journal styles or more generic styles such as the Council of Science Editors or the American Chemical Society. In addition, you can share your research easily, even leaving notes for your colleagues in the record for a particular article. Apparently, Thomson Scientific is overwhelmed with requests for lessons on Endnote Web. Therefore, they are offering a number of free Webinars through December. I attended one of these Webinars a few months ago and found it very useful. I highly recommend them for getting a basic understanding of the application. It will last about 45 minutes to an hour, and because it is a live Webinar, you have the ability to ask questions of the trainer. Dates are as follows:

  • Tuesday, December 11, 2007 , 2:00 pm, Eastern Standard Time
  • Wednesday, December 12, 2007, 2:30 pm, Eastern Standard Time
  • Thursday, December 13, 2007, 10:00 am, Eastern Standard Time
  • Thursday, December 20, 2007, 10:00 am, Eastern Standard Time
  • Thursday, December 20, 2007, 2:00 pm, Eastern Standard Time
To register, click here.

Wednesday, November 28, 2007

Biology Image Library

A subscription database launched by BioMed Central, Biology Image Library contains images, illustrations, and movies related to

  • Development Biology
  • Histology & Pathology
  • Immunology
  • Microbiology & Parasitology
  • Molecular & Cellular Biology
  • Neuroscience
  • Plant Biology
Resources found within the Biology Image Library are peer-reviewed to ensure quality. Professors and students can create image sets that can be implemented as a slideshow or downloaded for other educational purposes. Individuals can try the library for two weeks by visiting In addition, it would be possible to have a trial for Eckerd College if people seem interested. Please e-mail me if this sounds like an option you would like to try.

Tuesday, November 27, 2007

Introducing Nonlinear Biomedical Physics

A new open-access journal titled Nonlinear Biomedical Physics is being published by BioMed Central. The journal, founded by Zbigniew Czernicki, will focus on articles that offer a

  • better understanding of the physiological origin of complex nonlinear dynamics of living systems
  • calculation of quantitative measures of complex spatial and temporal behaviour and classification of different physiological and pathological states through nonlinear analysis of biosignals (EEG, EMG, HRV)
  • studies of the feasibility of applying complexity measures as diagnostic tools in Medicine, to characterize changes induced by pathologies, administered drugs, photo-therapy, anaesthesia, etc. by comparing experimentally observed behaviour with mathematical models' predictions and computer simulations
  • collective phenomena, self-organized ordering and synchronisation in biological systems
  • bioelectromagnetic phenomena and biomedical devices such as biosensors and pacemakers
  • nonlinear, non-Newtonian fluids in the body - respiration, blood circulation, CSF, lymph

Articles will be peer-reviewed by two experts within three weeks, a quick turn-around. After acceptance, the articles will be published online and immediately available through PubMed. This provides excellent exposure for authors, and easy access for students.

For more information, read the editorial from the Editors-in-Chief (one of whom is from our own state!):

Zbigniew Czernicki, Polish Academy of Sciences Medical Research Institute, Department of Neurosurgery, 80 Ceglowska Str., Warsaw, Poland

Wlodzimierz Klonowski, Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland

Larry Liebovitch, Florida Atlantic University, Center for Complex Systems and Brain Sciences, 777 Glades Road, Boca Raton, FL 33431, USA

Tuesday, November 20, 2007


Being a vegetarian, I thought gourds would better represent my Thanksgiving celebration. I do plan to make a baked squash polenta dish that I have never tried before. I am leaving tomorrow for Thanksgiving on Cedar Key in a cabin with a canoe.

I wish you all a happy celebration with your friends and family! See you next week!

Monday, November 19, 2007

Experiment with a free online citation manager: Connotea

Recently I have had a few discussions with other librarians and a faculty member about the possible effect of full-text access on serendipity. The young faculty member was especially concerned that students wouldn't have the experience of flipping through a journal and finding something unexpected that alters one's outlook or focus on research. Yet, in a recent meeting including students, the students all said they wanted full text access. Sometimes both print and electronic access is prohibitively expensive. Will we lose serendipity along the way?

After these conversations, I began to consider information seeking behaviors. In many studies, it has been shown that amongst faculty an "invisible college" exists, whereby much of their information comes from colleagues and conferences. Students, not yet part of the larger scientific network of their discipline, lack this access...and one may think then that serendipity should play an important role in their explorations. However, the Web is becoming more social, and perhaps that can make up for the serendipitous discovery in the library.

Take, for example, Connotea . I wrote a paper in library school on the value of social bookmarking in academia, and then promptly set it aside. I think I have shown Connotea to only one class in my library instruction this semester. I realized that is likely because I don't think of it as the type of research tool where you get the article you are looking for; rather to me it is a vehicle for exploration...and maybe that serendipitous discovery.

Connotea...what is it? Connotea is a

free online reference management for clinicians and scientists

With Connotea, you can save and share citations with your colleagues. Think of it as bookmarks that are accessible through any computer because they are Web-based. Some people might be familiar with or furl (which is the application where I place the NAS links). Connotea is a similar concept with a focus on academic citations.

Where does the exploration and serendipitous discovery come in? Connotea is searchable. You can search on a subject, a user, or a tag. For example, I searched on "crustaceans" in honor of a reference question that I had a few nights ago. Eleven article citations were found. In addition, though, the people who have these articles in their citations have tagged them with descriptive words or phrases. Connotea lists these hyperlinked tags. Some of the tags for the article I found were
  • Molecular Evolution ~ Molecular-Ecological Adaptation
  • crustaceans
  • toxicology
  • Vibrios
  • Phreatoicopsis raffae
  • Infection and or Contamination Control
  • research
  • Taxonomy~Phylogeny
  • Madagascar
  • Pathogen Characterizations and or MisCharacterizations
  • uploaded
  • Environmental disturbances-vector proliferation
Furthermore, the user names for the people who saved these articles are also hyperlinked. This allows you to click on a tag that interests you to see what articles might also have been given this tag. You can also click on the user name of the person who saved an article you found to be of interest. That way you can see what else he or she is reading. From there you might click on one of his or her other tags, and discover another user whose interests match your own. It is an expanding network. You can even subscribe to an RSS feed for a person or tag you would like to follow.

