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index.html
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---
layout: workshop # DON'T CHANGE THIS.
root: . # DON'T CHANGE THIS.
venue: "The Donald Danforth Plant Science Center"
address: "Mary and Oliver Langenberg Theater, 975 North Warson Road, St. Louis, MO" # street address of workshop (e.g., "123 Forth Street, Blimingen, Euphoria")
country: "us" # country (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en" # language (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "FIXME" # fractional latitude and longitude (e.g., "41.7901128,-87.6007318"; you can use http://www.latlong.net/)
humandate: "June 17, 2017" # human-readable date (e.g., "Feb 17-18, 2020")
humantime: "9:00 am - 5:00 pm" # human-readable time (e.g., "9:00 am - 4:30 pm")
startdate: 2017-06-17 # use YYYY-MM-DD format like 2015-01-01
enddate: 2017-06-17 # use YYYY-MM-DD format like 2015-01-02
instructor: ["Bo Ji", "Catalina Anghel"] # list of names like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Alex Harkess", "Patricia Baldrich"] # list of names like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: "catalina.v.anghel@gmail.com" # contact email address for workshop organizer, such as "grace@hopper.org"
etherpad: http://pad.software-carpentry.org/2017-06-17-stlouis # optional (insert the URL for your Etherpad if you're using one)
eventbrite: # optional (insert the alphanumeric key for Eventbrite registration, e.g., "1234567890AB")
---
<!--
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>
<a href=http://datacarpentry.org>Data Carpentry</a> workshops are for any researcher
who has data they want to analyze, and no prior computational experience is required.
This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.
</p>
<p>
The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover
data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows.
We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.
</p>
<p>
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
Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges
on. They should have a few specific software packages installed (listed
<a href="#setup">below</a>). They are also required to abide by
Data Carpentry's
<a href="{{site.dc_site}}/code-of-conduct/">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>
<hr/>
<h2>Etherpad</h2>
<!--
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>Link:</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 %}
<!--
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.
-->
<!-- DO NOT EDIT SURVEY LINKS -->
<h2>Surveys</h2>
<p>Please be sure to complete these surveys before and after the workshop.</p>
<p><a href='{{ site.dc_pre_survey }}'>Pre-workshop Survey</a></p>
<p><a href='{{ site.dc_post_survey }}'>Post-workshop Survey</a></p>
<div>
<h2>Schedule</h2>
</p>
<div class="row">
<div class="col-md-6">
<h3>Morning: 9:00AM - 12:00PM</h3>
<table class="table table-striped">
<!-- <tr>
<td colspan=2 style="background:gainsboro"><strong><em>8:30 - 9:00:</em></strong> Coffee & Sign In</td>
</tr> -->
<tr>
<td colspan=2 style="background:gainsboro"><strong>Module 1: </strong> Data and project organization</td>
</tr>
<!-- <tr>
<td colspan=2 style="background:gainsboro">
<ul>
<li>Good practices for data and project organization
</ul>
</td>
</tr> -->
<tr>
<td>
<a href="http://www.datacarpentry.org/2016-05-26-NIH/DataCarpentry_Intro.pdf">Intro to Data Carpentry</a>
</td>
<td>
Bo
</td>
</tr>
<tr>
<td>
<a href="http://www.datacarpentry.org/introduction-genomics/">Intro to Data</a> and
<a href="https://jasonjwilliamsny.github.io/tidiness-genomics/">Genomics Data Tidiness</a>
(brief overview)
</td>
<td>
Bo
</td>
</tr>
<tr>
<td colspan=2 style="background:gainsboro"><strong>Module 2: </strong>Using cloud computing for genomics</td>
<tr>
<td colspan=2 style="background:gainsboro">
<ul>
<li>understand what cloud computing is and why it's useful
<li>log in to remote computing resources
</ul>
</td>
</tr>
<tr>
<td>
<a href="https://jasonjwilliamsny.github.io/cloud-genomics/">Connecting to the Cloud in 5 Minutes or Less</a>
</td>
<td>
Bo
</td>
</tr>
<tr>
<td colspan=2 style="background:gainsboro"><strong>Module 3: </strong>Introduction to the command line</td>
<tr>
<!-- <td colspan=2 style="background:gainsboro">
<ul>
<li>learn commands for the command line
<li>learn to navigate at the command line
</ul>
</td> -->
</tr>
<tr>
<td>
<a href="http://www.datacarpentry.org/shell-genomics/lessons/">Using the Command Line (Shell)</a>
</td>
<td>
Bo (a short introduction by Catalina)
</td>
</tr>
<tr>
</table>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h3>Afternoon: 1PM - 5:00PM</h3>
<table class="table table-striped">
<tr>
<td colspan=2 style="background:gainsboro"><strong>Module 3, continued (if needed): </strong> Command line </td>
<tr>
</tr>
<tr>
<td>
<a href="http://www.datacarpentry.org/shell-genomics/lessons/">Using the Command Line (Shell)</a>
</td>
<td>
Catalina
</td>
</tr>
<tr>
<tr>
<td colspan=2 style="background:gainsboro"><strong>Module 4: </strong>Running bioinformatics programs and creating workflows
</td>
<tr>
<td colspan=2 style="background:gainsboro">
<ul>
<li>Quality control of NGS Data
<li>Automating a workflow
</ul>
</td>
</tr>
<tr>
<td>
<a href="https://jasonjwilliamsny.github.io/wrangling-genomics/00-readQC.html" target="_blank">QC of Sequence Data</a>
</td>
<td>
Catalina
</td>
<tr>
<tr>
<td>
<a href="https://jasonjwilliamsny.github.io/wrangling-genomics/01-automating_a_workflow.html" target="_blank">Automating Workflows</a>
(up until the shell script)
</td>
<td>
Catalina
</td>
</tr>
</table>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h3>Post Workshop</h3>
<table class="table table-striped">
<tr>
<td colspan=2 style="background:gainsboro">Alignment and Variant Calling </td>
</tr>
<td>
<a href="https://jasonjwilliamsny.github.io/wrangling-genomics/01-automating_a_workflow.html" target="_blank">Automating Workflows</a>
</td>
<td>
On Your Own
</td>
<tr>
<td>
<a href="https://jasonjwilliamsny.github.io/wrangling-genomics/02-variant-calling-workflow.html" target="_blank">Variant Calling</a>
</td>
<td>
On Your Own
</td>
</tr>
<tr>
<td colspan=2 style="background:gainsboro">How To Make This Work Your Own</td>
</tr>
<td>
<a href="https://jasonjwilliamsny.github.io/cloud-genomics/logging-onto-cloud.html"> Launching Your Own Cloud Instances</a>
</td>
<td>
On Your Own
</td>
<tr>
</table>
</div>
</div>
<!--
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>
<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>