Wednesday, February 27, 2008

New Book Profile: Population Ecology

New Book Profile

Title: Population Ecology: An Introduction to Computer Simulations (QH352.B458 2003: New Book shelf)
Author: Ruth Bernstein
Publisher: Wiley
Year: 2003
159 pages

Aimed at undergraduates with no prior experience, this text provides simple, straightforward instruction for using MATLAB to explore simulations in ecology, conservation, and population biology. Chapters include step-by-step code, as well as explanations of the equations used to create simulations. Each chapter has a specific goal dealing with topics such as population growth, population invasions, the Leslie Matrix, predator-prey dynamics, foraging, and more. Each chapter's exercise is meant to take no more than 2 hours, and the stepped approach is designed to keep the focus on the topics being studied rather than the computational aspect.

Tuesday, February 26, 2008

Visual biology protocols

I was reading The blog this morning and learned that Current Protocols from Wiley-Blackwell will collaborate with the Journal of Visualized Experiments to include video protocols in the journal. As cool as this sounded, I wondered more about Journal of Visualized Experiments (JoVE). I hope I am not the last one at Eckerd to discover this open access resource.

JoVE is an open access online journal that publishes biological experiments via video. The journal was developed in an attempt to alleviate some of the lengthy learning curve for new experimental methods. In addition, according to JoVE, the videos should assist issues of "reproducibility of biological experiments."

The first issue was published in December 2006 and since May 2007 has been published on a monthly basis. Site navigation is straightforward with options for exploring by issue, by category, or editor's picks. Categories are listed as follows:

  • Basic Protocols
  • Neuroscience
  • Developmental Biology
  • Cellular Biology
  • Plant Biology
  • Microbiology
  • Immunology
In addition, the option to subscribe by RSS feed is available.

Video articles also contain written instructions and a table for materials that includes company name and catalog number. I watched the Editor's Pick:
The fascinating and concise (~12 min.) video provided both microscopic images and animation to illustrate the techniques. The last section of the video involved a discussion of the techniques from the viewpoint of the lab assistant. In addition, there is a place for viewers to add comments or ask questions.

Perusal of a few videos seems to indicate that most are less than 20 minutes and some are less than 10 minutes, which makes them feasible for classroom or pre-experiment view, the latter being a suggestion made by a lecturer in a comment on blog.

Submission guidelines, of course, include the rules for making submission. In addition, they include a small section on how to cite one of the videos. There is an editorial review process for videos. The international editorial board consists of professors from Harvard, University of Kyoto, Centre National de la Recherche Scientifique, and more highly respected institutions.

Monday, February 25, 2008

Discussion on a gene-centric view of life

The provides an opportunity to hear a discussion between Craig Venter and Richard Dawkins, which took place at the Digital, Life, Design conference January in Munich.

Richard Dawkins published the groundbreaking work The Selfish Gene, which is available from our library, call number QH 437 .D38 1989.

Craig Venter was head of the team that decoded the human genome. One of his many projects today is collection and cataloging of genes from the ocean.

Some of the topics broached included the concept of the gene as information that can be stored digitally and rebuilt in laboratories. Possible applications discussed were the development of new energy sources that could help what some scientists deem an upcoming energy crisis. Another topic was the transfer of genes, not just between same species, but between other species, and possibly with extraterrestrial organisms. Audience members were also encouraged the question Venter and Dawkins. At the, people interested in this revolutionary discussion can watch it, or they can read the entire transcript.

Friday, February 22, 2008

Friday Fun: The T.W.I.N.K.I.E.S. Project

During a strenuous exam period, two students at Rice University set up a number of experiments entitled

Using the well-known snack cake, Christopher Scott Gouge and Todd William Stadler conduct numerous tests:

  • Rapid Oxidation Test
  • Solubility Test
  • Maximum Density Test
  • Resistivity Test
  • Gravitational Response Test
  • Radiation Test
  • Turing Test
Check it out!

Wednesday, February 20, 2008

Harvard votes for open access

In a great boon for the Open Access movement, the faculty of Harvard's College of Arts and Sciences has adopted a policy requiring researchers to provide their articles for an open-access institutional repository. Following NIH's new policy, this seems to represent major forward momentum in the efforts to revise the current publishing paradigm. In my opinion, it would be difficult and likely damaging to journals to refuse to publish NIH or Harvard researchers. Therefore, more journals should be looking at their copyright policies and allowing authors to place of peer-reviewed, published articles into open-access repositories. Perhaps some journals will decide to follow open-access publishing models, such as BioMed Central, many of whose journals are gaining rank in Journal Citation Reports.

For a Chronicle of Higher Learning report and very interesting commentary from major detractors, such as the president of the American Association of University Publishers Sandy Thatcher, to important promoters, such as Ray English, Director of Libraries at Oberlin College, visit their news blog.

For the text of the policy, visit Peter Suber's Open Access News blog.

