Anvi’o Workshop in Irvine, California

Posted on March 28, 2018 by Isabelle Laforest-L.

Where to find Anvi’o: http://merenlab.org/software/anvio/

What is Anvi’o: “Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.” (Definition taken directly from the software website)

On the 19th-20th of March 2018, I had the chance and privilege of attending a 2-days workshop on how to use Anvi’o as a tool to analyze my metagenomics data and produce cool figures. And Anvi’o is Open source! Open &*^$% Source! This is great that as a postdoc I get the chance to acquire new skills and I really appreciate the fact that my ACHRI and Cumming School of Medicine postdoctoral fellowship came with a 2K package to pay for workshops this year.

Here is the summary of my experience:

1. Meren is great but Anvi’o is greater.

I mean, the tutorial is smooth, well annotated in the website, and there is even a blog (with sassy humour all over it) written by users and managers alike.

Not only can you make amazing figures, and let’s be real, this helps to publish good papers, but you can also use Anvi’o to make sure your genome assembly is good. I haven’t had the time to explore yet all the possibilities Anvi’o offers, but it really seemed easy to explore and figure out. And the support community is real.

Only thing I would say, three days would be better. And I would liked to have a hands-on assignment on the third day where each participant would go through the whole process from the binning to the production of quality figures.

2. California, I miss you.

Coming from the Canadian winter… California smelled like summer, flowers, and earth. Wow. Can I go back?

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Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

Posted on March 13, 2018 by Isabelle Laforest-L.

New paper in mSystems!

This is my first perpective/comment. It was really fun to get the chance to contribute to the special issue on Early-Career Systems Microbiology Scientists.

Microbiome Keystone Symposia 2018

Posted on March 7, 2018 by Isabelle Laforest-L.

This week I am enjoying my first international conference on the human microbiome. This transition from plant microbiome to human microbiome has been challenging, I have to absorb an impressive amount of immunology and biochemistry knowledge, which was hidden deep in my previous undergraduate biology understanding.

The conference (Keystone) is in Banff and we are staying at the Fairmont which, I must say, is incredible. My poster session was filled with interesting interactions with fellow researchers in the human microbiome field also working on interkingdom interactions.

The University of Calgary is well represented at the meeting with all fantastic four PI of the microbiome core group present (Drs. Arrieta, Sycuro, McCoy, and Geuking), ass well as Dr. Hirota.

I think there is still a lot of improvement needed regarding the integration of real ecology in microbiome research. For what I see researchers use ecological buzz words but don’t investigate the concepts.