Difference between revisions of "2010 GMOD Summer School - Americas"

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== Cost ==
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== Costs ==
  
This course is ''free'' thanks to [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7234938&p_grant_num=1R01HG004483-01&p_query=&ticket=&p_audit_session_id=&p_keywords= NIH grant 1R01HG004483-01] under [http://biowiki.org/IanHolmes Ian Holmes], and to the grants of the individual instructors.
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This course is ''free'' thanks to  
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* [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7234938&p_grant_num=1R01HG004483-01&p_query=&ticket=&p_audit_session_id=&p_keywords= NIH grant 1R01HG004483-01] under [http://biowiki.org/IanHolmes Ian Holmes]
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* Financial support from [http://nescent.org NESCent]
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* The grants of the individual instructors
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== Sponsor ==
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{{ImageRight|NESCentLogo152.jpg|NESCent|140|http://nescent.org}}
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We would like to thank the [http://nescent.org National Evolutionary Synthesis Center (NESCent)] for hosting and financially supporting this course.  Travel scholarships for 3 participants were entirely funded by NESCent, as part of its [http://www.nescent.org/eog/ Education and Outreach] effort.  NESCent's [http://www.nescent.org/eog/ Education and Outreach Group] is committed to sharing the exciting evolutionary biology research occurring at NESCent and elsewhere.  In addition, NESCent is interested in outreach to groups who are underrepresented in evolutionary biology and improving evolution education, and offers resources for scientists, educators, and the general public that meet these goals.
  
 
== Travel, Lodging and Food ==
 
== Travel, Lodging and Food ==

Revision as of 00:08, 2 March 2010

2010SummerSchoolAmericas300.png
2010 GMOD Summer School - Americas
6-9 May, 2010
NESCent
Durham, NC, USA

__NOTITLE__

The 2010 GMOD Summer School - Americas will be held 6-9 May at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like previous GMOD Summer Schools, this course will focus on installing, configuring and integrating popular GMOD Components. Sessions will be taught by GMOD Component developers and GMOD staff. There is space in the course for 25 participants, and admission is competitive.


Applications

The deadline for applying to the summer school has now passed. However, you are encouraged to submit an application to get on the waiting list.

Admission to the course is competitive and is based on the strength of the application (especially the statement of interest). Last year there were over 50 applications for the 25 slots. The application deadline was the end of Monday, February 22, but you can still submit an application and get on the waiting list. Applicants will be notified of admission status by March 1.

Tentative Program

The program will feature 4 full days of hands-on training starting with an overview of GMOD, and then covering the installation, configuration, and administration of several popular GMOD Components.

This schedule is subject to change.

Date Time Session
Thursday
May 6
8:45am Introduction and Overview
Scott Cain and Dave Clements
Participant and instructor introductions, how the GMOD project works, what software tools are available in GMOD, how they interoperate, what resources are needed to get a GMOD installation up and running, and course overview
10:25am VMware and BioPerl Setup
Everyone
Get the GMOD Summer School VMware image up and running on your laptop, and then finish installation of BioPerl.
12:15pm Lunch
on your own
1:15pm MAKER I
Carson Holt
MAKER overview, installation, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality
4:30pm Social Hour w/ NESCent Staff
and then Dinner on your own
6:30pm MAKER II
Carson Holt
Advanced MAKER configuration, re-annotation options, and improving annotation quality
7:30pm Open Discussion and User Presentations
Everyone
This session is open to any and all questions you have on the GMOD Project, GMOD Components, and GMOD users. The instructors will come with their knowledge of GMOD and their opinions on the project's strengths, weaknesses, and future directions. Students will also have the opportunity to share work from their projects with the rest of the group.

We expect this session to be lively.

