Microbial 'omics

a post by A. Murat Eren (Meren)

Table of Contents

Here you can find a list of past and future anvi’o workshops and events.

October 2017, Brest (France)

Event EBAME Workshop on Computational Microbial Ecogenomics
Dates Oct 22 - 27, 2017
Place European Institute for Marine Sciences at Western Brittany University
More info http://pagesperso.univ-brest.fr/~maignien/ebame3.html

September 2017, Walnut Creek (USA)

Event Two-day Intense Anvi’o User Workshop
Dates Sep 25 - 26, 2017
Place Joint Genome Institute, Walnut Creek, California
More info http://merenlab.org/2017/05/17/anvio-workshop-at-jgi/

April 2017, Chicago (USA)

Event Two-day Intense Anvi’o User Workshop
Dates Apr 26 - 27, 2017
Place University of Chicago, Chicago, Illinois
More info http://merenlab.org/2017/03/23/anvio-workshop-at-uchicago/

Aftermath: Although how well we did to go through the workshop topics is open to discussion, we probably were most successful at making the most out of the cozy space that was available to us:

Workshop

Workshop

Which inspired this haiku from Jessica Mark Welch:

Thirty-eight people
Science, laughter, anvi'o
In a room for twelve
Jessica Mark Welch

Feb 2017, State College (USA)

Event Metagenomics hands-on Workshop
Dates Feb 9, 2017
Place Penn State University, State College, Pennsylvania
More info Please send an e-mail to meren @ uchicago.edu

Dec 2016, Boston (USA)

Event Workshop on Microbial Genome Sequencing
Dates Dec 15, 2016
Place Harvard Medical School, Boston, MA
More info http://cfar.globalhealth.harvard.edu/event/save-date-workshop-microbial-genome-sequencing

Sep 2016, Paris (France)

Event Summer School in Metagenomics
Dates September 12 - 16, 2016
Place Institut Pasteur, Paris, France
More info http://www.france-bioinformatique.fr/
Contact summer_school_metagenomics at groupes dot france-bioinformatique dot fr

There are some very exciting talks during this event. Just so you know.

Sep 2016, Bielefeld (Germany)

Event Joint de.NBI & DZIF training course on targeted and untargeted metagenome analysis
Dates August 29 - September 2, 2016
Place Universitätsstraße 25 (Room V0-133), 33615 Bielefeld, Germany
More info http://www.bioinformatics-platform.dzif.de/?p=1417
Contact Andreas Bremges (andreas.bremges at helmholtz-hzi dot de)

Aug 2016, Montréal (Canada)

The First Traditional Anvi’o Colloquium in Montréal” (hehe) has been quite fun. Myself, Tom Delmont and the 20-some participants of our tiny workshop were pleasantly surprised by the effort Nicolas Tromas put into arranging this event. I thank him and Jesse Shapiro very much for making this a possibility.

We talked a lot about challenges and opportunities emerge from metagenomics, and about using anvi’o as a workbench to explore complex metagenomic data. I thank all participants for their patience, great questions, and feedback!

During the workshop I lost a historical battle, and finally agreed to make the necessary changes for anvi-gen-variability-profile to also report dN/dS for each variable nucleotide position by default. I made very good arguments, but they didn’t work.

I also thank Adrien for this sketch, although it makes me look much cooler than I do:

Our workshop was right after ISME 2016 conference, during which we had many missed interactions with friends and colleagues, which made it totally worth carrying an anvi’o poster all they way to Montreal:

For people who are interested in a higher resolution, a PNG file for the poster is also here: eren-isme-poster-72dpi.png.


Event The First Traditional Anvi’o Colloquium in Montréal
Dates August 29 - 30, 2016
Place Uniersity of Montréal, Montréal, Canada
More info http://merenlab.org/2016/03/13/worskhop-at-montreal/
Contact Nicolas Tromas (tromas.nicolas at gmail dot com)

Aug 2016, Woods Hole (USA)

STAMPS was very exciting this year. This was the first time Tom and I presented anvi’o to a large crowd, and heard back some very encouraging feedbacks:

I guess we will continue working on anvi’o after these!

Here is a group photo (which is pretty much my job during every STAMPS course since 2011):

STAMPS 2016


Event STAMPS Course
Dates 3 - 13 August, 2016
Place Marine Biological Laboratory, Woods Hole, USA
More info https://stamps.mbl.edu/
Contact David Mark Welch (dmarkwelch at mbl dot edu)

July 2016, Hawai’i (USA)

ECOGEO covered multiple topics. The first day there was a UNIX tutorial by Ken, and lots of marker gene stuff from multiple people. The second day there were four modules: assembly, binning, annotation, and phylogenetics. I -for the first time- used anvi’o to compare binning tools.

Here is Ken teaching UNIX to the class the first day:

ECOGEO Ken


Event ECOGEO Workshop
Dates 25 - 26 July, 2016
Place Marine Biological Laboratory, Woods Hole, USA
More info http://earthcube.org/group/oceanography-geobiology-environmental-omics
Contact ECOGEO (ecogeo.rcn at gmail dot com)