Difference between revisions of "2012 GMOD Summer School"

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[[File:Summer-school-splash.jpg|center|2012 Summer School splash screen]]
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Snazzy logo here!<br />
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2012 GMOD Summer School, August 24-29, 2012
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__NOTITLE__
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{{TocRight}}
 
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= Introduction =
 
  
 
The GMOD Summer School is a five day course that covers the use of several widely used GMOD components in the context of a organism or clade database.  The course is taught by members of the projects' development teams.  Applications are competitive, since we generally receive many more applications that we have slots.
 
The GMOD Summer School is a five day course that covers the use of several widely used GMOD components in the context of a organism or clade database.  The course is taught by members of the projects' development teams.  Applications are competitive, since we generally receive many more applications that we have slots.
  
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= Application =
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[https://www.nescent.org/courses/2012/gmod/Main_Page GMOD 2012 Summer School wiki] (contents available to course participants only)
  
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The application is available as a [https://docs.google.com/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LUZxZW04Qm1yZXc6MQ Google form].  The deadline is July 9.
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[[File:GMOD-Summer-School-2012-group.jpg|800px|center|Students and tutors from the 2012 GMOD Summer School]]
  
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= Schedule =
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==The Course==
  
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<center>
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A 5 day hands-on course on GMOD component installation, configuration, and usage. Most sessions were four hours (a half day), and the evenings featured work sessions where the instructors for that day's topics were available to answer questions and help participants use the tools with their data. The instructors on the course were experienced component developers and GMOD project staff.
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{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
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! rowspan="1" style="background-color: #ffffaa" | Saturday<br />August 25
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! style="background-color: #ffffbb" | 8:30am-6:00pm<br />7:30pm-9pm
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! style="background-color: #ffffcc" align="center" rowspan="5" | '''[[2011 GMOD Spring Training]]'''
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<div style="font-weight: normal">A 5 day hands-on course on GMOD Component installation, configuration, and usage. The course will cover these components in detail:
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'''[[Apollo]] &bull; [[MAKER]] &bull; [[GBrowse]] &bull; [[Chado]] &bull; [[InterMine]] &bull; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]] &bull; [[SOBA]]'''
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The course covered the following topics in detail:
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</div>
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{| class="wikitable"
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! Topic
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! Tutorial
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! Instructor
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! Affiliation; GMOD role
 
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! rowspan="1" style="background-color: #ffffaa" | Sunday<br />August 26
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| Amazon Web Services set up || [[AWS_walkthrough|Tutorial]] || [[User:Scott|Scott Cain]] || [http://oicr.on.ca/ Ontario Institute for Cancer Research]<br>GMOD Project Coordinator; [[Chado]], [[GBrowse]]
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! style="background-color: #ffffbb" | 8:30am-6:00pm<br />7:30pm-9pm
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! rowspan="1" style="background-color: #ffffaa" | Monday<br />August 27
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| [[Chado]] || [[Chado Tutorial 2012|Tutorial]] || [[User:Scott|Scott Cain]] || [http://oicr.on.ca/ Ontario Institute for Cancer Research]<br>GMOD Project Coordinator; [[Chado]], [[GBrowse]]
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! style="background-color: #ffffbb" | 8:30am-6:00pm<br />7:30pm-9pm
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|-
 
