Difference between revisions of "2009 GMOD Summer School - Americas"

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| [[File:2009SummerSchoolAmericas300.png|center]]
 
| <span style="font-size: 200%; line-height: 120%"><b>2009 GMOD Summer School - Americas</b><br />16-19 July, 2009<br />[http://www.nescent.org/ NESCent]<br />Durham, NC, USA</span>
 
| <span style="font-size: 200%; line-height: 120%"><b>2009 GMOD Summer School - Americas</b><br />16-19 July, 2009<br />[http://www.nescent.org/ NESCent]<br />Durham, NC, USA</span>
 
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__NOTITLE__
 
  
The '''''2009 GMOD Summer School - Americas''''' will be held 16-19 July at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina.  Like the [[2008 GMOD Summer School]], this course will focus on installing, configuring and integrating popular [[GMOD Components]].
+
The '''''2009 GMOD Summer School - Americas''''' was held 16-19 July at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina.  Like the [[2008 GMOD Summer School]], this course focused on installing, configuring and integrating popular [[GMOD Components]].
  
Another [[GMOD Summer School]] is being offered in [[2009 GMOD Summer School - Europe|Oxford, UK in August]], as part of the [[GMOD Europe 2009]] week.
+
The course wiki is [https://www.nescent.org/courses/2009/gmod/Americas here] (login required).
  
{{2009SummerSchoolApplicationBlurb}}
+
Another [[GMOD Summer School]] was offered in [[2009 GMOD Summer School - Europe|Oxford, UK in August, 2009]], as part of [[GMOD Europe 2009]].
  
== Draft Program ==
+
== Program ==
 +
 
 +
The program featured 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]].
 +
<div class="emphasisbox">
 +
The summer school GMOD component sessions are available as [[Training and Outreach#Online Tutorials|online tutorials]].  To access the tutorials, follow the links for [[MAKER Tutorial|MAKER]], [[JBrowse Tutorial|JBrowse]], [[Chado Tutorial|Chado]], [[Apollo Tutorial|Apollo]], [[GBrowse Tutorial|GBrowse]], [[BioMart Tutorial|BioMart]], [[GBrowse_syn Tutorial|GBrowse_syn]], and [[Tripal Tutorial|Tripal]]
 +
</div>
  
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]].
 
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
|-
 
|-
! width="10%" style="background-color: #99ccff" | Date
 
 
! width="7%"  style="background-color: #99ccff" | Time
 
! width="7%"  style="background-color: #99ccff" | Time
! width="83%" style="background-color: #99ccff" | Session
+
! width="93%" style="background-color: #99ccff" | Session
 
|-
 
|-
| colspan="3" |
+
| colspan="2" |
 
|-
 
|-
! rowspan="8" style="background-color: #bbffff" | Thursday<br />July 16
+
! colspan="2" style="background-color: #bbffff" | Thursday<br />July 16
 +
|-
 
! style="background-color: #ccffff" | 8:45am
 
! style="background-color: #ccffff" | 8:45am
 
| style="background-color: #ddffff" align="center" | '''Introduction and Overview'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />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
 
| style="background-color: #ddffff" align="center" | '''Introduction and Overview'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />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
 
|-
 
|-
 
! style="background-color: #ccffff" | 10:25am
 
! style="background-color: #ccffff" | 10:25am
| style="background-color: #ddffff" align="center" | '''VMware and BioPerl Setup'''<br />'''Everyone'''<br />Get the GMOD Summer School [[#System Requirements|VMware]] image up and running on your laptop, and then finish installation of [[BioPerl]].
+
| style="background-color: #ddffff" align="center" | '''[[VMware]] and [[BioPerl]] Setup'''<br />'''Everyone'''<br />Get the GMOD Summer School [[#System Requirements|VMware]] image up and running on your laptop, and then finish installation of [[BioPerl]].
 
