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.