So I wouldn't recommend this to a student deep into their research necessarily, but I would recommend it to a student just exploring topics, looking for the focus for their own research. In addition, of course, I recommend it to anyone who might want to keep track of their citations online. Personally, I tend to prefer a bibliographic citation manager such as Endnote for this purpose because it creates a bibliography, but one nice thing about Connotea is your references can be exported into one of those programs.

Happy explorations!

Friday, November 16, 2007

Arsole, Dickite, and Erotic Acid...Oh my!

It's been a while since we've had a Fun Friday entry, so today I bring you Molecules with Silly or Unusual Names. Dr. Paul May from the University of Bristol has collected three Web pages worth of unusual molecule names. Many have equally amusing pictures illustrating the silliness. However, in addition, with the right plug-ins the 3-D structure files for the molecules can be downloaded.

Wednesday, November 14, 2007

Geology of the Everglades...

I have decided to occasionally profile new books that are added to our collection. Today's selection is the following:

Petuch, E. J., & Roberts, C. E. (2007). The geology of the Everglades and adjacent areas. Boca Raton, FL: CRC Press.

Petuch, Professor of Geology, and Roberts, Associate Professor of Geology, at the Department of Geosciences, Florida Atlantic University (Boca Raton, Florida), wrote 7 chapters detailing the geological development of the Everglades from late Paleogene to Holocene Southern Florida. The preface of this 212-page book acquaints us with the Everglades through an evocative line,

There is but one Everglades on this planet...
This work identifies the Everglades as a marine environment that must be studied from an oceanographic perspective. According to Petuch and Roberts, what was essentially an enclosed sea was flooded 12 times, providing layers of unique ecosystems.

The introduction serves as both a historical overview and a literature review. Students will find the exposure to the historical aspects of the geological foundation to the Everglades useful to understanding and researching its formation.

The book also comes with a DVD that includes and Powerpoint and a Quicktime video depicting the development of the Florida peninsula using simulated space shuttle photography.

Students at Eckerd are likely to find this book especially fascinating as it deals with areas close to home. In addition, most of the research on the area is relatively new, providing fascinating exposure to the development of an area of study within geology.

Tuesday, November 13, 2007

Eigenfactor measures journal influence

As I have mentioned in a previous blog post, Eckerd College does not subscribe to Journal Citation Reports (JCR) from Thomson ISI. JCR give the impact factors for journals indexed by Thomson ISI. Because we are looking at some of our indices and databases, I wanted a way to recognize commonly used journals in certain disciplines. I discovered a recent article by an associate professor of biology at the University of Washington:

Bergstrom, C. G. (2007). Eigenfactor: Measuring the value and prestige of scholarly journals. College & Research Libraries News 68(5),314-316.

Bergstrom (2007) discusses an algorithm for ranking journal that is similar to the manner in which Google ranks Web pages. Citations stand in for hyperlinks in tracing influential journals. Bergstrom and colleagues call the ranking, Eigenfactor, and make it freely available at The Eigenfactor looks at citations over a five-year period, and measures

the importance of a citation by the influence of the citing journal divided by the total number of citations appearing in that journal (Bergstrom, 2007, p.314).
According to Bergstrom (2007), the Eigenfactor indicates the amount of use a journal is getting by scholars. It is unclear whether scholars or researchers are thought to be faculty only, faculty and graduate students, or include undergraduate students also.
A second measurement calculated is Article Influence, which more closely correlates to ISI impact factor. The Article Influence
is proportional to the Eigenfactor divided by the number of articles (Bergstrom, 2007, p. 315).
Finally, the application compares actual journal prices with their influence.

At, an additional feature allows interactive mapping of the scientific flow of information. The image below is a static map of the sciences in 2004. To create this map, 6,362,307 citations were partitioned into 82 modules. For more information on mapping, see the paper: M. Rosvall and C. T. Bergstrom (2007) Maps of information flow reveal community structure in complex networks arXiv physics.soc-ph/0707.0609v1

Monday, November 12, 2007

Training for new WoS interface

A trainer from Web of Science will be here in January to train for the new interface. I know it seems like ages ago that I first discussed the new interface on this blog. The interface was originally going to be rolled out sooner, but now we can expect to see it in January. However, if you have not had a chance to work with it yet, you can access the new interface from the current one. There is a button at the top of the screen that will link you to the new interface.

The training will be Wednesday, January 16 from 1:30-3 at the library. Students and faculty are welcome. Let me know if you are interested in attending.

Monday, November 5, 2007

Credo Reference added to virtual Reference Shelf

Eckerd College has recently purchased Credo Reference, an online interdisciplinary reference resource. Credo Reference is available to all members of the Eckerd community on campus, or off campus, by using your e-mail user name and password.

To reach Credo Reference, choose the link Reference Shelf from the home page (as seen below).

Once you reach our virtual reference shelf, you will see Credo Reference as the first link listed under Encyclopedias and Dictionaries.

In Credo Reference, you can search all 289 reference books, or you can narrow your search to all the science reference books (complete title list below), or one particular reference book. Many results have images or even video links included. For example, I searched "Comet" in the Astronomy Encyclopedia to find an entry on Comet Holmes, which has been prevalent in recent news. In addition to an entry on this comet, more than 100 other entries, many with images, were available.

Credo also include concept map searching. The image below shows an example concept map for photosynthesis. Each dot represents a concept that is linked to photosynthesis. This feature is a fun way for you to explore larger concepts that you are trying to focus for a research paper. To see a larger image of the concept map, click on the map.