|-
 
|-
 
! style="background-color: #ccffff" | 12:15pm
 
! style="background-color: #ccffff" | 12:15pm
Line 35: Line 38:
 
|-
 
|-
 
! style="background-color: #ccffff" | 1:15pm
 
! style="background-color: #ccffff" | 1:15pm
| style="background-color: #ddffff" align="center" | '''[[MAKER]] I'''<br />[[User:Carsonholt|Carson Holt]]<br />Maker overview, installation, and basic configuration for annotating genomic sequence
+
| style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER I]]'''<br />[[User:Carsonholt|Carson Holt]]<br />[[MAKER]] overview, installation, and basic configuration for annotating genomic sequence
 
|-
 
|-
 
! style="background-color: #ccffff" | 4:30pm
 
! style="background-color: #ccffff" | 4:30pm
Line 41: Line 44:
 
|-
 
|-
 
! style="background-color: #ccffff" | 6:30pm
 
! style="background-color: #ccffff" | 6:30pm
| style="background-color: #ddffff" align="center" | '''[[MAKER]] II'''<br />[[User:Carsonholt|Carson Holt]]<br />Advanced Maker configuration, re-annotation options, and improving annotation quality
+
| style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER II]]'''<br />[[User:Carsonholt|Carson Holt]]<br />Advanced [[MAKER]] configuration, re-annotation options, and improving annotation quality
 
|-
 
|-
 
! style="background-color: #ccffff" | 7:30pm
 
! style="background-color: #ccffff" | 7:30pm
| style="background-color: #ddffff" align="center" | '''[[JBrowse]]'''<br />[[User:MitchSkinner|Mitch Skinner]]<br />JBrowse installation, configuration and administration; converting [[GFF3]] to [[Glossary#JSON|JSON]] and loading it into JBrowse.
+
| style="background-color: #ddffff" align="center" | '''[[JBrowse Tutorial|JBrowse]]'''<br />[[User:MitchSkinner|Mitch Skinner]]<br />[[JBrowse]] installation, configuration and administration; converting [[GFF3]] to [[Glossary#JSON|JSON]] and loading it into JBrowse.
 
|-
 
|-
 
! style="background-color: #ccffff" | 9:00pm
 
! style="background-color: #ccffff" | 9:00pm
 
| style="background-color: #ddffff" align="center" | Day ends
 
| style="background-color: #ddffff" align="center" | Day ends
 
|-
 
|-
| colspan="3" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="background-color: #bbffcc"| Friday<br />July 17
 
|-
 
|-
! rowspan="7" style="background-color: #bbffcc"| Friday<br />July 17
 
 
! style="background-color: #ccffdd" | 8:45am
 
! style="background-color: #ccffdd" | 8:45am
| style="background-color: #ddffdd" align="center" | '''[[Chado]] I'''<br />[[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
+
| style="background-color: #ddffdd" align="center" | '''[[Chado Tutorial|Chado I]]'''<br />[[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
 
|-
 
|-
 
! style="background-color: #ccffdd" | 12:30pm
 
! style="background-color: #ccffdd" | 12:30pm
Line 59: Line 63:
 
|-
 
|-
 
! style="background-color: #ccffdd" | 1:30pm
 
! style="background-color: #ccffdd" | 1:30pm
| style="background-color: #ddffdd" align="center" | '''[[Chado]] II'''<br />[[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
+
| style="background-color: #ddffdd" align="center" | '''[[Chado Tutorial|Chado II]]'''<br />[[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
 
|-
 
|-
 
! style="background-color: #ccffdd" | 3:00pm
 
! style="background-color: #ccffdd" | 3:00pm
| style="background-color: #ddffdd" align="center" | '''[[Apollo]] I'''<br />[[User:Elee|Ed Lee]]<br />Overview, basic installation, basic configuration, reading/writing data, and remote analyses.
+
| style="background-color: #ddffdd" align="center" | '''[[Apollo Tutorial|Apollo I]]'''<br />[[User:Elee|Ed Lee]]<br />Overview, basic installation, basic configuration, reading/writing data, and remote analyses.
 
|-
 
|-
 
! style="background-color: #ccffdd" | 5:30pm
 
! style="background-color: #ccffdd" | 5:30pm
Line 68: Line 72:
 
|-
 
|-
 
! style="background-color: #ccffdd" | 7:00pm
 
! style="background-color: #ccffdd" | 7:00pm
| style="background-color: #ddffdd" align="center" | '''[[Apollo]] II'''<br />[[User:Elee|Ed Lee]]<br />Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance.
+
| style="background-color: #ddffdd" align="center" | '''[[Apollo Tutorial|Apollo II]]'''<br />[[User:Elee|Ed Lee]]<br />Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance.
 
