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---
layout: workshop
root: .
venue: Stony Brook University
address: Wang Center - Lecture Hall 2; 100 Nicolls Road, Stony Brook, NY 11790
country: United-States
language: en
latlng: 40.916011, -73.119883
humandate: January 19-20
humantime: 9:00 am - 4:30 pm
startdate: 2016-01-19
enddate: 2016-01-19
instructor: ["Jason Williams", "Sheldon McKay","Matthew Aiello-Lammens"]
helper: ["Joslynn Lee", "Laura Graham", "Jonathan Borrelli"]
contact: williams@cshl.edu
etherpad: http://pad.software-carpentry.org/2016-01-19-sbu
eventbrite: 19896547108
day1_am: "data and project organization"
day1_pm: "using cloud computing and the command line"
day2_am: "running bioinformatics pipelines at the command line"
day2_pm: "data analysis and visualization with R"
---
<!--
HEADER
Edit the values in the block above to be appropriate for your
workshop. Run 'tools/check' *before* committing to make sure that
changes are good.
-->
<!--
EVENTBRITE
This block includes the Eventbrite registration widget if
'eventbrite' has been set in the header. You can delete it if you
are not using Eventbrite, or leave it in, since it will not be
displayed if the 'eventbrite' field in the header is not set.
-->
{% if page.eventbrite %}
<iframe
src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt"
frameborder="0"
width="100%"
height="206px"
scrolling="auto">
</iframe>
{% endif %}
<h2>General Information</h2>
<!--
INTRODUCTION
Edit the general explanatory paragraph below if you want to change
the pitch.
-->
<p>
This Genomics Data Carpentry workshop is for learning how to manage and
analyze genomic data. This hands-on workshop requires no prior computational experience and teaches basic concepts, skills and tools for working more
effectively with genomic data.
</p>
<p>
We will cover {{page.day1_am}}, {{page.day1_pm}}, {{page.day2_am}}, and {{page.day2_pm}}.
Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.
</p>
<!--
AUDIENCE
Explain who your audience is. (In particular, tell readers if the
workshop is only open to people from a particular institution.
-->
<p>
<strong>Who:</strong>
The course is aimed at graduate students and other researchers.
</p>
<!--
LOCATION
This block displays the address and links to maps showing directions
if the latitude and longitude of the workshop have been set. You
can use http://itouchmap.com/latlong.html to find the lat/long of an
address.
-->
{% if page.latlng %}
<p>
<strong>Where:</strong>
{{page.address}}.
Get directions with
<a href="//www.openstreetmap.org/?mlat={{page.latlng | replace:',','&mlon='}}&zoom=16">OpenStreetMap</a>
or
<a href="//maps.google.com/maps?q={{page.latlng}}">Google Maps</a>.
</p>
{% endif %}
<!--
SPECIAL REQUIREMENTS
Modify the block below if there are any special requirements.
-->
<p>
<strong>Requirements:</strong> Participants must bring a laptop with
a few specific software packages installed (will be listed
<a href="#setup">below</a> soon). They are also required to abide by
Data Carpentry's
<a href="{{site.swc_site}}/conduct.html">Code of Conduct</a>.
</p>
<!--
CONTACT EMAIL ADDRESS
Display the contact email address set in the header. If an address
isn't set in the header, the Software Carpentry admin address is
used.
-->
<p>
<strong>Contact</strong>:
Please mail
{% if page.contact %}
<a href='mailto:{{page.contact}}'>{{page.contact}}</a>
{% else %}
<a href='mailto:{{site.contact}}'>{{site.contact}}</a>
{% endif %}
for more information.
</p>
<p>
<strong>Fee:</strong>
Fees will cover coffee/snacks. Waivers can be requested by contacting organizer.
</p>
<hr/>
<!--
SCHEDULE
Show the workshop's schedule. Edit the items and times in the table
to match your plans. You may also want to change 'Day 1' and 'Day
2' to be actual dates or days of the week.