8:30pm Day ends
Friday
May 7
8:45am GBrowse
Scott Cain
1:00pm Lunch
on your own
2:00pm Galaxy
James Taylor
Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
6:00pm JBrowse
Mitch Skinner
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
8:00pm Day ends
Saturday
May 8
8:45am Chado I
Scott Cain and Dave Clements
1:00pm Lunch
on your own
2:00pm Chado II
Scott Cain and Dave Clements
3:00pm Apollo
Ed Lee
Overview, basic installation, basic configuration, reading/writing data, and remote analyses. Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance.
7:30pm Day ends
Sunday
May 9
8:45am GBrowse_syn
Sheldon McKay
12:30pm Lunch
on your own
1:30pm Tripal
Stephen Ficklin
Tripal is a web front end to Chado databases built on Drupal. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration.
6:00pm Wrapup and Resources
Dave Clements and Scott Cain
6:30pm Summer School Ends

Instructors

The tentative list of instructors includes

Instructor GMOD Affiliation Affiliation
Scott Cain GMOD Project Coordinator; Chado, GBrowse Ontario Institute for Cancer Research
Dave Clements GMOD Help Desk National Evolutionary Synthesis Center (NESCent)
Stephen Ficklin Tripal Clemson University Genomics Institute
Carson Holt MAKER University of Utah
Ed Lee Apollo developer Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn, GBrowse Cold Spring Harbor Laboratory
Mitch Skinner JBrowse University of California, Berkeley
James Taylor Galaxy Emory University

Prerequisites

The course requires a minimal level of Linux systems administration knowledge (see Computing Requirements). By "a minimal level of Linux systems administration knowledge" we mean that participants should be

  1. Comfortable with the Linux command line interface, and
  2. Comfortable installing packages under Linux.

A good benchmark for this level of knowledge is that you should be able to get a basic GBrowse installation (that is, GBrowse without MySQL) up and running with the example GBrowse data. This also requires installing Apache, and BioPerl and all its dependencies.

System Requirements

VMware

Participants are required to bring their own laptops, already capable of running a VMware system image.

The course starts with getting a VMware image (built specifically for the course) up and running on your machine. We then build upon that image in each succeeding session.

VMware on Windows and Linux

Windows http://www.microsoft.com/}} Linux}} A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it. There are multiple versions. Be sure to download a version that can run on your laptop.


VMware on Mac OS X

Apple http://www.apple.com/macosx/}} Participants can also bring newer Macs with Intel processors. The Intel processor is a requirement for all the packages discussed below. There is no free VMware player that runs directly under Mac OS X. However, there are several other options, all of which require an Intel Mac:
VMware Fusion
Fusion http://www.vmware.com/products/fusion/}}  VMware Fusion ($80/corporate, $40/Academic) allows you to run VMware images (as well as Windows and Linux) under Mac OS. We recommend this option for Mac users. There is a fully functional, 30 day free trial version of VMware Fusion available for download.
VirtualBox
VirtualBox-logo.png VirtualBox is free and open source, and runs on Intel Macs (and Windows, Linux and Solaris too). It claims to be capable of running VMware images, but we have not tested this with our images.

Costs

This course is free thanks to

NESCent

We would like to thank the National Evolutionary Synthesis Center (NESCent) for hosting and financially supporting this course. Travel scholarships for 3 participants were entirely funded by NESCent, as part of its Education and Outreach effort. NESCent's Education and Outreach Group is committed to sharing the exciting evolutionary biology research occurring at NESCent and elsewhere. In addition, NESCent is interested in outreach to groups who are underrepresented in evolutionary biology and improving evolution education, and offers resources for scientists, educators, and the general public that meet these goals.

Travel, Lodging and Food

The course will be held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. The closest airport is Raleigh-Durham International Airport (RDU), a 30 minute drive from NESCent.

Participants will be responsible for their own travel, lodging and some meal costs. We will offer a block of rooms in a local hotel at a discounted rate of around $85/night, including tax. Participants can share a room to further reduce their costs. The hotel is within walking distance and also will have a free shuttle service to NESCent.

A light breakfast will be provided everyday. For other meals, NESCent is adjacent to Durham's 9th Street District, which offers many dining options, and a grocery store.