|-
 
|-
 
! style="background-color: #ccffdd" | 9:00pm
 
! style="background-color: #ccffdd" | 9:00pm
 
| style="background-color: #ddffdd" align="center" | Day ends
 
| style="background-color: #ddffdd" align="center" | Day ends
 
|-
 
|-
| colspan="3" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="background-color: #ffffaa" | Saturday<br />July 18
 
|-
 
|-
! rowspan="7" style="background-color: #ffffaa" | Saturday<br />July 18
 
 
! style="background-color: #ffffbb" | 8:45am
 
! style="background-color: #ffffbb" | 8:45am
| style="background-color: #ffffcc" align="center" |'''[[GBrowse]] I'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]<br />
+
| style="background-color: #ffffcc" align="center" |'''[[GBrowse Tutorial|GBrowse I]]'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]<br />
 
|-
 
|-
 
! style="background-color: #ffffbb" | 12:30pm
 
! style="background-color: #ffffbb" | 12:30pm
Line 83: Line 88:
 
|-
 
|-
 
! style="background-color: #ffffbb" | 1:30pm
 
! style="background-color: #ffffbb" | 1:30pm
| style="background-color: #ffffcc" align="center" |'''[[GBrowse]] II'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]
+
| style="background-color: #ffffcc" align="center" |'''[[GBrowse Tutorial|GBrowse II]]'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]
 
|-
 
|-
 
! style="background-color: #ffffbb" | 2:30pm
 
! style="background-color: #ffffbb" | 2:30pm
| style="background-color: #ffffcc" align="center" |'''[[BioMart]]'''<br />[[User:Junjun|Junjun Zhang]]<br />Introduction; exploring over 20 public databases through BioMart central portal; system installation; accessing BioMart server via API, webservice and [[DAS]]; configuration of BioMart server including federation; demonstration of creating data mart.
+
| style="background-color: #ffffcc" align="center" |'''[[BioMart Tutorial|BioMart]]'''<br />[[User:Junjun|Junjun Zhang]]<br />Introduction; exploring over 20 public databases through [[BioMart]] central portal; system installation; accessing BioMart server via API, webservice and [[DAS]]; configuration of BioMart server including federation; demonstration of creating data mart.
 
|-
 
|-
 
! style="background-color: #ffffbb" | 6:00pm
 
! style="background-color: #ffffbb" | 6:00pm
Line 98: Line 103:
 
| style="background-color: #ffffcc" align="center" |Day ends
 
| style="background-color: #ffffcc" align="center" |Day ends
 
|-
 
|-
| colspan="3" |
+
| colspan=2" |
 +
|-
 +
! colspan="2" style="background-color: #ffccaa" | Sunday<br />July 19
 
|-
 
|-
! rowspan="5" style="background-color: #ffccaa" | Sunday<br />July 19
 
 
! style="background-color: #ffddcc" | 8:45am
 
! style="background-color: #ffddcc" | 8:45am
| style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]]
+
| style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn Tutorial|GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]]
 
|-
 
|-
 
! style="background-color: #ffddcc" | 12:30pm
 
! style="background-color: #ffddcc" | 12:30pm
Line 108: Line 114:
 
|-
 
|-
 
! style="background-color: #ffddcc" | 1:30pm
 
! style="background-color: #ffddcc" | 1:30pm
| style="background-color: #ffeedd" align="center" |'''[[User:Sficklin#Tripal|Tripal]]'''<br />[[User:sficklin|Stephen Ficklin]]<br />Tripal is a web front end to [[Chado]] databases built on [http://www.drupal.org/ Drupal]. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration.
+
| style="background-color: #ffeedd" align="center" |'''[[Tripal Tutorial|Tripal]]'''<br />[[User:sficklin|Stephen Ficklin]]<br />[[Tripal]] is a web front end to [[Chado]] databases built on [http://www.drupal.org/ Drupal]. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration.
 
|-
 
|-
 
! style="background-color: #ffddcc" | 6:00pm
 
! style="background-color: #ffddcc" | 6:00pm
Line 126: Line 132:
 
|-
 
|-
 
| [[User:Scott|Scott Cain]]
 
| [[User:Scott|Scott Cain]]
| GMOD Project Coordinator
+
| GMOD Project Coordinator; [[Chado]] develoepr
 
| [http://www.oicr.on.ca/ Ontario Institute for Cancer Research]
 
| [http://www.oicr.on.ca/ Ontario Institute for Cancer Research]
 
|-
 
|-
Line 134: Line 140:
 
|-
 
|-
 
| [[User:sficklin|Stephen Ficklin]]
 