-->
<h2>Agenda and Lessons</h2>
<div class="row">
<div class="col-md-6">
<h3>Day 1: 9AM - 5PM</h3>
<table class="table table-striped">
<tr>
<td colspan=2 style="background:gainsboro">Intro, Data Processing, and Organization</td>
</tr>
<tr>
<td>
<a href="http://ucbpsych.qualtrics.com/SE/?SID=SV_5AYslF7f7XLwSQB">Pre-Survey (only take if you did not complete the link sent via email)</a>
</td>
<td>
</td>
</tr>
<tr>
<td>
<a href="./DataCarpentry_Intro.pdf">Intro to Data Carpentry</a>
</td>
<td>
Jason
</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/datadescription-genomics/blob/master/lessons/01-intro-to-ecoli-evo-experient.md">Introduction
</td>
<td>
Jason
</td>
</tr>
</tr>
<tr>
<td>
<a href="http://www.datacarpentry.org/2015-08-24-ISU/lessons/00-intro-to-data-tidy.html">
Data tidiness</a>
</td>
<td>
Jason
</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/datadescription-genomics/blob/master/lessons/02-examining-sra-runtable.md">
Getting started with the data
</a>
</td>
<td>
Jason
</td>
</tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/organization-genomics/blob/gh-pages/lessons/01_intro_organization.md">
Getting your project started
</a>
</td>
<td>
Jason
</td>
</tr>
<tr>
<td>
<a href="http://www.datacarpentry.org/shell-genomics/lessons/">
Command line exploration of the data (unix shell)
</a>
</td>
<td>
Sheldon
</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/wrangling-genomics/blob/gh-pages/lessons/00-readQC.md">
Quality Control of NGS Data
</a>
</td>
<td>
Jason
</td>
</tr>
<tr>
</table>
</p>
<p>
<h3>Day 2: 9AM - 5PM</h3>
<table class="table table-striped">
<tr>
<td colspan=2 style="background:gainsboro">NGS Data analysis</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/knowyourdata-genomics/blob/gh-pages/lessons/01-know_your_data.md">
Know your data
</a>
</td>
<td>
Jason
</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/wrangling-genomics/blob/gh-pages/lessons/01-automating_a_workflow.md">
Automating a workflow with a shell script
</a>
</td>
<td>
Sheldon
</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/wrangling-genomics/blob/gh-pages/lessons/02-variant-calling-workflow.md">
Automating a variant calling workflow
</a>
</td>
<td>
Sheldon
</td>
</tr>
<tr>
<td colspan=2 style="background:gainsboro">
{{page.day2_pm}}
</td>
</tr>
<tr>
<td>
<a href=http://mlammens.github.io/R-genomics/>Data analysis and visualization with R</a>
</td>
<td>
Matthew
</td>
</tr>
<tr>
<td colspan=2 style="background:gainsboro">
Wrap-up
</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/cloud-genomics/blob/master/lessons/05.Data-rountripping.md">
Moving Your Data</a>
</td>
<td>
Jason
</td>
</tr>
<tr>
<td>
<a href="http://ucbpsych.qualtrics.com/SE/?SID=SV_01xBhX3mMHjeBH7">Please complete the post-workshop Survey
</td>
<td>
Everyone
</td>
</table>
<h3>Post-Workshop (or using these lessons on your own)</h3>
<table class="table table-striped">
<tr>
<td colspan=2 style="background:gainsboro">Launching cloud instances after the workshop</td>
</tr>
<tr>
<td>
<a href="https://github.com/JasonJWilliamsNY/cloud-genomics/blob/master/lessons/1.logging-onto-cloud.md">
Launching your own instance</a><br>
Note: Start here if you are working on the lessons on your own
</td>
<td>
On your own
</td>
</tr>
</table>
</p></a>
<!--
ETHERPAD
Display the Etherpad for the workshop. You can set this up in
advance or on the first day; either way, make sure you push changes
to GitHub after you have its URL. To create an Etherpad, go to
http://etherpad.mozilla.org/YYYY-MM-DD-site
where 'YYYY-MM-DD-site' is the identifier for your workshop (e.g.,
'2015-06-10-esu'.
