Difference between revisions of "User:Scott/Schedule Draft"

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Dave leaves on the 28th
 +
Sheldon arrives on the 27th
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{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
|-
 
|-
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| colspan="3" |
 
| colspan="3" |
 
|-
 
|-
−
! rowspan="10" style="background-color: #bbffff" | Friday<br />August 24
+
! rowspan="9" style="background-color: #bbffff" | Saturday<br />August 25
 
! style="background-color: #ccffff" | 8:30am
 
! style="background-color: #ccffff" | 8:30am
−
| style="background-color: #ddffff" align="center" | '''[[Introduction]] and [[GMOD Overview|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 [[GMOD Overview|Overview]]'''<br />[[User:Scott|Scott Cain]] and [[User:Girlwithglasses|Amelia Ireland]]<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" | 10:40am
 
! style="background-color: #ccffff" | 10:40am
−
| style="background-color: #ddffff" align="center" | '''[[VMware Setup]]'''<br />'''Everyone'''<br />Get the GMOD course VMware image up and running on your laptop.
+
| style="background-color: #ddffff" align="center" | '''[[AWS Setup]]'''<br />'''Everyone'''<br />Get the GMOD course AWS images up and running.
 
|-
 
|-
 
! style="background-color: #ccffff" | 11:45pm
 
! style="background-color: #ccffff" | 11:45pm
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| style="background-color: #ddffff" align="center" | '''[[GFF3]] and [[SOBA]]'''<br />'''[[User:Scott|Scott Cain]] and [[User:Bmoore|Barry Moore]]'''<br />GFF3 is the standard genome annotation format used by GMOD's genomic tools and many others.  [[SOBA]] is a [[GFF3]] analysis package.
 
| style="background-color: #ddffff" align="center" | '''[[GFF3]] and [[SOBA]]'''<br />'''[[User:Scott|Scott Cain]] and [[User:Bmoore|Barry Moore]]'''<br />GFF3 is the standard genome annotation format used by GMOD's genomic tools and many others.  [[SOBA]] is a [[GFF3]] analysis package.
 
|-
 
|-
−
! style="background-color: #ccffff" | 2:45pm
+
! style="background-color: #ccffdd" | 8:30am
−
| style="background-color: #ddffff" align="center" | '''[[JBrowse]]'''<br />[[User:MitchSkinner|Mitch Skinner]]<br />[[gmod:JBrowse|JBrowse]] installation, configuration and administration; converting [[gmod:GFF3|GFF3]] to [[gmod:Glossary#JSON|JSON]] and loading it into JBrowse.
+
| style="background-color: #ddffdd" align="center" | '''[[MAKER]]'''<br />[[User:Bmoore|Barry Moore]] and [[User:Daniel_Ence|Daniel Ence]]<br />[[gmod:MAKER|MAKER]] overview, installation, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality; Advanced [[gmod:MAKER|MAKER]] configuration, re-annotation options, and improving annotation quality
 
|-
 
|-
 
! style="background-color: #ccffff" | 4:00pm
 
! style="background-color: #ccffff" | 4:00pm
 
| style="background-color: #ddffff" align="center" | '''Reception'''<br />Get to know your fellow course participants ''and'' [http://nescent.org/dir/ NESCent researchers].  That, and, free beer.
 
| style="background-color: #ddffff" align="center" | '''Reception'''<br />Get to know your fellow course participants ''and'' [http://nescent.org/dir/ NESCent researchers].  That, and, free beer.
−
|-
 
−
! style="background-color: #ccffff" | 5:00pm
 
−
| style="background-color: #ddffff" align="center" | '''[[JBrowse]] II'''<br />[[User:MitchSkinner|Mitch Skinner]]
 
 
|-
 
|-
 
! style="background-color: #ccffff" | 6:00pm
 
! style="background-color: #ccffff" | 6:00pm
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|-
 
|-
 
! style="background-color: #ccffff" | 7:30pm
 
! style="background-color: #ccffff" | 7:30pm
−
| style="background-color: #ddffff" align="center" | '''[[GFF3]], [[SOBA]] and [[JBrowse]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
+
| style="background-color: #ddffff" align="center" | '''[[GFF3]], [[SOBA]] and [[MAKER]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
 
|-
 
|-
 
! style="background-color: #ccffff" | 9:00pm
 
! style="background-color: #ccffff" | 9:00pm
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| colspan="3" |
 
| colspan="3" |
 
|-
 
|-
−
! rowspan="7" style="background-color: #bbffcc" | Wednesday<br />March 9
+
! rowspan="7" style="background-color: #bbffcc" | Sunday<br />August 26
 
|-
 
|-
−
! style="background-color: #ccffdd" | 8:30am
+
! style="background-color: #ffffbb" | 8:30am
−
| style="background-color: #ddffdd" align="center" | '''[[MAKER]]'''<br />[[User:Bmoore|Barry Moore]]<br />[[gmod:MAKER|MAKER]] overview, installation, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality; Advanced [[gmod:MAKER|MAKER]] configuration, re-annotation options, and improving annotation quality
+
| style="background-color: #ffffcc" align="center" |'''[[Tripal]]'''<br />[[User:Sficklin|Stephen Ficklin]]<br />[[gmod:Tripal|Tripal]] is a web front end to [[gmod:Chado|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: #ccffdd" | 12:30pm
 