| [[User:sficklin|Stephen Ficklin]]
| Lead [[User:Sficklin#Tripal|Tripal]] developer
+
| [[Tripal]] developer
 
| [http://www.genome.clemson.edu/ Clemson University Genomics Institute]
 
| [http://www.genome.clemson.edu/ Clemson University Genomics Institute]
 
|-
 
|-
 
| [[User:Carsonholt|Carson Holt]]
 
| [[User:Carsonholt|Carson Holt]]
| Lead [[MAKER]] developer
+
| [[MAKER]] developer
 
| [http://www.utah.edu University of Utah]
 
| [http://www.utah.edu University of Utah]
 
|-
 
|-
 
| [[User:Elee|Ed Lee]]
 
| [[User:Elee|Ed Lee]]
| Lead [[Apollo]] developer
+
| [[Apollo]] developer
 
| [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)]
 
| [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)]
 
|-
 
|-
 
| [[User:Mckays|Sheldon McKay]]
 
| [[User:Mckays|Sheldon McKay]]
| Lead [[GBrowse_syn]] developer, [[GBrowse]] developer
+
| [[GBrowse_syn]] developer, [[GBrowse]] developer
 
| [http://cshl.edu Cold Spring Harbor Laboratory]
 
| [http://cshl.edu Cold Spring Harbor Laboratory]
 
|-
 
|-
 
| [[User:Jorvis|Joshua Orvis]]
 
| [[User:Jorvis|Joshua Orvis]]
| Lead [[Ergatis]] developer and power [[Chado]] user
+
| [[Ergatis]] developer and power [[Chado]] user
 
| [http://www.igs.umaryland.edu/ Institute for Genome Sciences]
 
| [http://www.igs.umaryland.edu/ Institute for Genome Sciences]
 +
|-
 +
| [[User:MitchSkinner|Mitch Skinner]]
 +
| [[JBrowse]] developer
 +
| [http://berkeley.edu University of California, Berkeley]
 
|-
 
|-
 
| [[User:Junjun|Junjun Zhang]]
 
| [[User:Junjun|Junjun Zhang]]
Line 166: Line 176:
  
 
{|
 
{|
| {{#icon: VmwareLogoSmall.jpg|VMware||http://www.vmware.com}}
+
| [[File:VmwareLogoSmall.jpg|link=http://www.vmware.com|VMware]]
|''Participants are required to bring their own laptops, already capable of running a [http://www.vmware.com VMware] system image.''
+
|''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.
+
The course started with getting a [ftp://ftp.gmod.org/pub/gmod/Courses/2009/SummerSchoolAmericas/GmodSumSch2009Amer1.zip VMware image built specifically for the course] up and running on your machine.  We then built upon that image in each succeeding session.
  
 
{{2009SummerSchoolSystemOptions|$80}}
 
{{2009SummerSchoolSystemOptions|$80}}
 
== Applications ==
 
 
{{2009SummerSchoolApplicationStatus}}
 
  
 
== Cost ==
 
== Cost ==
  
This course will be ''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.
+
This course was ''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.
  
Participants are responsible for their own travel, lodging, and living expenses.  Some travel scholarships are available for participants from underrepresented groups.  Please indicate on your application if you would like to be considered for this option.
+
== Feedback ==
  
== Travel, Lodging and Food ==
+
17 of 25 students provided feedback on the course.
  
The course will be held at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, United States.  The closest airport is [http://www.rdu.com/ 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 $79/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.
+
'''Q: Would you recommend [[GMOD Summer School]] to others?'''
 +
{| class="wikitable"
 +
! No
 +
! Yes, with reservations
 +
! Yes
 +
! No opinion
 +
|-
 +
| 0%
 +
| 12%
 +
! 88%
 +
| 0%
 +
|}
  
Some meals are included in the summer school.  For meals that aren't, NESCent is adjacent to [http://www.ninthst.com/ Durham's 9<sup>th</sup> Street District], which offers many dining options.
 