The science titles included in Credo are listed below:

  • Academic Press Dictionary of Science and Technology
  • Astronomy Encyclopedia
  • Atlas of the Universe
  • Collins Dictionary of Astronomy
  • Collins Dictionary of Biology
  • Dictionary of Astronomy, Peter Collin Publishing
  • Dictionary of Developmental Biology and Embryology, Wiley
  • Encyclopedia of Paleontology
  • Guide to Gems
  • Guide to Global Hazards
  • Guide to Minerals, Rocks and Fossils
  • Guide to Seashells of the World
  • Guide to Stars and Planets
  • Guide to the Oceans
  • Illustrated Dictionary of Science, Andromeda
  • McGraw-Hill Concise Encyclopedia of Science and Technology
  • McGraw-Hill Dictionary of Scientific and Technical Terms
  • Reader's Guide to the History of Science
  • The American Heritage Science Dictionary
  • The Cambridge Dictionary of Scientists
  • The Macquarie Dictionary of Trees & Shrubs
  • The New Penguin Dictionary of Science
  • The Penguin Dictionary of Mathematics
  • The Penguin Dictionary of Physics

Thursday, November 1, 2007

Open collection of crystal structures

Following the supposition that crystal structures are facts, and therefore not subject to copyright, Nick Day, while a PhD student, developed CrystalEye. CrystalEye collects the Crystallographic Information Framework (CIF) files from published articles. Using a web spider, CrystalEye gathers these files from five publishers: Acta Crystallographica, American Chemical Society, Chemical Society of Japan, Elsevier, and Royal Society of Chemistry. Currently, nearly 100,000 structures reside on CrystalEye. Future plans include aggregation from institutional repositories.

CrystalEye provides several access points to its data. You can search either by using simplified molecular input line entry specification (SMILES) or cell parameters. In addition, you can browse by journal and issue. Results are neatly packaged in a clickable chart form (see image below--click on image to see it larger).

Clicking the summary will yield more information, such as the DOI number of the article containing the structure, data collection parameters, refinement results, as well as a javascript application that allows you to change the number of unit cells along an axis and view the structure.

As a big proponent of using RSS feeds to collect information that personally appeals to you, I was thrilled to see the RSS feed function available. You can subscribe to a feed by journal, compound class, atoms, or bonds. For example, you can subscribe to a feed that will notify you of any CIF files added to CrystalEye that contain a bond between aluminum and silver.

CrystalEye also create histograms for bond lengths involving different atoms. The histograms are clickable so you can be linked to the structures that fit the specific parameters you clicked on.

For people interested in the development, technology, and future plans for the beta site, Day has a wiki page with more information.

Wednesday, October 31, 2007

Happy Halloween From NSF (and me)

Happy Halloween, Eckerd!

It's a grey, windy day, perfect for this spooky night. The National Science Foundation has put together a "ghoulish" newsletter. Find out why we like scary movies, how to be eco-friendly for Halloween, and the truth behind monsters.

Tuesday, October 30, 2007

The best of algal blooms

If you're a marine science or environmental studies student interested in marine issues, and you are not familiar with SeaWeb, I would like to introduce you to this excellent resource via algal blooms. Red tide...It's something we know well here on the coast. A family I know lives on Boca Ciega Bay, and a bad red tide can mean dead fish on their little beach, horrendous smells, and more.

SeaWeb was mentioned in another recent blog post, as the sponsor of the the Marine Photobank. SeaWeb is a nonprofit working for healthy oceans. The Web site is full of information and resources, such as its program "Too precious to wear," which highlights the plight of corals being used for jewelry and furniture accessories.

One of my favorite resources offered by SeaWeb is Ocean Citations. Ocean Citations lists literature on topics dealing with marine and coastal environmental issues. The 2007 list on algal bloom contains 17 citations from high-profile journals such as Limnology and Oceanography and Ambio. At least 3 of the articles study Florida and the marine areas near Eckerd. Other topics for citations include marine mining, introduced species, fisheries, and more. What an easy way to find specific resources!

In addition, users can sign up to receive updates on citation lists and others valuable resources. If we don't own a journal, remember you can always order the article on interlibrary loan. Take a moment to check out the best of 2007 in algal bloom literature and surf around SeaWeb to see how it can help you in your studies.

Saturday, October 27, 2007

Scitopia reaches final version

It has been a crazy week with meetings for me first in Ohio and then in Fort Myers. Therefore, instead of my take on the new Scitopia, I am going to direct you to an excellent article in Information Today. In brief, Scitopia has improved the XML to provide more exact results. The patent search includes Japanese and European patents, as well as those in the United States. In addition, the article claims that in comparison to one expensive database, the coverage is better. No names are used but at Eckerd, I know for our subject guides, I will be directing you to Scitopia over a few smaller search pages such as SIAM or AGU, since Scitopia covers their content.

Friday, October 19, 2007

Biological and ecological data comes recommended

NatureServe Explorer was brought to my attention through a reference librarian journal, Reference & User Services Quarterly. According to the review,

With its colorful Web site and troves of animal, plants, and ecological data, NatureServe, a nonprofit conservation organization, is a superb resource for academics and members of the public.
From my experimentation with the Web site, I feel Eckerd students studying animals and plants from an environmental perspective will find this free site extremely helpful. The Online Encyclopedia of Life provides information on 70,000+ species of plants and animals. Information is not comprehensive for all entries, however many entries include conservation status, distribution, ecology & life history, and population delineation. Maps and images are also prevalent. For example, I decided to search for Roseate Spoonbill because I saw one on campus the other day. The search allows common or scientific names. As shown in the distribution map below, populations in Illinois (dark blue) are "presumed extirpated," in Florida (orange) are "imperiled," in Mississippi (red) are "critically imperiled," in Louisiana (yellow) are "vulnerable," and in Texas (green) are "apparently secure."

Ridgely, R.S., T.F. Allnutt, T. Brooks, D.K. McNicol, D.W. Mehlman, B.E. Young, and J.R. Zook. 2003. Digital Distribution Maps of the Birds of the Western Hemisphere, version 1.0. NatureServe, Arlington, Virginia, USA.

You can also search by ecological systems as defined by ECOLOGICAL SYSTEMS OF THE UNITED STATES: A WORKING CLASSIFICATION OF U.S. TERRESTRIAL SYSTEMS . I found this search more difficult to use, but the option to search by state was effective. In this manner, I was able to access data about the ecosystem "Southwest Florida Dune and Coastal Grassland." I learned the vegetation distinctive to this area, as well its lack of distinctive animal species.

