Quick post – potentially useful new tool – Bio-Community Perl Toolkit

Just found an interesting new paper via automated Google Scholar searches: The Bio-Community Perl toolkit for microbial ecology. By Florent Angly, Christopher Fields, and Gene Tyson in Bioinformatics.

Here is the abstract:

Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio- Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly-used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio- Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A README file describes software installation and how to contribute.

Seems like it has potential for those working on microbial ecology.

New Paper

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.