<commit_before>---
layout: post
title: Microbial 'Omics Workshop
modified: 2018-07-23
excerpt: "A light introduction to questions of microbial ecology and microbial omics through the story of crassphage"
comments: true
authors: [alon]
categories: [anvio]
---

{% capture images %}{{site.url}}/images/anvio/2018-07-23-microbial-omics-workshop{% endcapture %}

{% include _toc.html %}

{% include _join-anvio-slack.html %}

{:.notice}
This workshop was developed as part of the BRI class for the University of Chicago Biophysical Sciences Graduate Program first year students in the fall quarter of 2018. The workshop was planned for 20 hours in-class, and the students were expected to do additional work on assignment outside of class hours.

The general goals of this workshop are:
1. Introduce the students to some of the microbial ecology and microbial omics type of work that is being done in the Meren Lab.
2. Learn a new practical tool (snakemake) through some hands-on experience.

The specific goals of this workshop are:
1. Get familiar with some basic questions of microbial ecology.
2. Learn how questions of microbial ecology are addressed using 'omics approahces through the example of [crassphage](https://en.wikipedia.org/wiki/CrAssphage).
3. Learn, through the example of [snakemake](https://snakemake.readthedocs.io/en/stable/), how workflow managment tools help us streamline the analysis of large collection of genomic samples.
4.  Learn how large datasets could serve as an input to machine learning algorithms, and help us address questions of microbial ecology.

## Introduction to microbial ecology

The introduction will include a lecture by Dr. Eren. Slides are available [here]().

## Crassphage

Slides for the introduction to crassphage could be found [here]().

The background includes review of these crassphage related papers:

[![crassphage_paper]({{images}}/crassphage_paper.png)]( {{images}}/crassphage_paper.png){:.center-img .width-120}



<commit_msg>added section "prepare your Mac"<commit_after>---
layout: post
title: Microbial 'Omics Workshop
modified: 2018-07-23
excerpt: "A light introduction to questions of microbial ecology and microbial omics through the story of crassphage"
comments: true
authors: [alon]
categories: [anvio]
---

{% capture images %}{{site.url}}/images/anvio/2018-07-23-microbial-omics-workshop{% endcapture %}

{% include _toc.html %}

{% include _join-anvio-slack.html %}

{:.notice}
This workshop was developed as part of the BRI class for the University of Chicago Biophysical Sciences Graduate Program first year students in the fall quarter of 2018. The workshop was planned for 20 hours in-class, and the students were expected to do additional work on assignment outside of class hours.

The general goals of this workshop are:
1. Introduce the students to some of the microbial ecology and microbial omics type of work that is being done in the Meren Lab.
2. Learn a new practical tool (snakemake) through some hands-on experience.

The specific goals of this workshop are:
1. Get familiar with some basic questions of microbial ecology.
2. Learn how questions of microbial ecology are addressed using 'omics approahces through the example of [crassphage](https://en.wikipedia.org/wiki/CrAssphage).
3. Learn, through the example of [snakemake](https://snakemake.readthedocs.io/en/stable/), how workflow managment tools help us streamline the analysis of large collection of genomic samples.
4.  Learn how large datasets could serve as an input to machine learning algorithms, and help us address questions of microbial ecology.

## Prepare your Mac

For this workshop you are required to install the following things:

### brew

For more details refer to [https://brew.sh/](https://brew.sh/)

### anvi'o dependencies

samtools: [http://localhost:4000/2016/06/18/installing-third-party-software/#samtools](http://localhost:4000/2016/06/18/installing-third-party-software/#samtools)

prodigal: [http://localhost:4000/2016/06/18/installing-third-party-software/#prodigal](http://localhost:4000/2016/06/18/installing-third-party-software/#prodigal)

HMMER: [http://localhost:4000/2016/06/18/installing-third-party-software/#hmmer](http://localhost:4000/2016/06/18/installing-third-party-software/#hmmer)

GSL: [http://localhost:4000/2016/06/18/installing-third-party-software/#gnu-scientific-library](http://localhost:4000/2016/06/18/installing-third-party-software/#gnu-scientific-library)

Numpy: [http://localhost:4000/2016/06/18/installing-third-party-software/#numpy](http://localhost:4000/2016/06/18/installing-third-party-software/#numpy)

Cython: [http://localhost:4000/2016/06/18/installing-third-party-software/#cython](http://localhost:4000/2016/06/18/installing-third-party-software/#cython)



Refer to: [http://localhost:4000/2016/06/26/installation-v2/#painless-installation-with-homebrew](http://localhost:4000/2016/06/26/installation-v2/#painless-installation-with-homebrew)

## Introduction to microbial ecology

The introduction will include a lecture by Dr. Eren. Slides are available [here]().

## Crassphage

Slides for the introduction to crassphage could be found [here]().

The background includes review of these crassphage related papers:

[![crassphage_paper]({{images}}/crassphage_paper.png)]( {{images}}/crassphage_paper.png){:.center-img .width-120}




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