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! rowspan="1" style="background-color: #ffffaa" | Tuesday<br />August 28
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| [[Galaxy]] || [[Galaxy Tutorial 2012|Tutorial]] || [[User:Clements|Dave Clements]] || [http://galaxyproject.org/ Galaxy Project], [http://emory.edu/ Emory University]<br>[[Galaxy]]
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! style="background-color: #ffffbb" | 8:30am-6:00pm<br />7:30pm-9pm
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! rowspan="1" style="background-color: #ffffaa" | Friday<br />August 29
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| [[GBrowse]] || [[GBrowse Tutorial 2012|Tutorial]] || [[User:Scott|Scott Cain]] || [http://oicr.on.ca/ Ontario Institute for Cancer Research]<br>GMOD Project Coordinator; [[Chado]], [[GBrowse]]
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! style="background-color: #ffffbb" | 8:30am-6:30pm
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</center>
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Most sessions will last half a day. Each night the instructors for that day's topics will be available to answer questions and help participants use the tools with their data.
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= Instructors =
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Sessions are taught by experienced component developers and GMOD project staff:
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<center>
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{| class="wikitable"
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! Instructor
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! GMOD Affiliation
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! Affiliation
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| [[User:Scott|Scott Cain]]
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| [[GBrowse syn]] || [[GBrowse_syn Tutorial 2012|Tutorial]] || [[User:Mckays|Sheldon McKay]] || [http://iplantcollaborative.org iPlant Collaborative], [http://www.cshl.edu CSHL]<br>[[GBrowse_syn]], [[GBrowse]]
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| GMOD Project Coordinator; [[Chado]], [[GBrowse]]
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| [http://www.oicr.on.ca/ Ontario Institute for Cancer Research]
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| [[User:Clements|Dave Clements]]
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| [[GFF3]] || [[GFF Tutorial 2012|Tutorial]] || [[User:Scott|Scott Cain]] || [http://oicr.on.ca/ Ontario Institute for Cancer Research]<br>GMOD Project Coordinator; [[Chado]], [[GBrowse]]
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| [[Galaxy]]
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| [http://usegalaxy.org/ Galaxy, Emory University]
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| [[User:sficklin|Stephen Ficklin]]
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| [[JBrowse]] || [[JBrowse Tutorial 2012|Tutorial]] || [[User:RBuels|Robert Buels]] || [http://berkeley.edu University of California, Berkeley]<br>[[JBrowse]]
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| [[Tripal]]
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| [http://www.wsu.edu Washington State University]
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| Alex Kalderimis
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| [[MAKER]] || [[MAKER Tutorial 2012|Tutorial]] || [[User:Bmoore|Barry Moore]] || [http://utah.edu University of Utah]<br>[[MAKER]]
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| [[InterMine]]
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| [http://flymine.org FlyMine]
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| [[User:Bmoore|Barry Moore]]
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| [[SOBA]] || [[SOBA Tutorial 2012|Tutorial]] || [[User:Bmoore|Barry Moore]] || [http://www.utah.edu University of Utah]<br>[[MAKER]]
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| [[MAKER]]
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| [http://www.utah.edu University of Utah]
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| [[User:Elee|Ed Lee]]
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| [[Tripal]] || [[Tripal Tutorial (v1.0)|Tutorial]] || [[User:sficklin|Stephen Ficklin]] || [http://www.wsu.edu Washington State University]<br>[[Tripal]]
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| [[Apollo]]
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| [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)]
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| [[User:Mckays|Sheldon McKay]]
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| [[WebApollo]] || [[WebApollo Tutorial 2012|Tutorial]] || [[User:Elee|Ed Lee]] || [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)]<br>[[Apollo]], [[WebApollo]]
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| [[GBrowse_syn]], [[GBrowse]]
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| [http://iplantcollaborarive iPlant Collaborative]
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|-
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| [[User:RBuels|Robert Buels]]
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| [[JBrowse]]
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| [http://berkeley.edu University of California, Berkeley]
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</center>
 
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= Prerequisites =
 
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<div class="emphasisbox">
 
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''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
 
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# Comfortable with the Linux command line interface, and
 
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# Comfortable installing packages under Linux.
 
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''A good benchmark for this level of knowledge is that you should be able to get a basic [[GBrowse Install HOWTO|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.
 
