Friday, May 30, 2008

Blog hiatus

As May draws to a close, the students are gone, and many of the faculty are leaving as well. I, myself, will be gone part of June and all of July. Therefore, the NAS Library News blog will be on hiatus for the next two months. I will return in August with news for Autumn Term. Have a wonderful summer!

Tuesday, May 27, 2008

Time to vote for Eckerd

It is time for The Scientist's survey on the Best Places to Work in Academia. Click here to take part. You may have to register (it's free) to reach the article. Sometimes, I am asked to log in and sometimes I am not.

Sunday, May 25, 2008

Mars library a gift to future explorers

Mars as taken by the Hubble Space Telescope. Photo Credit: NASA, Dr. Nicholas Short's Remote Sensing Tutorial.

When I was in library school, an administration class had us creating our own libraries, that is, collection development, writing position descriptions, working with budgets, describing mission, etc. A friend and fellow graduate assistant created a library in space. It was generally known as the most far out (no pun intended) and clever library planned in the class, at least in my time at USF. However, it was also considered by some to be the least likely to ever exist. As of today, though, Mars will play host to a library of earthly creations. The Planetary Society has created the Vision of Mars library on DVD, which traveled to the planet on the rover Phoenix. The press release from the Planetary Society has information about the contents and purpose of the library.

Friday, May 23, 2008

Chemistry on your MP3 player

The Chemistry Heritage Foundation produces weekly podcasts on the past, present and future of Chemistry. The show, Distillations, in production for about half a year, is hosted by a historian and former naval officer Robert Hicks. Episodes are just over ten minutes long and cover a wide range of topics, such as entropy, pharmaceuticals, color, nutrition, and more. The podcasts are accessible to laypeople with an interest in chemistry and a basic upper middle school science education. Every topic features a related element, and references are provided for each week's topic to permit further study on topics of interest.

Wednesday, May 21, 2008

Tutorials for Gene Research

Through a collaboration between MIT Engineering and Science Libraries and Harvard's Countway Library, brief video tutorials of UCSC Genome Browser and NCBI BLAST are now available. The UCSC Genome browser provide access to reference sequences for a number of genomes. Tutorials provided for this browser are as follows:

  • Getting DNA Sequence
  • Using Annotation Tracks
  • Intron-Exon Boundaries
  • Searching with BLAT
NCBI's BLAST is a tool for nucleotide or protein comparisons. The tutorials related to BLAST are as follows:

  • BLAST Link
  • Do I Need BLAST? The Use of the Related Sequences Tool
  • Nucleotide BLAST
  • Nucleotide BLAST: Algorithm Comparison

Tuesday, May 20, 2008

Life Sciences search engine: NextBio

Image from NextBio content:

According to its FAQ page, NextBio
makes massive amounts of disparate biological, clinical and chemical data from public and proprietary sources searchable, regardless of data type and origin, and empowers scientists to quickly understand their own experimental results within the context of other research.
NextBio provides an open access platform for biology research with excellent search and organizational features. A smart search box displays the most likely terms as you type (see below), identified by categories, such as tissue, gene, disease, etc.

Results are displayed by summary allowing the researcher to refine through drill-down options in various categories. Results include raw data and literature from various public resources and any contributed data from individual scientists. A fabulous demo of basic features is available from the creators so I will not explain the entire process here.

NextBio offers free registration that turns on organizational features. Once registered, you can bookmark, organize, and make notes on your search results. In addition, you can upload your own data for comparison if you permit that data to be accessed. If you want to keep your data private, a fee is assessed. A number of large research institution, both private and educational, are using NextBio for project coordination and collaboration.

Tuesday, May 13, 2008

Presentation on Open Science Notebook

Jean-Claude Bradley, Associate Professor of Chemistry at Drexel University, spoke on Open Science Notebook at the 5th Annual Scholarly Communication Symposium: Scholar2Scholar: How Web 2.0 is Changing Scholarly Communication. The webcast for this presentation is available for free. This presentation focuses on the use of open application for science collaboration and dissemination. Bradley's work involves the synthesis of new anti-malarial agents. He glosses over the research itself, however those interested can reach his experiments via his open notebook.

He touts openness as a way to make experimentation easier through collaboration. In addition, the data published can be used by other researchers to, for example, create their own hypothetical models. Another way such information is being used is for classroom lab components that can be cross-referenced with the experimental process reported originally.

Bradley also discusses how the technology is useful for keeping records and noting changes to experiments, promoting funding efforts, and discussing peer-reviewed literature. In addition, through the use of open technologies, dissemination is done through large engines like Google.

The webcast is about 30 minutes with corresponding slides.