-->
{% if page.etherpad %}
<p>
<strong>Etherpad:</strong> <a href="{{page.etherpad}}">{{page.etherpad}}</a>.
<br/>
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
</p>
{% endif %}
<hr/>
<!--
SYLLABUS
Show what topics will be covered.
1. If your workshop is R rather than Python, remove the comment
around that section and put a comment around the Python section.
2. Some workshops will delete SQL.
3. Please make sure the list of topics is synchronized with what you
intend to teach.
4. You may need to move the div's with class="col-md-6" around inside
the div's with class="row" to balance the multi-column layout.
This is one of the places where people frequently make mistakes, so
please preview your site before committing, and make sure to run
'tools/check' as well.
-->
<!--
<h2>Syllabus</h2>
<div class="row">
<div class="col-md-6">
<h3>The Unix Shell</h3>
<ul>
<li>Files and directories</li>
<li>History and tab completion</li>
<li>Pipes and redirection</li>
<li>Looping over files</li>
<li>Creating and running shell scripts</li>
<li>Finding things</li>
<li><a href="{{site.swc_lessons}}/ref/01-shell.html">Reference...</a></li>
</ul>
</div>
<div class="col-md-6">
<h3>Programming in Python</h3>
<ul>
<li>Using libraries</li>
<li>Working with arrays</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Defensive programming</li>
<li>Using Python from the command line</li>
<li><a href="{{site.swc_lessons}}/ref/03-python.html">Reference...</a></li>
</ul>
</div>
<div class="col-md-6">
<h3>Programming in R</h3>
<ul>
<li>Working with vectors and data frames</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Using R from the command line</li>
<li><a href="{{site.swc_lessons}}/ref/06-R.html">Reference...</a></li>
</ul>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h3>Version Control with Git</h3>
<ul>
<li>Creating a repository</li>
<li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
<li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
<li>Ignoring files</li>
<li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
<li>Resolving conflicts</li>
<li>Open licenses</li>
<li>Where to host work, and why</li>
<li><a href="{{site.swc_lessons}}/ref/02-git.html">Reference...</a></li>
</ul>
</div>
<div class="col-md-6">
<h3>Managing Data with SQL</h3>
<ul>
<li>Reading and sorting data</li>
<li>Filtering with <code>where</code></li>
<li>Calculating new values on the fly</li>
<li>Handling missing values</li>
<li>Combining values using aggregation</li>
<li>Combining information from multiple tables using <code>join</code></li>
<li>Creating, modifying, and deleting data</li>
<li>Programming with databases</li>
<li><a href="{{site.swc_lessons}}/ref/04-sql.html">Reference...</a></li>
</ul>
</div>
</div>
<hr/>
-->
<!--
SETUP
Delete irrelevant sections from the setup instructions. Each
section is inside a 'div' without any classes to make the beginning
and end easier to find.
This is the other place where people frequently make mistakes, so
please preview your site before committing, and make sure to run
'tools/check' as well.
-->
<h2 id="setup">Setup</h2>
</div>
</div>
<p>
To participate in a Data Carpentry workshop, you will need working copies of the
described software. Please make sure to install everything (or at least to download
the installers) before the start of your workshop. Participants should bring and use
their own laptops to insure the proper setup of tools for an efficient workflow
once you leave the workshop.
<p>
Please follow these <a href=install.html>Setup Instructions</a>
<p>
We maintain a list of common issues that occur during installation as a reference for instructors
that may be useful on the
<a href = "https://github.com/swcarpentry/workshop-template/wiki/Configuration-Problems-and-Solutions">Configuration Problems and Solutions wiki page</a>.
</p>