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</div>
 
  
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= System Requirements =
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==Course Work==
  
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Previous incarnations of this course used VMware images.  The 2012 instance will use the Amazon Web Service (aka, the cloud).  The only software required to be on students' laptops is a ssh client (like putty for Windows, or the builtin ssh client in the Mac OS), a web browser (preferably up to date (and avoiding Internet Explorer is a good idea)), and possibly (depending on what we do) Java.
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The 2012 Summer School used Amazon Web Services to host virtual GMOD instances containing the software and demo data used during the course. See [[Cloud|GMOD in the Cloud]] for more information on the GMOD Amazon Machine Images available to the public. The tutorials used on the course are available on this wiki for interested persons to work through.
  
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= Costs =
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==Sponsors==
  
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There will be a tuition of $300 charged for the course to cover expenses, primarily instructor travel expenses.
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[[File:NESCentLogo152.jpg|100px|right|link=http://nescent.org|NESCent]]
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GMOD thanks the [http://nescent.org National Evolutionary Synthesis Center (NESCent)] for its continued support of the GMOD project and for providing the venue for this course. 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.
  
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= Travel, Lodging and Meals =
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GMOD thanks the generous grant from the Amazon [http://aws.amazon.com/grants/ AWS in Education program], which provided free compute time on Amazon Web Services for the course tutors and participants.
  
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Suggestions for travel into the Durham, NC area will be forthcoming, as well as a suggested hotel.
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[[Category:Education and Outreach]]
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[[Category:Events]]
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[[Category:Tutorials]]
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[[Category:2012 Summer School]]
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[[Category:GMOD Schools]]

Latest revision as of 18:09, 8 January 2014

2012 Summer School splash screen


The GMOD Summer School is a five day course that covers the use of several widely used GMOD components in the context of a organism or clade database. The course is taught by members of the projects' development teams. Applications are competitive, since we generally receive many more applications that we have slots.

GMOD 2012 Summer School wiki (contents available to course participants only)

Students and tutors from the 2012 GMOD Summer School

The Course

A 5 day hands-on course on GMOD component installation, configuration, and usage. Most sessions were four hours (a half day), and the evenings featured work sessions where the instructors for that day's topics were available to answer questions and help participants use the tools with their data. The instructors on the course were experienced component developers and GMOD project staff.

The course covered the following topics in detail:

Topic Tutorial Instructor Affiliation; GMOD role
Amazon Web Services set up Tutorial Scott Cain Ontario Institute for Cancer Research
GMOD Project Coordinator; Chado, GBrowse
Chado Tutorial Scott Cain Ontario Institute for Cancer Research
GMOD Project Coordinator; Chado, GBrowse
Galaxy Tutorial Dave Clements Galaxy Project, Emory University
Galaxy
GBrowse Tutorial Scott Cain Ontario Institute for Cancer Research
GMOD Project Coordinator; Chado, GBrowse
GBrowse syn Tutorial Sheldon McKay iPlant Collaborative, CSHL
GBrowse_syn, GBrowse
GFF3 Tutorial Scott Cain Ontario Institute for Cancer Research
GMOD Project Coordinator; Chado, GBrowse
JBrowse Tutorial Robert Buels University of California, Berkeley
JBrowse
MAKER Tutorial Barry Moore University of Utah
MAKER
SOBA Tutorial Barry Moore University of Utah
MAKER
Tripal Tutorial Stephen Ficklin Washington State University
Tripal
WebApollo Tutorial Ed Lee Berkeley Bioinformatics Open-source Projects (BBOP)
Apollo, WebApollo

Course Work

The 2012 Summer School used Amazon Web Services to host virtual GMOD instances containing the software and demo data used during the course. See GMOD in the Cloud for more information on the GMOD Amazon Machine Images available to the public. The tutorials used on the course are available on this wiki for interested persons to work through.

Sponsors

NESCent

GMOD thanks the National Evolutionary Synthesis Center (NESCent) for its continued support of the GMOD project and for providing the venue for this course. 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.

GMOD thanks the generous grant from the Amazon AWS in Education program, which provided free compute time on Amazon Web Services for the course tutors and participants.

Retrieved from "http://gmod.org/mediawiki/index.php?title=2012_GMOD_Summer_School&oldid=25056"