It is important to choose "New Search" even if you have moved from one search tab to another. Otherwise the parameters of your first search seem to remain.

A second component for this product is InfoNatura, which provides information on birds, mammals, and amphibians in Latin America. My first search was for Galapagos Sealion, since I had a student Meebo me a question on these mammals a few days ago. I was curious to see how much this might have helped the student. I was disappointed to find the information on this animal very limited. On subsequent searches within InfoNatura, I found some species with more data, but overall this aspect of the database seemed less extensive than what is available for North America and Canada.

Thursday, October 18, 2007

Formula of belief

An exhibit put together by The World Question Center and the Serpentine Gallery in London displays the formulas, equations, or algorithms from more than 80 scientists and premier thinkers. At once, it reminded me of the "This I believe" media project, whereby people offer their deeply held beliefs in a oral essay. Yet, these formulas are much simpler, much more exact, and in some ways, more beautiful. The breadth of formulas is astounding: from ones describing the path to happiness to work philosophies to formulas I can't understand at all. Take a moment to check them out for yourself. Make sure to scroll to the bottom of the page to see the full set. And if, by chance, you are inspired to share your own formula, I would be happy to put it up on this blog.

Tuesday, October 16, 2007

Open Access publishing for Eckerd

As a participant in The Oberlin Group, a consortium of liberal arts college libraries, Eckerd College is a Supporter Level member of Biomed Central (BMC). What does this mean for our researchers? We receive a discount for publishing in any one of 182 peer-reviewed, open access journals published by BMC. As a supporting member, The Oberlin Group has its own Web page, where its researchers are featured. Functionality on the page filters articles that Oberlin Group researchers have published recently, as well as articles that have been accessed the most within a month and a year. This feature provides extra exposure to authors from Oberlin Group institutions.

According to BioMed Central, some of the reasons for publishing in a BMC open-access journal are the speed of publication, international exposure, a highly dedicated promotional process undertaken by BMC, inclusion in major bibliographic indices (e.g., PubMed), and now, and the addition of a Thomson ISI impact factors for some journals. Additional promotion is available through BioMed's "Highly accessed" designation, which can be mentioned as a measurement when authors refer to their work.

Authors for BMC retain copyright over their own work through a Creative Commons license. Work published in BMC journals are made available for free through BMC permanently. Works are archived in various locations so if BMC loses control of its works, open access articles will remain available through other venues.

Some of the recent titles from Oberlin Groups researchers include the following:

Toward the automated generation of genome-scale metabolic networks in the SEED
Matthew DeJongh1, Kevin Formsma1,2, Paul Boillot1, John Gould1, Matthew Rycenga3,4 and Aaron Best2

  1. Department of Computer Science, Hope College
  2. Department of Biology, Hope College
  3. Department of Chemistry, Hope College
  4. Department of Chemistry, University of Washington
BMC Bioinformatics 2007, 8:139 doi:10.1186/1471-2105-8-139

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas
Nichole L King, EricWDeutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B Martin, Bong Kim, Hookeun Lee, Brian Raught, and Ruedi Aebersold

Abstract: We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.

Genome Biology 2006, 7:R106 (doi:10.1186/gb-2006-7-11-r106)

Monday, October 15, 2007

Blog Action Day!

photo/Rob Partington for CC:Attribution-ShareAlike

I have to admit, I forgot about Blog Action Day in which participants would blog about environmental issues on October 15, 2007. Fortunately, as karma would have it, this weekend, my significant other and I made some environmental pledges to ourselves. Baby steps, as we say. It seems appropriate to discuss some of them on Blog Action Day. There are more than 16,000 blogs participating, and that doesn't include people like me who never registered their blog. The resources for Blog Action Day are excellent. I particular like TreeHugger's How to Green Guides, including How to Green Your Pet; How to Green Your Meals; and How to Green Your Sex.

So what are we doing? We are riding bikes or public transportation at least 3 days a week to work. Furthermore, same rules apply for anything within 5 miles of our house. No more running out for milk in the car. If we have more shopping than can fit on a bike, we plan it around other car activities, such as a day when someone might be driving to work. We are no longer using disposable napkins or sponges. We have cloth napkins, and I am knitting washable cotton cloths for cleaning dishes. We will hang up a clothesline instead of drying our reusables in the dryer. Finally we joined the new Pinellas Sweetwater farm, community-supported organic farming.

Is this all that can be done to promote a sustainable lifestyle? Not by a long shot! But with smaller goals, we can work toward a greener way to live. Once we incorporate a few lifestyle changes, perhaps others will become easier. We have decided on a reward if we stick to our goals. If it works, I will report in about 4 months.

I would love to hear some of the things Eckerd students are doing to keep the campus green.

Friday, October 12, 2007

2007 Nobel Peace Prize

Because the Peace Prize this year has been awarded for efforts to disseminate and collate information on global change, I thought it appropriate for this blog. Both the Natural Sciences Collegium and Eckerd College have been proponents of environmental wellness. This year's award will be split between Al Gore Jr. and the Intergovernmental Panel on Climate Change (IPCC). The IPCC was established in 1988 by the World Meteorological Organization and the United Nations Environment Programme. The organization publishes assessments based on peer-reviewed literature. Al Gore has dedicated a portion of his career to the effects of climate change, most recently with a book and an Academy-award winning movie.

Wednesday, October 10, 2007

2007 Nobel Prize in Chemistry

German surface chemist Gerhard Ertl is the single recipient of this year's Nobel Prize in Chemistry. According to the Royal Swedish Academy of the Sciences,

This year’s chemistry laureate Gerhard Ertl has succeeded in providing a detailed description of how chemical reactions take place on surfaces and has in this way laid the foundation of modern surface chemistry. He is awarded the prize for showing how reliable results can be obtained in this area of research.