Swarthmore, a college classified similarly to Eckerd by the Carnegie Foundation, published an editorial urging its students to follow Harvard's lead.

Students and faculty interested in learning more about open access should visit the SPARC (Scholarly Publishing and Academic Resources Coalition) Web site. I would also be happy to come to a class or have a discussion lunch to discuss this issue.

Issues in Science and Technology Librarianship webliography on Open access

Friday, February 15, 2008

Statistics Library

Started in 1989 as an email service, StatLib is evolving into a powerful Internet tool. Hosted by Carnegie Mellon University and maintained by Pantelis Vlachos, a research scientist in Carnegie Mellon's Department of Statistics, StatLib contains freely available software and data sets for statisticians. The majority of both the software and data sets are affiliated with a published papers or books. For example, one dataset is described as

A collection of the data sets used in the book Analyzing Categorical Data, by Jeffrey S. Simonoff, Springer-Verlag, New York, 2003.
To fully understand the context and/or development of the resources, articles can be obtained from the library or Interlibrary Loan. Software is divided mainly by method, such as MATLAB extensions, multivariate archive, and more.

In addition, the site provides access to the Data and Story Library (DASL). Searchable by topics and statistical method used, DASL offers stories that are linked to data files.
Stories are abstracts that discuss the statistical concepts of a particular datafile. (from DASL)

Thursday, February 14, 2008

I heart Eckerd

Happy Valentine's Day!

Hearty links for Eckerd:

Wednesday, February 13, 2008

Make 2009 a Year of Science

Polls indicate that national scientific literacy is low in the United States. In an effort to engage and teach the public about scientific activities and research, the Coalition on the Public Understanding of Science (COPUS) was formed between universities and colleges, scientific organizations, businesses, media, and museums and libraries. The group is planning the 2009 Year of Science showcase as part of their effort.

Local participants include the Science Center of Pinellas County and the Pinellas County Environmental Land Division. Some planned activities for the year include the following:

  • AAPT High School Physics Photo Contest
  • Cafe Scientifique
  • Darwin Day
  • Launch of the Understanding Science Web site
COPUS is looking for more participants and events to make this a real national occasion. I think it would be excellent if NAS registers any events that they have planned, and perhaps even plan some events in conjunction with other local participants.

Monday, February 11, 2008

The Elements Song--Animated

I am thrilled that so many classes are coming to see me this semester. Unfortunately, it also means I have been spending a lot more time planning than blogging! I promise to have so more substantial blog posts soon, but to entertain you for now, visit Mike Stanfill's animated version of Tom Lehrer's Elements song. It's catchy and fun!

Wednesday, February 6, 2008

New Web of Science interface finally here

As promised, when you log in to Web of Science, you will now see the new interface pictured below:

Recorded classes are available from the vendor, Thomson ISI, at the following links:

Students or faculty should feel free to sign up for any classes. In addition, I am available to help you, your study group, or an entire class. Contact me to set up a time.

Monday, February 4, 2008

Ocean energy

An interesting article in today's St. Pete Times reveals the efforts the state and entrepreneurs are making towards a new alternative energy through ocean turbines. According to the article "Gulf Stream Turbines Might Whirl Out Energy" by David Adams, turbines on the bottom of the ocean situated within the Gulf Stream could produce as much as a third of Florida's energy. However, the application of this idea is still some way off. Major donors, including the state of Florida, are becoming involved in research done at Sea Tech, Florida Atlantic University, and a prototype might be tested later this year to determine effect on fish populations. To read the entire article, go the the library home page. Use the drop database menu to access America's Newspapers. Choose St. Petersburg Times, and search on the title of the article.

Friday, February 1, 2008

New twist on classroom assignments

While perusing another science librarian's blog, I came across an entry introducing his ninth-grade son's blog: Space Exploration and Us! I bring this to the attention of the Eckerd community because I think it is a great way to use new technology in the classroom. In this case, the student decided that the active component of his semester-long project would be this blog. Eckerd students might find this an unusual way to approach one of the less restrictive writing assignments they are given. Approach your professor with this idea and see what they say. Direct them to this blog if you think it will help!

In addition, I can see professors using this model to introduce unique assignments to classes, especially those classes where writing a research paper does not seem to fit. As a liberal arts college, we often question whether students are getting enough writing experience, especially those in the sciences. For example, chemistry professors often do not see writing assignments fit into some of their classes. However, with a blog, students could explore one topic over an entire semester. And the blogs would serve a study guides for the entire class. Or math professors--who often struggle with students who aren't majoring in math--could have students write an interdisciplinary blog that explores how math integrates with their chosen major.

Another Web 2.0 idea is the wiki. At Eckerd, we have our own academic wiki, and NAS' own Steve Weppner serves as its extremely helpful and knowledgeable guru. For a class in the humanities, I helped a professor create a wiki template for his class to complete as part of their project. This sort of assignment could easily be adapted for the sciences, and again, would serve a student-created study guides for final exams.