! style="background-color: #ccffdd" | 12:30pm
 
| style="background-color: #ddffdd" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
| style="background-color: #ddffdd" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
|-
 
|-
−
! style="background-color: #ccffdd" | 1:45pm
+
! style="background-color: #ccffff" | 1:45pm
−
| style="background-color: #ddffdd" align="center" | '''[[Chado]]'''<br />[[User:ScottCain|Scott Cain]]
+
| style="background-color: #ddffff" align="center" | '''[[JBrowse]]'''<br />[[User:RobertBuels|Rob Buels]]<br />[[gmod:JBrowse|JBrowse]] installation, configuration and administration; converting [[gmod:GFF3|GFF3]] to [[gmod:Glossary#JSON|JSON]] and loading it into JBrowse.
 
|-
 
|-
 
! style="background-color: #ccffdd" | 6:00pm
 
! style="background-color: #ccffdd" | 6:00pm
Line 55: Line 56:
 
|-
 
|-
 
! style="background-color: #ccffdd" | 7:30pm
 
! style="background-color: #ccffdd" | 7:30pm
−
| style="background-color: #ddffdd" align="center" | '''[[MAKER]] and [[Chado]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
+
| style="background-color: #ddffdd" align="center" | '''[[JBrowse]] and [[Tripal]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
 
|-
 
|-
 
! style="background-color: #ccffdd" | 9:00pm
 
! style="background-color: #ccffdd" | 9:00pm
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| colspan="3" |
 
| colspan="3" |
 
|-
 
|-
−
! rowspan="7" style="background-color: #ffffaa"| Thursday<br />March 10
+
! rowspan="7" style="background-color: #ffffaa"| Monday<br />August 27
 
|-
 
|-
−
! style="background-color: #ffffbb" | 8:30am
+
! style="background-color: #ffddcc" | 8:30am
−
| style="background-color: #ffffcc" align="center" |'''[[Tripal]]'''<br />[[User:Sficklin|Stephen Ficklin]]<br />[[gmod:Tripal|Tripal]] is a web front end to [[gmod:Chado|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" | '''[[Apollo]]'''<br />[[User:Elee|Ed Lee]]<br />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.
 
|-
 
|-
 
! style="background-color: #ffffbb" | 12:30pm
 
! style="background-color: #ffffbb" | 12:30pm
 
| style="background-color: #ffffcc" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
| style="background-color: #ffffcc" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
|-
 
|-
−
! style="background-color: #ffffbb" | 1:45pm
+
! style="background-color: #ffcccc" | 1:45pm
−
| style="background-color: #ffffcc" align="center" |'''[[InterMine]]'''<br />[[User:Alex@flymine.org|Alex Kalderimis]]<br />[[gmod:InterMine|InterMine]] installation and configuration.
+
| style="background-color: #ffdddd" align="center" |'''[[Galaxy]]'''<br />[[User:Clements|Dave Clements]]<br />Introduction; Installation and configuration of [[gmod:Galaxy|Galaxy]]; Defining your own tools; ...
 
|-
 
|-
 
! style="background-color: #ffffbb" | 6:00pm
 
! style="background-color: #ffffbb" | 6:00pm
Line 77: Line 78:
 
|-
 
|-
 
! style="background-color: #ffffbb" | 7:30pm
 
! style="background-color: #ffffbb" | 7:30pm
−
| style="background-color: #ffffcc" align="center" | '''[[Tripal]] and [[InterMine]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
+
| style="background-color: #ffffcc" align="center" | '''[[Galaxy]] and [[Apollo]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
 
|-
 
|-
 
! style="background-color: #ffffbb" | 9:00pm
 
! style="background-color: #ffffbb" | 9:00pm
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| colspan="3" |
 
| colspan="3" |
 
|-
 
|-
−
! rowspan="9" style="background-color: #ffccaa" | Friday<br />March 11
+
! rowspan="7" style="background-color: #ffccaa" | Tuesday<br />August 28
 
|-
 
|-
 
! style="background-color: #ffddcc" | 8:30am
 
! style="background-color: #ffddcc" | 8:30am
Line 92: Line 93:
 
| style="background-color: #ffeedd" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
| style="background-color: #ffeedd" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
|-
 
|-
−
! style="background-color: #ffddcc" | 1:45pm
+
! style="background-color: #ffcccc" | 1:45am
−
| style="background-color: #ffeedd" align="center" | '''[[Apollo]]'''<br />[[User:Elee|Ed Lee]]<br />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.
+
| style="background-color: #ffdddd" align="center" |'''[[GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]]
−
|-
+
−
! style="background-color: #ffddcc" | 3:45pm
+
−
| style="background-color: #ffeedd" align="center" | '''[http://www.ilovelocopops.com/ Locopops Break]'''
+
−
|-
+
−
! style="background-color: #ffddcc" | 4:15pm
+
−
| style="background-color: #ffeedd" align="center" | '''[[Apollo]] II'''<br />[[User:Elee|Ed Lee]]
+
 
|-
 
|-
 
! style="background-color: #ffddcc" | 6:00pm
 
! style="background-color: #ffddcc" | 6:00pm
Line 105: Line 100:
 
|-
 
|-
 
! style="background-color: #ffddcc" | 7:30pm
 
! style="background-color: #ffddcc" | 7:30pm
−
| style="background-color: #ffeedd" align="center" | '''[[GBrowse]] and [[Apollo]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
+
| style="background-color: #ffeedd" align="center" | '''[[GBrowse]] and [[GBrowse_syn]] Work Session'''<br />Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data.  The instructors for the day will be available.
 