Surface reactions are vital in many processes today
  • in catalytic cleaning carbon monoxide oxidates on platinum,
  • freons used in air conditioning systems, for instance, reduce the ozone layer by reacting on the surfaces of small ice crystals,
  • rusting takes place when an iron surface is exposed to oxygen,
  • surface reactions are used in the electronics industry to manufacture semiconductor materials for components,
  • artificial fertilizers contain ammonia which is produced when nitrogen and hydrogen react on an iron surface,
  • renewable fuels can be produced using catalytic surfaces.

Image and quotes from The Royal Swedish Academy of Sciences. (2007). Information for the public: the Nobel Prize in Chemistry 2007. Retrieved from

Ertl laid the groundwork for a branch of chemistry that is difficult to quantify, yet has extremely practical applications. Ertl's modelling of hydrogen reaction on metal surfaces in the 1970s advanced conversations on catalytic mechanisms. A much more thorough discussion of Ertl's contributions for both scientists and the public is available here.

Tuesday, October 9, 2007

2007 Nobel Prize in Physics

(pictures from Nobel

The Nobel Prize in Physics will be split between a French and a German physicist, Albert Fert and Peter Grunberg, respectively, for

the discovery of Giant Magnetoresistance
With this discovery, the ability to read data on hard drives became more refined, and therefore, applicable to smaller storage devices such as your ipod. The Nobel Prize Web site has an excellent article on the science behind Giant Magnetoresistance (GMR) available here.

Monday, October 8, 2007

Marine photos available for educational use

The Delray Beach, Florida, ocean outfall discharges 13 million gallons per day of treated sewage up-current of a coral reef./ Jim Cagle, Palm Beach Reef Rescue/Marine Photobank

Marine Photobank provides easily accessible images of human effect on marine life. Photographers--some professional, some amateur,some researchers from universities and nonprofits--furnish photos of sea lions wrapped in filament, otters blanketed in oil, corals bleaching, hurricanes swirling over land, and many more. According to the organization's mission statement:

The Marine Photobank aims to literally shed light through photos on pressing marine issues and human-related impacts on the ocean ecosystem.

In frustration over the lack of compelling images, philanthropist and photographer Wolcott Henry joined Green Media Toolshed to collect images that document the widespread destruction throughout the world's oceans and coastlines. In 2004, the photobank became part of SeaWeb, a nonprofit advancing the cause of ocean conservation.

Users can register to both download and upload photographs. There are two types of download registrations, one in which you designate your photo use as nonprofit (e.g., in an educational context) and one in which you designate your use for the media or other for-profit use. Upon registering for nonprofit, your membership must be accepted by the organization. In my case, this took approximately 24 hours. I did not register to upload photos, but students and faculty who spend time photographing research may want to contribute to this database.

Photographs will be excellent for presentations made by either students or faculty on marine and coastal issues. The site offers an extensive collection of exceptional, vivid, and troubling images. The images are arranged in subject galleries, such as Reefs in Peril, Deep Sea Habitat, and Coast Development, which makes for easy browsing. In addition, the search function permits searching by keywords, concepts, or photo ID number.

Some images have been turned into "photo stories," which may be best described as downloadable informational posters on a marine issue. In addition, educational materials for classroom use are under development. Another cool feature is the photo wishlist. Members can request certain images. Currently, there is a lengthy wishlist, so prospective photographers also might be interested to see what members wish for.

Furthermore, I see Marine Photobank serving a social/networking function also. Photographers are listed, some with biographies and contact links. Many of the photographers are also researchers, providing a method of finding people studying issues that you might also find interesting, hope to study, or are studying yourself.

2007 Nobel Prize in Medicine or Physiology

This morning the Nobel Prize for Medicine or Physiology was awarded to Mario R. Capecchi, Martin J. Evans, and Oliver Smithies for

their discoveries of "principles for introducing specific gene modifications in mice by the use of embryonic stem cells"

An excellent summary and illustration of the research done by these scientists is available at the Nobel Prize Web site. The prize money will be split equally three ways between Capecchi, who is a U.S. citizen born in Italy, Evans, a British citizen, and Smithies, a U.S. citizen born in the United Kingdom.

Friday, October 5, 2007

The house that Flickr built

This Friday I bring you a super cool demo for an application under development called Photosynth. Microsoft Labs architect, Blaise Aguera y Arcas, demonstrates how Photosynth reconstructed a three-dimensional model of Notre Dame using photos from Flickr.

Thursday, October 4, 2007

Computational Science for the classroom

Computational Science Education Reference Desk (CSERD) is dedicated to introducing students to computational science, especially through its use in the classroom. According to CSERD, computational science involves the use of a computational architecture in combination with an algorithm to solve a scientific problem. For a more thorough definition, as well as a model, see the article from CSERD at CSERD is a partnership of National Science Digital Library, the Virtual Reference Desk, and the Gateway to Educational Materials.

At the CSERD site (, both students and faculty can browse resources by subject, educational level, resource type, audience, or any configuration of these. In addition to providing resources, CSERD offers the opportunity for students and/or faculty to review and add resources. Once a user registers at no cost, they are able to conduct the following tasks:

Ask and answer questions in the forum.
Review material in the catalog.
Add items to the catalog.
Submit modules to be included in CSERD's resources.
Submit in depth verification, validation, and accreditation reviews.

CSERD tracks user participation and will submit letters to appropriate administrators regarding contribution.

Wednesday, October 3, 2007

NCSE promotes evolution education

September 29 through October 6 marks the American Libraries Association's Banned Books week. In honor of this event, I did a brief database search on the censorship and science. One idea the emerged was the national discussion on evolution versus creationism/ intelligent design in science classrooms of public schools. Therefore, I decided to introduce a Web site that, in the organization's words, educates "the press and public about the scientific, educational, and legal aspects of the creation and evolution controversy, and supply needed information and advice to defend good science education at local, state, and national levels." This organization is the National Center for Science Education (NCSE). Often in my library instruction, I discuss the evaluation of Web sites and their possible bias. In this vein, I would like to note that this organization is firmly on the side of evolution as necessity in science classrooms. Therefore, arguments for the teaching of creationism are not present.

