http://bioinformatics.whatheblog.com One base pair at a time... Tue, 20 Oct 2009 05:37:10 +0000 http://backend.userland.com/rss092 en MEGAN MEtaGenome ANalyzer. A stand-alone metagenome analysis tool. Metagenomics and Our Microbial Planet A website on metagenomics and the vital role of microbes on Earth from the National Academies. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet A report released by the National Research Council in March 2007. ... http://bioinformatics.whatheblog.com/2009/10/metagenomics-resources/ With IBM tossing it's hat into the ring of "next-next-generation" sequencing, I'm starting to get lost as to which generation is which. For the moment, I'm sort of lumping things together, while I wait to see how the field plays out. In my mind, first generation is anything that requires ... http://bioinformatics.whatheblog.com/2009/10/next-gen-sequencing/ There was an article on probiotics in the New York Times today. By Tara Parker-Pope it addresses some important issues rarely covered in the press about probiotics (see Well - Probiotics - Looking Underneath the Yogurt Label - NYTimes.com). On the one hand, the article does a decent job of pointing ... http://bioinformatics.whatheblog.com/2009/10/nytimes-on-probiotics/ Sure, James Watson has been known, especially recently, to say some outrageous things. But here is something I think everyone, scientists and the public should read - an opinoin piece in the NY Times today by Watson ( Op-Ed Contributor - To Fight Cancer, Know the Enemy - NYTimes.com) This piece ... http://bioinformatics.whatheblog.com/2009/10/new-look-at-cancer-biology/ The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing Dethlefsen L, Huse S, Sogin ML, Relman DA PLoS Biology Vol. 6, No. 11, e280 doi:10.1371/journal.pbio.0060280 A paper in PLOS Biology from the Relman lab investigates the effect of a treatment with the antibiotic ciprofloxacin ... http://bioinformatics.whatheblog.com/2009/10/the-pervasive-effects-of-an-antibiotic-on-the-human-gut-microbiota/ The format of Windows and Unix text files differs slightly. In Windows, lines end with both the line feed and carriage return ASCII characters, but Unix uses only a line feed. As a consequence, some Windows applications will not show the line breaks in Unix-format files. Likewise, Unix ... http://bioinformatics.whatheblog.com/2009/04/how-do-i-convert-between-unix-and-windows-text-files/ Linux? You geeks use Linux? If you work in science, and you work on big datasets (such as analyzing next generation sequencing data), chances are that you use Linux for some of your work. I frequent several of our lab's Red Hat servers for data analysis and code development purposes. However, ... http://bioinformatics.whatheblog.com/2009/03/linux-whos-on-the-server/ http://bioinformatics.whatheblog.com/2009/02/craig-venter-on-the-verge-of-creating-synthetic-life/ Something I came across. Integrated solutions * CLCbio Genomics Workbench - de novo and reference assembly of Sanger, 454, Solexa, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, browser and other features. Runs on Windows, Mac OS X and Linux. * NextGENe - de ... http://bioinformatics.whatheblog.com/2009/02/next-gen-tools/ Firefox?!?! I know what you're thinking. "Come on. A browser? As a bioinformatics tool?" You might actually be surprised. I think that most people that do research spend at least some amount of time online trying to track down information. Maybe it's  protein name, or DNA elements in a chromosome segment. ... http://bioinformatics.whatheblog.com/2009/02/bioinformatics-tool-chest-why-you-should-be-using-firefox/