Friday, May 9, 2008

Good luck on exams...

Hurray! the last day of classes. We just had our library party for work scholars and spirits were high. Classes are over! Remember that the library is open late tonight and tomorrow night, until 1 am, and opening early on Sunday (10 am). We will be open Sunday to Thursday until 1 am as usual. Best of luck next week as you complete your exams next week!

Thursday, May 8, 2008

Cleaner interface for arXive

IOP (Institute of Physics) has developed an interface known as eprintweb for accessing e-prints uploaded to arXive. In its beta form, eprintweb offers an easier, better-looking platform for accessing eprints in 17 physical and mathematical disciplines.*

Features available in eprintweb include the following:

  • RSS feeds: By subscribing to a particular feed channel, researchers can remain informed of newly submitted papers.
  • Personalization: After signing up for a free account, users can create bookmarks and email alerts, as well as customize settings
  • DOIs: Linking through DOI number to the published article is available
Search features mimic common database interfaces, providing several search boxes with drop-down menus to identify your search area, whether it be author, title, subject, affiliation, abstract, and more. Boolean logic (AND, OR, NOT) can be used to further refine search statements. In addition, the archive allows user to browse by date and subject category, and the author tab permits easy browsing by category and author name.

For students unfamiliar with eprints and preprints, it is important to note that some of the material may not have been peer-reviewed. According to Richard Luce(1), the term "preprints" generally describes either material that has been accepted for publication or material submitted but has yet to be accepted (or rejected). In arXiv, the papers often have comments describing their publication status, but not always. Richard Luce(1) identifies eprints as preprints, published works, and unpublished works distributed electronically by an author, often for archiving purposes.

*Categories are as listed:
  • Astrophysics (astro-ph)
  • Condensed Matter (cond-mat)
  • Computer Research Repository (CoRR)
  • General Relativity and Quantum Cosmology (gr-qc)
  • High Energy Physics - Experiment (hep-ex)
  • High Energy Physics - Lattice (hep-lat)
  • High Energy Physics - Phenomenology (hep-ph)
  • High Energy Physics - Theory (hep-th)
  • Mathematics (math)
  • Mathematical Physics (math-ph)
  • Nonlinear Sciences (nlin)
  • Nuclear Experiment (nucl-ex)
  • Nuclear Theory (nucl-th)
  • Physics (physics)
  • Quantitative Biology (q-bio)
  • Quantum Physics (quant-ph)
  • Statistics (stat)
1. Luce, R. (2001) E-prints intersect the digital library: inside the Los Alamos arXiv. Issues in Science and Technology Librarianship, 29. Retrieved May 8, 2008, from

Monday, May 5, 2008

Science and the presidential election

Members of the scientific community likely have concerns that should be important to all U.S. citizens as the election nears. The American Association for the Advancement of Science has created a guide for Science and Technology in the Presidential Election. Each of the major party candidates, as well as some lesser known candidates and former candidates, are profiled, using their campaign Web sites and other news sources as noted. Issues are covered in xx categories:

  • Competitiveness and Innovation
  • STEM (science, technology, engineering, and math) Education and Workforce
  • Better Health for Americans
  • Energy and Environment
  • National and Homeland Security
Full-text reports are available as well as links to relevant news stories. In addition, this guide is a portal to additional resources provided by a number of organizations.

Friday, May 2, 2008

Friday Fun: Insultingly Stupid Movie Physics

The weather is gorgeous, my office smells like gardenias (courtesy of another professor), and all in all, it is a day to enjoy life, possibly through some harmless mocking. Enter Insultingly Stupid Movie Physics. This site--and as of December 2007, a book--examine the plausibility of action seen in movies. The authors, self-proclaimed technonerds, have developed a simple rating system:

  • GP = Good physics in general

  • PGP = Pretty good physics (just enough flaws to be fun)

  • PGP-13 = Children under 13 might be tricked into thinking the physics were pretty good; parental guidance is suggested

  • RP = Retch

  • XP = Obviously physics from an unknown universe

  • NR = Unrated. When a movie is obviously a parody, fantasy, cartoon or is clearly based on a comic book it can't be rated but may still have some interesting physics worth discussing.

Newer movies are reviewed individually in addition to treatises on generally bad movies physics, such as explosions, laser beams, flashing bullets, etc.

Not without educational merit, the site also offers information on movie physics in the classroom and recommendations for people interested in studying basic physics on their own (i.e., adults who never took physics or at least don't remember actually taking physics, and now wish they did).

Get together with your physics study group this weekend, choose a good physics movie to watch, and discuss those concepts that are sure to show up on your upcoming final exams.