The Web site for NSCE includes news on the debate divided by state and national issues, an events pages, and a resources page. In addition, the journal of the organization Creation/Evolution Journal is available in full text from 1980-1990. Furthermore, full text to some important works on this topic are also available, such as Eugenie C. Scott's article "Antievolutionism and Creationism in the United States" (Annu. Rev. Anthropol. 1997. 26:263-89).

Friday, September 28, 2007

Vote for the cutest baby animals

For a little Friday cheer, take a minute to check out's cute baby animals. Take the opportunity to see a baby anteater, porcupine, and panda. C'mon, who doesn't love baby animals?

Thursday, September 27, 2007

Endnote Web available to Eckerd

Endnote Web is a bibliographic citation manager available within Web of Science (Science Citation Index). As a web-based application, it is available from any computer, and it easily integrates with Endnote on your desktop. Use of Endnote Web requires a FREE registration through Web of Science. As long as you are affiliated with Eckerd, this account will remain available to you. It can hold up to 10,000 references.

Once you have logged into your account, you can import references from Web of Science seamlessly. However, you can also import from other databases. Generally this involves saving the reference as a text file, and importing, using one of the provided filters within Endnote Web. The filters correspond to individual databases. In addition, the option to enter references by hand is also available.

After importing references, they can be arranged in folders that you have created. References can be stored in one, or more than one folder, when applicable.

Endnote Web will utilize stored references to create a bibliography. The bibliography will be output according to your specifications: the folder you choose, the style you choose, and the output format you choose. More than 100 journal styles are available for your choice, as well as more encompassing styles, such as ACS or APA. The same folder of references can be formatted for one journal style and then reformatted for another. In addition, bibliographies can be output as HTML, rich text, or plain text.

A final feature available with Endnote Web is the Cite While You Write downloadable plug-in for Microsoft Word. This will allow you to add citations directly into your text, which will be formatted by the program. Then the citations are used to create you bibliography. This eliminates common mistakes, such as spelling an author's name one way in the text and another in your reference list. In addition, using this software, you will know that all references you cited are in the bibliography.

Personally, I am a fan of Refworks, another Web-based bibliographic utility, but it is not free. This program comes with our Web of Science package and can be used by all students and faculty. I am available for training on this utility. Just give me a call!

Tuesday, September 25, 2007

Blog celebrates National Chemistry Week

National Chemistry Week will be celebrated October 21-27 this year with the theme "The Many Faces of Chemistry." A Science and Technology librarian at Iowa State University has launched a blog in honor of the event. In addition, a facebook group has been started for people interested in celebrating chemistry.

Monday, September 24, 2007

Free tutorial covers academic publishing process

More on publishing...PRIMO, the Peer-Reviewed Instructional Materials Online Site of the Month, chose Publish, Not Perish for August. This tutorial was created by librarians at the University of Colorado. Five modules address the oft-confusing world of scholarly publishing. Module 1 covers the scholarly communication field as a whole, spending extra time on new business models, such as open access. This module would be helpful for undergraduate students, as well as grads and new faculty. It gives an overview of the types of journals and journal articles that are being published, and that a student might access for class research. Modules 2 to 5 move from the broad overview into process-based approach for publishing. These sections of the tutorials are better suited for graduate students and new faculty who plan to publish soon. Tips include better ways to manage your time, how to conduct journal research, and where the ideas come from. The final module offers advice on how to create a personal publishing plan. This can help modulate fear and provide a working goal. The tutorial will take at least an hour to complete so set aside some time to work through the exercises. To access Publish, Not Perish, visit At the start of the tutorial, you are asked to enter your campus information. People not affiliated with University of Colorado can put "Other" and then the name of their own institution. There is no charge for the tutorial.

Thursday, September 20, 2007

New approach to citation measurement

I was recently asked about a journal's impact factor. Eckerd does not subscribe to Journal Citation Report from Thomson ISI, which presents impact factors in a neat package. I have spent some time, definitely not enough, looking into other measurements and measurement systems. I found an interesting, free, downloadable program by Anne-Wil Harzing, called Publish or Perish, that uses Google Scholar for calculations over Thomson ISI. The program calculates citations per paper, per year, as well as the h-index and g-index (Leo Egghe, Theory and practice of the g-index, Scientometrics, Vol. 69, No 1 [2006], pp. 131-152; Harzing offers a white paper comparing the use of Google Scholar and Thomson databases for calculations. According to Harzing, some of the major advantages to Google Scholar include the capture of articles in non-ISI-indexed journals and capture of book chapters, whereas some of the problems associated with Google Scholar include capture of nonscholarly works and length of time between updates.

I conducted a little experiment with one of our Marine Science professors, Shannon Gowans. Using Web of Science Cited Reference Search from 1999 to 2007, I found she had 68 citations to 9 articles. Using Publish or Perish, I found 154 citations to 10 articles. This is a large difference, and I am curious as to the reasons. I hope to look more into this topic, especially if it will help Eckerd faculty.

Wednesday, September 19, 2007

APA provides examples for digital resources

The best feature to the new APA style guide are the numerous examples for uniquely electronic resources. In the past, we were guessing at the way a blog should be listed in our references. Now we have examples for not only blogs but also e-books, gray literature, white papers, raw data, course materials, preprints, and online bibliographies, to name only a few. APA also strives to simplify the electronic reference process. The name of the database where you retrieved an article is no longer necessary, unless it is an unknown or limited location. The retrieval date can be left off articles or books that are in their final form. To save space, home page URLs are favored for online reference sources, over lengthy addresses to the exact article. I guess APA thinks we, as researchers, are intelligent enough to look up a particular article once we get to the home page of a reference resource. Another major change is the use of Digital Object Indentifiers (DOI) over URLs when possible. DOI numbers, as they are commonly called, were created to assign a permanent identifier to an electronic object that may change title, URL, etc. The DOI number should be a constant form of identification. Journals that use DOI numbers will place the number on the first page of the article. An example of a DOI number can be seen below.