|-
 
|-
 
! style="background-color: #ffddcc" | 9:00pm
 
! style="background-color: #ffddcc" | 9:00pm
Line 112: Line 107:
 
| colspan="3" |
 
| colspan="3" |
 
|-
 
|-
−
! rowspan="6" style="background-color: #ffbbbb" | Saturday<br />March 12
+
! rowspan="7" style="background-color: #ffbbbb" | Wednesday<br />August 29
−
! style="background-color: #ffcccc" | 8:30am
+
|-
−
| style="background-color: #ffdddd" align="center" |'''[[GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]]
+
! style="background-color: #ccffdd" | 1:45pm
 +
| style="background-color: #ddffdd" align="center" | '''[[Chado]]'''<br />[[User:ScottCain|Scott Cain]]
 
|-
 
|-
 
! style="background-color: #ffcccc" | 12:30pm
 
! style="background-color: #ffcccc" | 12:30pm
 
| style="background-color: #ffdddd" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
| style="background-color: #ffdddd" align="center" | '''Lunch'''<br />on your own, on nearby Ninth Street
 
|-
 
|-
−
! style="background-color: #ffcccc" | 1:45pm
+
! style="background-color: #ffffbb" | 8:30am
−
| style="background-color: #ffdddd" align="center" |'''[[Galaxy]]'''<br />[[User:Clements|Dave Clements]]<br />Introduction; Installation and configuration of [[gmod:Galaxy|Galaxy]]; Defining your own tools; ...
+
| style="background-color: #ffffcc" align="center" |'''Student presentations, questions, etc.'''<br />Some time at the end of the class to clear up lingering questions or brag about cool things you've done.
 
|-
 
|-
 
! style="background-color: #ffcccc" | 5:45pm
 
! style="background-color: #ffcccc" | 5:45pm

Latest revision as of 19:48, 21 August 2012

Dave leaves on the 28th Sheldon arrives on the 27th


Date Time Session
Saturday
August 25 		8:30am Introduction and Overview
Scott Cain and Amelia Ireland
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
10:40am AWS Setup
Everyone
Get the GMOD course AWS images up and running.
11:45pm Lunch
Catered, at NESCent
1:00pm GFF3 and SOBA
Scott Cain and Barry Moore
GFF3 is the standard genome annotation format used by GMOD's genomic tools and many others. SOBA is a GFF3 analysis package.
8:30am MAKER
Barry Moore and Daniel Ence
MAKER overview, installation, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality; Advanced MAKER configuration, re-annotation options, and improving annotation quality
4:00pm Reception
Get to know your fellow course participants and NESCent researchers. That, and, free beer.
6:00pm Dinner
on your own, on nearby Ninth Street
7:30pm GFF3, SOBA and MAKER Work Session
Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data. The instructors for the day will be available.
9:00pm Day ends
Sunday
August 26
8:30am 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.
12:30pm Lunch
on your own, on nearby Ninth Street
1:45pm JBrowse
Rob Buels
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
6:00pm Dinner
on your own, on nearby Ninth Street
7:30pm JBrowse and Tripal Work Session
Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data. The instructors for the day will be available.
9:00pm Day ends
Monday
August 27
8:30am 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.
12:30pm Lunch
on your own, on nearby Ninth Street
1:45pm Galaxy
Dave Clements
Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
6:00pm Dinner
on your own, on nearby Ninth Street
7:30pm Galaxy and Apollo Work Session
Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data. The instructors for the day will be available.
9:00pm Day ends
Tuesday
August 28
8:30am GBrowse
Scott Cain
12:30pm Lunch
on your own, on nearby Ninth Street
1:45am GBrowse_syn
Sheldon McKay
6:00pm Dinner
on your own, on nearby Ninth Street
7:30pm GBrowse and GBrowse_syn Work Session
Your chance to ask more detailed questions and apply what you learned in today's sessions to your own data. The instructors for the day will be available.
9:00pm Day ends
Wednesday
August 29
1:45pm Chado
Scott Cain
12:30pm Lunch
on your own, on nearby Ninth Street
8:30am Student presentations, questions, etc.
Some time at the end of the class to clear up lingering questions or brag about cool things you've done.
5:45pm Resources and Wrapup
Scott Cain
6:30 Spring Training Ends
7:00 pm Closing Dinner
Retrieved from "http://gmod.org/mediawiki/index.php?title=User:Scott/Schedule_Draft&oldid=21120"