Tip of the Week: Searching for Microbes by Characteristic
Recently I was watching a show about the beginning of life on Earth, and they were talking about how important Cyanobacteria was for making oxygen available for other life forms. As they talked about astrobiology and the search for other inhabitable planets, it occurred to me that I know a way of searching for microbes associated with such studies, or a variety of other categories for that matter, different than through a mere keyword search of PubMed. For my tip of the week, I want to show you how to use the Integrated Microbial Genomes (IMG) system to search for microbes associated with some basic characteristic or relevance, such as acid loving or causing disease.
If you want to learn more after watching this tip, you can read the recent publication by the Joint Genome Institute (JGI).
Markowitz, V.M., Szeto, E., Palaniappan, K., Grechkin, Y., Chu, K., Chen, I.A., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K., Ivanova, N.N., Kyrpides, N.C. (2007). The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Research, 36(Database), D528-D533. DOI: 10.1093/nar/gkm846
http://img.jgi.doe.gov/cgi-bin/pub/main.cgi
Comments
Comment from Trey
Time February 8, 2008 at 4:34 PM
We are looking at a simple way to do these. Jing/Screencast allows us to do this very quickly and with a minimum of hassle.
I’ll look into some other ways such as SciVee, etc. We’ll get back to you!
Comment from JamesH
Time February 9, 2008 at 12:19 PM
The screencast plays fine after the Friday Feb 9th update of firefox and shockwave under Ubuntu 7.10 (firefox 2.0.0.12 and shockwave 9.0.48.0.2).
Comment from Jennifer
Time February 12, 2008 at 1:34 PM
Hey, I just found a post on the Jing blog that addresses not being able to see Jing movies – you have to have the latest Flash player. You can check the post out at http://blog.jingproject.com/2008/01/jing_videos_dont_display.html.
Hope that helps!
Comment from Chris Lasher
Time February 12, 2008 at 4:20 PM
I found the root of the problem: the latest Flash plugin failed to install from the Ubuntu repositories due to a failed md5sum. This is described in a bug report at http://tinyurl.com/yqtjyh
I found a package containing a fix and now the screencast plays well. Thanks!
Comment from Chris Lasher
Time February 8, 2008 at 4:13 PM
I’m having trouble viewing your screencast at screencast.com under Ubuntu 7.10 with Firefox 2.0 and the Adobe Flash plugin. Would you be willing to upload it to another site, perhaps on YouTube, Google Video, or ShowMeDo.com?