Category Archives: Bioinformatics

Three Enterotypes (So Far)

Biologists are beginning to make a thorough exploration of the human microbiome, the approximately hundred trillion bacterial cells associated with each human body. Yesterday members of the Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium published a paper in Nature stating … Continue reading

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Visualizing Biological Data

On March 16–19, 2011, the Workshop on Visualizing Biological Data was held at the Broad Institute in Cambridge, Massachusetts, less than a mile from where I work. I am deeply interested in this topic, and I would have loved to … Continue reading

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Why Bosco Thinks Python Is Good

Bosco Ho, who writes the Trapped in the USA blog, yesterday posted his best-of list covering eight years of blogging. Hey, I just realized that I’ve had this blog for more than 8 years, but never put out a best-of … Continue reading

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More Accurate Multiple Sequence Alignment

The 20 June 2008 issue of Science contains a paper by Art Löytynoja and Nick Goldman titled “Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.” The authors tackled the difficult problem of how to handle correctly the … Continue reading

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Book Review: Learning Python, 3rd Edition (1)

Utterly bewitched by this dramatic and thrilling panel from an xkcd.com comic strip, I have decided that it is time I learned the Python programming language. I come to Python as a bioinformatics scientist who is experienced in C, C++, … Continue reading

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Book Review: Web Database Applications with PHP and MySQL

Web Database Applications with PHP and MySQL, 2nd Edition, was written by Hugh E. Williams and David Lane and published by O’Reilly in May, 2004. I purchased this book in 2005 when I was doing some consulting for a microarray … Continue reading

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Re: Notes to a Young Computational Biologist

This is a story of how clueless I can be, but how sometimes, given a sufficient number of opportunities, I can become clueful again. On 13 March 2007, Bosco Ho wrote a post entitled “Notes to a Young Computational Biologist” … Continue reading

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