Welcome to CME at MSU MSU's home

Tiedje Symposium Group Photo
CME members and alumni at the 2011 Tiedje Symposium,
October 29th, East Lansing, Michigan
(photo by Kurt Stepnitz, © All rights reserved by TGsymposium)
Visit the Tiedje Lab site

   Announcements

human gut

Visit the new SCFAdb (Short Chain Fatty Acid Database)

with over 18,000 sequences collected and analyzed in research sponsored by NIH Human Microbiome Project Demonstration Project (UH3 DK083993) and the University of Chicago Digestive Disease Research Core Center (P30DK42086).

Note: This database performs best in Chrome or Firefox browsers.

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RDPlogoRDP (Ribosomal Database Project) - NEW RDP Release 11, update 3 contains 3,019,928 aligned and annotated Bacterial and Archaeal small-subunit rRNA sequences, with additions made monthly. The Bacteria and Archaea hierarchy model used by RDP Classifier and RDP Hierarchy Browser has been updated to training set No. 10. The new addition includes 14 new bacterial phyla and 1 new archaeal phylum, and 159 new genera. The former phylum Nitrospira is renamed to Nitrospirae. The former candidate phyla OP11, TM7, OD1, WS3 are now the new bacterial phyla Microgenomates, Candidatus Saccharibacteria, Parcubacteria, Latescibacteria.

Announcing the RDP Fungal LSU Classifier (large subunit rRNA gene): 102,901 Fungal 28S rRNAs. New Warcup Fungal ITS training set to classify fungal ITS sequences is released. Available on the RDP Classifier page. RDP SOAP web services for Seqmatch and Classifier are available.

Instructors: try our new "Assignment Generator" for your class. Find sequences from completed genomes by searching with the GenBank Project ID and view sequences from the Whole Genome Project with our new Genome Viewer. http://rdp.cme.msu.edu

Check out the new tools in our Functional Gene Pipeline and RDPipeline. Source code of RDP Classifier is freely available from SourceForge and a GitHub repository of our latest tools for customizable command-line processing of your sequences.

Also new: A comprehensive tutorial using RDPTools output with Phyloseq package. Visit all our Workflow Tutorials at:
http://rdp.cme.msu.edu/tutorials/RDPtutorial_CONTENTS.html

CMEIAS logoCheck our newest version of the Center for Microbial Ecology Image Analysis System (CMEIAS software), designed to strengthen microscopy-based approaches for understanding microbial ecology. To learn more about CMEIAS and download its free program files and operator manuals, go to http://cme.msu.edu/cmeias/

We are pleased to announce the release of CMEIAS Quadrat Maker v1.0, a free, improved computing technology, uniquely designed to aid in preparing digital images for quadrat-based spatial distribution analysis.

CMEIAS QuadMakerPerforms three major routines: 1) significantly facilitates the task of optimizing the grid dimensions of the raster that divides digital landscape images into contiguous quadrats with optimal spatial resolution of foreground objects by avoiding their over- or under-sampling of points; 2) produces and saves an indexed image of the original landscape overlaid with the optimized grid-lattice that is annotation to indicate each quadrat’s location; and 3) produces individual image files of each quadrat sample saved with column-row location that are now ready for plot-based spatial pattern analysis of the landscape domain. Input images can be 8-bit grayscale or 24-bit RGB color in tiff, bmp, jpg or png format. Grid specifications, quadrat size in pixels, and percentage of the landscape area represented by each quadrat are automatically displayed in the GUI as the grid optimization procedure is interactively performed, and are also provided as a saved, output txt table.

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TIEDJE SYMPOSIUM: A Success!
A day of reunion and celebration, Saturday, October 29, 2011, in honor of Jim Tiedje (not a retirement!). A day full of talks and posters from former and present Tiedje lab personnel followed by a reception and dinner at the Kellogg Center. Check the agenda at http://tiedjesymposium.mmg.msu.edu


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AMAZING! We now have three distinguished faculty members who have been elected to the prestigious National Academy of Sciences! Congratulations to newest academy member, Dr. Richard Lenski (see article, May 2006), as he joins two other CME faculty members, Dr. James M. Tiedje and Dr. Michael F. Thomashow who were elected in 2003. (see article, May 2003)

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bullet What is the CME?  A brief description of the Center's organization and activities.
bullet Research Program:  Descriptions of CME research initiatives.
bullet Graduate Education:  Information about the CME graduate education program.
bullet Industrial Outreach:  Collaborations between CME and industry.
bullet Educational Outreach:  CME activities targeted toward young people and educators. Visit the Microbe Zoo!

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::  International Program  ::  Related Websites  ::

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Please contact rdpstaff@msu.edu with any questions, comments,
or suggestions regarding this page - last updated 19 Sept 2014.