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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| <span style="font-size: 200%; line-height: 120%"><b>2012 GMOD Summer School</b><br />August 24-29, 2012<br />[http://www.nescent.org/ NESCent]<br />Durham, NC, USA</span><br />
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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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[https://www.nescent.org/courses/2012/gmod/Main_Page GMOD 2012 Summer School wiki]
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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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= Introduction =
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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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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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==The Course==
  
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= Application =
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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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The application period is now closed, though if you would like to be placed on a waiting list, you can still fill it out.  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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The course covered the following topics in detail:
  
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= Schedule =
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{| class="wikitable"
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! Topic
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<center>
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! Tutorial
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{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
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! Instructor
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! Affiliation; GMOD role
 
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! rowspan="1" style="background-color: #ffffaa" | Saturday<br />August 25
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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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! style="background-color: #ffffcc" align="center" rowspan="5" | '''[[2012 GMOD Summer School]]'''
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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; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]] &bull; [[SOBA]]'''
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</div>
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! rowspan="1" style="background-color: #ffffaa" | Sunday<br />August 26
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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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! rowspan="1" style="background-color: #ffffaa" | Monday<br />August 27
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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" | Tuesday<br />August 28
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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-6:00pm<br />7:30pm-9pm
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! rowspan="1" style="background-color: #ffffaa" | Wednesday<br />August 29
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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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! 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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| [[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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| GMOD Project Coordinator; [[Chado]], [[GBrowse]]
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| [http://oicr.on.ca/ Ontario Institute for Cancer Research]
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| [[User:Clements|Dave Clements]]
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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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| [[Galaxy]]
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| [http://galaxyproject.org/ Galaxy Project], [http://emory.edu/ Emory University]
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| [[User:sficklin|Stephen Ficklin]]
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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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| [[Tripal]]
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| [http://www.wsu.edu Washington State University]
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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://iplantcollaborative.org iPlant Collaborative], [http://www.cshl.edu CSHL]
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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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| [[User:Daniel Ence|Daniel Ence]]
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| [[MAKER]]
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| [http://utah.edu University of Utah]
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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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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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= Costs =
 
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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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= Travel, Lodging and Meals =
 
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==Getting from Duke Tower to NESCent==
 
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While there is a shuttle mentioned below that you can take to and from Duke Tower, I will be walking to NESCent in the morning.  Since we have a start time of 8:30, I was planning on leaving Duke Tower promptly at 8:00.  For anybody who would like to walk with me, we'll meet in the courtyard by the tower and walk from there.  On Monday morning, I'll be wearing my GMOD shirt, so I'll be easy to recognize.
 
  
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==Hotel==
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==Course Work==
  
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NESCent has reserved a block of rooms at [http://duketower.com/ Duke Tower] for participants. Mention NESCent/GMOD when booking your room. The rooms are suite-style, with a separate living room and kitchen. Some rooms have two double beds, so participants could share a room to reduce costs. There is a shuttle between NESCent and Duke Tower ($2.00 per room; per trip), or the hotel is a 25 minute walk through the lovely [https://maps.google.com/maps?saddr=807+W+Trinity+Ave,+Durham,+North+Carolina+27701+(Duke+Tower+Hotel)&daddr=2024+W+Main+St,+Durham,+NC+27705&hl=en&sll=36.0056,-78.914015&sspn=0.013609,0.03238&geocode=FWFkJQIdjANM-yHQLsgj-ICvIClPC6kedeSsiTHQLsgj-ICvIA%3BFcBsJQIdOLlL-ynRTfbNAOSsiTGQRAw6gUnjOw&dirflg=w&mra=prev&t=m&z=16 Trinity Park neighborhood and East Campus] (''I will be walking, since it is a short walk and quite pleasant--Scott''). You are, of course, free to choose alternate accommodations in Durham, although most less expensive options may require a car for transportation.
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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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'''Some information from the hotel:'''
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==Sponsors==
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* Check in time is 3:00pm and check out time is 11am.
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* If you arrive after hours, you will check in with the guard by paging him from the telephone located near the office door. There are posted instructions for the paging system. The guard will meet you at the office and give you your key.
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* Please be sure to bring all personal toiletries, we supply only small bars of soap. There is no hairdryer in the unit.
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* There is a full kitchen including a coffee maker and filters, but we do not supply coffee.
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* There is wired high-speed internet access in all units at no charge. You may borrow an Ethernet cable from the business office.
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* There is a coin-operated laundry here on the property. You may exchange dollars for quarters with us in the office.
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* The Tower Cafe is open For Continental Breakfast - $5.00 Per Adult.
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= Feedback =
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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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{{2010GMODCourseFeedback|Previous [[GMOD Schools]] Feedback}}
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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.
  
 
[[Category:Education and Outreach]]
 
[[Category:Education and Outreach]]
 
[[Category:Events]]
 
[[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"