To read more about DOI numbers, see

Tuesday, September 18, 2007

WebCam provides glimpse of underwater research

The St. Petersburg Times featured an article about Aquarius Reef Base. Starting Monday, six researchers will be eating, sleeping, and conducting research under the Atlantic, south of the Florida Keys. In addition, the scientists will have classroom sessions via a live feed. The article from Associated Press detailing the mission is available here. NOAA's home page for the Aquarius base is The schedule for the shows can be located here.

Picture from Associated Press

Monday, September 17, 2007

I Can't Believe It!

I started out writing a very different blog post this morning, but with Eckerd internet acting a little funky, I decided to wait on my posting. That gave me the time to discover something entirely different. "Top" lists are extremely popular in our culture, from David Lettermen to the chain-letter-like Internet "memes." Alex Boese has published on his site the Top 20 Most Bizarre Experiments of All Time. Boese maintains the Museum of Hoaxes Web site, however this list is based on his actual research for a book titled Elephants on Acid: And Other Bizarre Experiments.

While each experiment mentioned is truly disturbing, I think what I found to be the most disquieting were the two-headed dog and monkey-head transplant experiments. The fact that the United States looked at an experiment where a puppy's head was grafted to a larger dog as a challenge in science experimentation--a challenge which lead to the grafting of a monkey head onto a different body--seems unbelievable. The Cold War era inspired such terror in people that many decisions were questionable at best. The McCarthy trials were, of course, the seminal example, but the advent of these experiments shows how far Cold War fear drove even so-called rational disciplines.

Friday, September 14, 2007

Dino burgers anyone?

For a little Friday fun, I thought you might enjoy a little comic strip offering an alternative explanation to the extinction of dinosaurs:

Wednesday, September 12, 2007

Free webliographies created by librarians

ISTL Web guides:

Science and Technology librarians have their own journal called Issues in Science and Technology Librarianship (ISTL). A regular feature in this journal is the webliography. Librarians create Internet-accessible annotated lists of resources in science- and technology-related disciplines. The webliographies are peer-reviewed. Students and faculty alike may find some interesting and formerly unknown resources by perusing these guides. Keep in mind that some of these guides date back to 1997. However, the date is clearly visible so you will know the age of the information before accessing the web guide.

Tuesday, September 11, 2007

APA Style Electronic reference

American Psychological Association has published a supplement to its 5th edition style guide. It is called APA Style Guide for Electronic Resources. The library has purchased a copy. It is available via PDF, and at this time, we are not sure how we will allow people to access it. To purchase your own copy, visit

I am working on figuring out the new parts of the style, and I hope to be able to let people know soon. I have already heard that APA is recommending DOI numbers instead of URLs. Soon I will be asking NAS faculty at Eckerd which style guide they ask their students to use, since I have noted we do not own the Council of Science Editors manual or the American Medical Association manual.

Friday, September 7, 2007

Play the virtual autopsy game

For Friday fun, I thought I would introduce you to the virtual autopsy game ( This game was created at the University of Leicester in England for undergraduate students in th Clinical Division of Pathology.

Eighteen cases are available for students to study. First, you are presented with a case history.

After reading the case history, you can click on the interactive cadaver to see what was discovered in the autopsy.

Once you have completed your "autopsy," You can try to determine the cause of death. Many choices are offered, and when you get one wrong, there are hints to help you make a better choice.

So have fun this Friday!

Wednesday, September 5, 2007

Societies join to create federated search

Although active for a few months now, I thought many people at Eckerd might not be aware of Scitopia. Scitopia ( offers free federated searching throughout 13 scholarly societies. The federated search engine allows access into the digital libraries of member societies. Member societies include the following:

  • Acoustical Society of America
  • American Geophysical Union
  • American Institute of Aeronautics and Astronautics
  • American Institute of Physics
  • American Physical Society
  • American Society of Civil Engineers
  • American Society of Mechanical Engineers
  • American Vacuum Society
  • The Electrochemical Society
  • The Institute of Electrical and Electronics Engineers
  • Institute of Physics Publishing
  • Optical Society of America
  • Society of Automotive Engineers
  • Society for Industrial and Applied Mathematics
  • SPIE

Once citations have been located, Scitopia will connect to the full text if we subscribe to the journal electronically. This should work automatically if you are in the library or on campus. From off campus, you will have to log in using your Eckerd email address. For example, I searched for an article from the Journal of Applied Physics. Searching by title, I was able to pull up the citation and link directly the article PDF.

What happens if you cannot access the full text? There are two options. First, check to see if the journal is available in print from Eckerd College Library. If not, you can order the article through interlibrary loan. Not sure how to do that? Chat with me on Meebo via my home page. Visit the library Web site, click on staff and then my name for all contact info.

Tuesday, September 4, 2007

Peer review for students

I recently discovered an education resource that proposes to lessen the time a professor reads papers by creating a system of peer review. Calibrated Peer Review (CPR) was created by Orville L. Chapman, a Professor of Organic Chemistry at UCLA and a member of the National Academy. For future scientists, this seems a wonderful way to gain understanding of the peer-review process and the varied aspects of scholarly communication.

The process follows a four-step process. Students will write an essay or paper. They will then work through some calibration essays to understand how to review the work of others. Next, the students will evaluate their peers, and finally they evaluate their own work. This entire assignment yields a scored result via the program.

In addition, a library of assignments is available through the CPR database. Sample assignments are available at the Web site. Although CPR can be used by any discipline, sample assignments are predominantly in the sciences. This resource may be helpful for professors at Eckerd College who are trying to incorporate writing into classes that do not traditionally use writing. For example, the following assignment was developed for calculus:

Title: Calculus I: Damped Oscillator

Assignment Goals
The goal of this assignment is for students to

* read and understand the verbal description of a physical situation, in particular that of a damped oscillator,
* modify a mathematical model based on physical assumptions,
* explain relationships between representations, in particular between the physical situation, the formula modeling it and its graph,
* articulate mathematical ideas and techniques using appropriate vocabulary,
* read critically and assess the reasonableness of mathematical assertions, and
* evaluate the students' own writing and that of their peers for completeness and correctness.

