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Current Issue - May 15, 2008 (Vol. 28, No. 10 )

BEST OF THE WEB

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In each print issue of GEN, our Best of the Web columnist reviews selected websites of interest. Dr. Ahern's informed and humorous opinions, now available online, make for one of Genetic Engineering & Biotechnology News most popular features.* Suggestions of websites for review are welcome and should be addressed to .

We've created a database of past reviews, making it quick and easy for you to find websites in a specific category of interest. To view the Best of the Web Database, click here.

  • Key
  • Strong Points
  • Weak Points
  • Ratings
  • Excellent
  • Very Good
  • Good
  • Very thorough, well organized
  • Figures uninspired
  • Rating
  • Biochemistry Course
  • www.med.unibs.it/~marchesi/subjects.html
  • The title of this one won’t win any prizes, but it is otherwise a nicely put together online set of information about biochemistry. Organized for teaching a course at the University of Brescia in Italy, the site greets visitors with a generic, gray opening page peppered with hyperlinks to numerous areas of biochemistry interest, including hemoglobin, DNA metabolism, muscle biochemistry, and many more. Over 50 aspects of the subject are covered. Clicking on a hyperlink brings up long pages of information including figures describing the topics in detail. While I wouldn’t use the material at the site as the only source of information for teaching the subject, I do find it to be an outstanding supplement to the material I cover in my courses. The only downside besides the vanilla interface is that the figures are pretty plain-Jane. Otherwise, this is a superb site.
  • Good coverage of topic
  • Nothing significant
  • Rating
  • Eicosanoids
  • www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/prostag.htm
  • If there’s a class of biochemicals whose effects are more diverse than those of the eicosanoids, I don’t know what it would be, other than perhaps the steroid hormones. The eicosanoids are 20 carbon compounds derived from arachidonic acid that are commonly associated with pain and inflammation. They include the prostaglandins, the thromboxanes, the prostacyclins, and the leukotrienes. They are implicated in processes as diverse as asthma (leukotrienes), uterine contraction (prostaglandins), and platelet stickiness (thromboxanes). Some of them like prostaglandins have been of tremendous interest over the past decade or so in general pain and are a target for NSAIDs such as aspirin, ibuprofen, and the now out-of-favor Cox II inhibitors like Vioxx. On the Eicosanoids page, what you think you’ll get is just what you do get. Sometimes it’s good not to be surprised, and this is one of those times. The site does a great job of going over the various forms of these compounds and the effects they produce. A very informative site even if the subject itself is rather limited in scope.
  • Great for programmers
  • Needs more breadth
  • Rating
  • Inforbiomatica
  • www.moseshohman.com/blog
  • Inforbiomatica is an interesting blog on software development. Hosted by Moses Hohman, the focus is primarily on bioinformatics and discussions are, not surprisingly, techie in nature. That may be putting it mildly. Let’s just say that if you’re not a programmer, you’ll probably have your head spinning as you look through the offerings of the site. Programmers have a language all their own, so it is useful for bioinformatics programmers to have a place to exchange ideas, such as here. Not everything is programming-related, though. Some of the posts are almost philosophical in nature. I liked the random category where he discusses the derivation of the word “meteorite;” in Korean it literally means star feces. As you can probably gather, there is a lot here to like, and archives dating back to 2004 are available for viewing. Worth a look-see, even if you’re not a programmer.
  • Interesting software
  • Narrow focus
  • Rating
  • Propeller Twist Blog
  • fjossinet.u-strasbg.fr
  • From Fabrice Jossinet, an assistant professor at the Université Louis Pasteur in Strasbourg, comes this blog dealing with Sequence to Structure (S2S)—a software to “display, manipulate, and interconnect RNA data from the sequence to the structure.” For the uninitiated, this may be a little vague, so I’ll try to interpret. The aim here is to provide RNA researchers with relevant structure information. RNA of course is very different from DNA in several respects. Most of these derive from alternative base pairings enabled by replacing T with U, the 2´ oxygen of ribose (not in deoxyribose), and the usually single-stranded nature of RNA. As a result of these differences, there are a lot more considerations to predicting RNA structure over DNA structure. Indeed, RNA can form much more elaborate 3-D structures than duplex DNA. S2S is written in Java to facilitate cross-platform usage and currently runs on Linux and Mac OSX systems. At the site, visitors can download the software for free and learn a lot more about it than I can describe in this limited space. Definitely worth a look if you’re interested in RNA structure.
  • Abundance of well-organized information about Japan
  • Needs to have more scientific content
  • Rating
  • Science Links Japan
  • sciencelinks.jp
  • If you’re looking for evidence that English is the universal language of science, you’ll have to go no further than Science Links Japan, which is not only written completely in English, but a Japanese translation isn’t even visible at the site. Self-described as a “Gateway to Japan’s Scientific and Technical Information,” Science Links Japan lives up to its billing as a central point of access to science in the country. The opening page splits coverage among topic areas of News, Press Releases, Opinions, and Links. It also provides access to a bibliographic database and links to over 450 journals, institutes, job info, and a database of researchers. Whew. This site takes no prisoners. Subsections are too numerous to mention but they include intellectual property links, online journals, surveys, and white papers relevant to Japan over 30 portal sites. If you’re looking for info about Japanese science, you’ll almost certainly find it here.
  • Thorough approach
  • Most parts need beefing up
  • Rating
  • Virtual Chembook
  • www.elmhurst.edu/~chm/vchembook
  • In terms of virtual content, Virtual Chembook is a sprawling effort from Elmhurst University that goes beyond the bounds of chemistry. The opening page, which is visually uninspiring, has topic areas arranged into three main categories in table form: General Chemistry, Organic/Biochemistry, and Miscellaneous. Underneath those are dozens of subtopics, including Solutions/Solubility, Molecular Geometry, Carbohydrates, Enzymes, Global Warming, and Drug Chemistry. Clicking on subtopics brings up primary information, which is adequate but not as in-depth as that in the previous site and of limited use for teaching, other than for parenthetical, basic information. While Virtual Chembook is good, the individual subsections are somewhat lacking, making yet another case where the whole is greater than the sum of its parts.

*The opinions expressed are solely those of the author(s) and should not be construed as reflecting the viewpoints of either the publisher, Genetic Engineering & Biotechnology News, the Mary Ann Liebert, Inc., publishing house, or employees or affiliates thereof.

 

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