  
{{2008GMODSummerSchoolFeedback‎}}
+
'''Q: Please rate the quality of the sessions overall, from 1 (very poor) to 3 (average) to 5 (very good), or N.A. if you have no opinion.'''
 +
 
 +
{| class="wikitable"
 +
! Very Poor<br />1
 +
! (Poor)<br />2
 +
! Average<br />3
 +
! (Good)<br />4
 +
! Very Good<br />5
 +
! N.A.
 +
|-
 +
| 0%
 +
| 0%
 +
| 12%
 +
! 59%
 +
| 23%
 +
| 6%
 +
|}
  
 +
[[Category:Tutorials]]
 
[[Category:Education and Outreach]]
 
[[Category:Education and Outreach]]
 +
[[Category:Events]]
 +
[[Category:GMOD Schools]]

Latest revision as of 22:13, 16 April 2014

2009SummerSchoolAmericas300.png
2009 GMOD Summer School - Americas
16-19 July, 2009
NESCent
Durham, NC, USA

The 2009 GMOD Summer School - Americas was held 16-19 July at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like the 2008 GMOD Summer School, this course focused on installing, configuring and integrating popular GMOD Components.

The course wiki is here (login required).

Another GMOD Summer School was offered in Oxford, UK in August, 2009, as part of GMOD Europe 2009.

Program

The program featured 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.

The summer school GMOD component sessions are available as online tutorials. To access the tutorials, follow the links for MAKER, JBrowse, Chado, Apollo, GBrowse, BioMart, GBrowse_syn, and Tripal

Time Session
Thursday
July 16
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, and basic configuration for annotating genomic sequence
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 JBrowse
Mitch Skinner
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
9:00pm Day ends
Friday
July 17
8:45am Chado I
Scott Cain, Joshua Orvis, and Dave Clements
12:30pm Lunch
on your own
1:30pm Chado II
Scott Cain, Joshua Orvis, and Dave Clements
3:00pm Apollo I
Ed Lee
Overview, basic installation, basic configuration, reading/writing data, and remote analyses.
5:30pm Dinner
on your own
7:00pm Apollo II
Ed Lee
Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance.
9:00pm Day ends
Saturday
July 18
8:45am GBrowse I
Scott Cain and Sheldon McKay
12:30pm Lunch
on your own
1:30pm GBrowse II
Scott Cain and Sheldon McKay
2:30pm BioMart
Junjun Zhang
Introduction; exploring over 20 public databases through BioMart central portal; system installation; accessing BioMart server via API, webservice and DAS; configuration of BioMart server including federation; demonstration of creating data mart.
6:00pm Dinner
on your own
7:30pm Open Discussion and User Presentations
Everyone
This optional 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.

9:00pm Day ends
Sunday
July 19
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

Instructor GMOD Affiliation Affiliation
Scott Cain GMOD Project Coordinator; Chado develoepr Ontario Institute for Cancer Research
Dave Clements GMOD Help Desk National Evolutionary Synthesis Center (NESCent)
Stephen Ficklin Tripal developer Clemson University Genomics Institute
Carson Holt MAKER developer University of Utah
Ed Lee Apollo developer Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn developer, GBrowse developer Cold Spring Harbor Laboratory
Joshua Orvis Ergatis developer and power Chado user Institute for Genome Sciences
Mitch Skinner JBrowse developer University of California, Berkeley
Junjun Zhang BioMart developer Ontario Institute for Cancer Research

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 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.

Getting a basic GBrowse up and running on your system will be assigned as homework to be done prior to the course's start.

System Requirements

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

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

VMware on Windows and Linux
Windoze
Linux
A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it.


VMware on Mac OS X

Participants can also bring newer Macs with Intel processors. The Intel processor is a requirement for all the packages discussed below.

Apple
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
VMWareFusionsLogo.jpg
VMware Fusion ($80) allows you to run VMware images, 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.


Mac OS 10.5 (Leopard) and Boot Camp
Boot Camp

The Leopard release of Mac OS (10.5) includes Boot Camp, a feature that allows you to boot your Mac into another operating system, including Windows or Linux. From there you can install the VMware player for your OS.*

* Apple tells you that you can partition your disk drive at any time using Boot Camp. In practice, this appears to only work easily when you first get your system.

Cost

This course was free thanks to NIH grant 1R01HG004483-01 under Ian Holmes, and to the grants of the individual instructors.

Feedback

17 of 25 students provided feedback on the course.


Q: Would you recommend GMOD Summer School to others?

No Yes, with reservations Yes No opinion
0% 12% 88% 0%


Q: Please rate the quality of the sessions overall, from 1 (very poor) to 3 (average) to 5 (very good), or N.A. if you have no opinion.

Very Poor
1
(Poor)
2
Average
3
(Good)
4
Very Good
5
N.A.
0% 0% 12% 59% 23% 6%