In addition, professors can build their own assignments. Eckerd College is not signed up for CPR, but it easily could be. Let me know if you are interested.

Monday, September 3, 2007

Happy Fall Semester!

On the first day of the Fall semester, I want to welcome back students and faculty. Remember I am here to assist you with research and instruction. Best of luck to you all.

Thursday, August 30, 2007

Sign up now for library instruction

I've already seen upperclassmen and -women unloading their cars while relieved freshmen, finished with their Autumn Term class, play baseball in their bare feet outside the library windows. The Fall Semester is nearly upon us, and as you finalize your syllabi, remember to include library instruction. I prefer to design instruction around your class assignments so give me a call or send me an e-mail so we can chat. The library classroom is already being booked so if you want to have your preferred time, get in touch with me as soon as possible. However, instruction is most effective when it can be immediately applied to an assignment. If your major research paper is not due until the end of the term, you may want to put off instruction for a month or so. Or plan two instructions, one as an introduction and then a refresher/Q&A class when your students are in the midst of the assignment. Furthermore, if you prefer, keep in mind that I can teach in your classroom if you have access to the Internet and a projector screen.

Tuesday, August 28, 2007

Live science from a researcher near you

YouTube is famously popular. Who hasn’t gotten links to hilarious, pathetic, or just plain strange YouTube videos in their email?

The National Science Foundation, Public Library of Science (PLoS), and the San Diego Supercomputer Center have teamed up to launch what bloggers and journalists are billing as the “YouTube for Scientists.” In SciVee, scientists can upload multimedia video podcasts that are associated with papers that they have published on PLoS. SciVee is structured to build communities among scientists through communication and discussion surrounding shared research interests. The SciVee “About Us” ( page has an excellent graphic that demonstrates their mission well:

I have watched a couple of videos on SciVee. There are not many, however this resource has only been available for about a week. Time will tell whether scientists will find this method of communication useful and comfortable. From what I have seen, there are differences in presentation quality and approaches. Some have chosen to give a straightforward lecture, while others have used photographs, slides, music, and animations to illustrate their paper. For example, in a video linked to a paper entitled “Order in Spontaneous Behavior” by Alexander Maye, Chih-hao Hsieh, George Sugihara, Bj√∂rn Brembs, I was able to see video of a fruit fly glued to a mechanism that measured head movements. This video illustrated the author’s device much better than a written description.

I am interested to see how the scientific community takes to this new dissemination medium. I hope the Eckerd community will check it out and leave me some comments.

SciVee (

Scifinder Scholar 2007 expands search features

The 2007 version of Scifinder Scholar has a number of new features to simplify your research process. Now when you locate a substance, you can extend your search by clicking on the structure.

In this screenshot, by clicking on cyclobutane, a drop-down menu for a number of search possibilities appears. By choosing, “explore” or “refine” you will automatically open the drawing window where you can alter the chemical structure to conduct more searches. The drop-down also offers you a number of other options. For example,

when you click on references, you are offered choices to create a more precise search (as seen below). Using the provided subject categories, one can search cyclobutane associated with adverse effect, including toxicity.

Another new feature is categorize. The categorize feature will analyze the subject terms of references you have retrieved and provide bar graph analysis per subject word. Using this analysis, you can combine subcategories to further refine your search. Scifinder Scholar has provided a PDF documenting slides on these new features. To access the slides, click here.

In addition, to sign up for webinars from the vendor, visit here.

Remember, I can instruct your class on this or other databases. Contact me to set up a lesson.

Thursday, August 23, 2007

New interface for Web of Science

ISI Web of Science has thoroughly updated its user interface. Presently, the old version and the new version are running concurrently. To access the new version, you have two choices:

1. Go to the library home page. Choose "Web of Science" from the drop-down menu QUICK JUMP: GO DIRECTLY TO A DATABASE. Once you have entered the old version, click the button on the top of the screen to access the new version.

2. Use the following URL from a computer on campus:

Upon entering the new version, the most noticeable feature is the availability of several search boxes (Figure 1). In addition, additional databases, such as ISIHighlyCited are no longer present on the introductory page. To access additional resources, one must use the “Additional Resources” tab. The new interface implemented by ISI Web of Science mimics some familiar databases owned by Eckerd College, such as Wilson’s General Science Full Text. The drop-down menu to the right of the search boxes allows the user to choose specific options, such as topic, author, language, and several more.

Figure 1. Initial search interface for the new version of Web of Science (click to see a larger image)

In addition, the results screen offers more new elements (Figure 2). A sidebar easily allows you to refine your results by subject areas, document types, authors, and more. An “Analyze Results” buttons provides a bar graph of your results filtered by your choice of data.

Figure 2. Results screen

Web of Science vendor Thomson Scientific is offering recorded training demos that you must sign up to access at In addition, I have acquired some Powerpoint slides on the new interface, which I can send to you if you email me: Don’t forget, though, your friendly librarian is always available to give instruction to you or your classes!

Tuesday, August 21, 2007

Zotero keeps track of your research

When I was in grad school, I wrote my first paper using handwritten notecards. It had been ten years since I was in school. I thought someone must have created an electronic research tool. I downloaded a few trials from, however I did not find a system that allowed me to keep my citation information linked to my notes, something that would allow me to search my own notes, capture screen shots that would link to citation information, or let me drop that citation information into my research paper with a simple mouse click. Zotero, created at the Center for History and New Media at George Mason University, claims to do all of these things. (Of that I have graduated).

Zotero is a Firefox plug-in that works with your browser window. Free to users, it downloads in a matter of minutes. This morning I downloaded the plug-in and began using it for some research on chronic daily headache.

Click the screen shot above to see the full screen with Zotero in use. Notice the notes attached to the article Managing the "difficult" headache patient. I have experimented for a short time this morning, but initially I feel that the potential for this tool is great. However, I have not used it enough yet to see how well it lives up to its potential. I will continue to use it in my daily work and post an update in a month or so.

For those interested, there is a video tour on the zotero site:

If you do test it out, let me know what you think of it.