Difference between revisions of "User:Smith"
 
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Design and outline of tutorials for geWorkbench
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==Resources:==
  
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Tutorial Design considerations -
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http://geworkbench.org =
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1. Probably best not to use detailed section numbers, since we cannot autoupdate them in this wiki. Instead, rely on links?
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http://wiki.c2b2.columbia.edu/workbench
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2. Each section should list example data files needed, and these should be part of distribution.
 
  
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http://wiki.c2b2.columbia.edu/workbook/index.php/Genomics_Workbook
  
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Outline for tutorials
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https://sharepoint.c2b2.columbia.edu/c2b2/default.aspx
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        2.1 Before You Begin
 
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        2.2 Getting Started
 
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              Is caWorkbench downloaded and installed?  Link to download and installation
 
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              Important concepts:
 
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                  Use of activated phenotype and marker panels throughout application.
 
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                      What is default active set if no panels are active?
 
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                      Note that there is a new "plot" button that is available only when a gene panel is active.
 
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              The  menu bar - point out that some commands are available both from the menu bar and by right-clicking on a dataset....
 
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        2.3 Loading Data
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http://wiki.c2b2.columbia.edu/mantis/
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              2.3.1 File types supported
 
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                    Expression
 
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                        Affymetrix MAS5/GCOS (text files output by Affymetrix software)
 
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                        Affymetrix File Matrix (.exp)(a geWorkbench defined format)
 
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                        RMAExpress Processed File
 
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                        GenePix
 
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                        Note - the type "Normalized no-confidence expression matix" has switched the phenotype and gene labels -don't use until fixed.
 
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                    Genotypic
 
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                        Genotypic data files - is this working?
 
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                    Sequence
 
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                        Fasta
 
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                    Pattern Detection
 
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                        Pattern Files
 
  
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              2.3.2 Loading MAS5/GCOS type files
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http://wiki.c2b2.columbia.edu/mantis/view_all_bug_page.php
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                        Use the 10 cardiomyopathy files from Harvard.
 
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                        What happens the first time a new chip-type is loaded - how long does it take, what is happening, what internal files are being built?
 
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              2.3.3 Merging loaded data
 
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              2.3.4 Loading matrix format files
 
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                        Include webmatrix2000G?, webmatrix4000G? and webmatrix.exp?
 
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                    Note - explain matrix format in an appendix
 
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              2.3.5 Other file types supportedLoading RMAExpress files
 
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                    Must generate an example RMAExpress file, start with harvard cardio files?
 
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        2.4 Working with Marker and Phenotype Panels
 
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                    Use the cardiomyopathy dataset created in 2.3
 
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                2.4.1 Creating Phenotype Panels
 
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                2.4.2 Assigning Case/Control status
 
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                2.4.3 Activating a phenotype panel
 
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                2.4.4 Creating Gene/Marker Panels
 
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                2.4.5 Activating a phenotype panel
 
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        2.5 Saving data files
 
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                Use the cardiomyopathy dataset annotated in 2.4
 
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                2.5.1 Save to matrix file
 
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          2.5 Visualize Gene Expression
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http://wiki.c2b2.columbia.edu/mantis/login_page.php
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          2.6 Filter and Normalize Data
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                2.6.1 Normalize
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http://wiki.c2b2.columbia.edu/isrce/index.php/MARINa,_IDEA,_CUPID_Grid_Service_Implementation
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                2.6.2 Filter
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          2.7 Clustering Gene Expression Data
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          2.8 Differential Expression
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http://gforge.nci.nih.gov
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                2.8.1 T Test
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          2.9 Regulatory Network
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http://gforge.nci.nih.gov/projects/geworkbench
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          2.10 Integrated Annotation Information
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          2.11 Enrichment Analysis
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http://wiki.c2b2.columbia.edu/informatics/
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          2.12 Sequence Analysis
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same as
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          2.13 Pattern Discovery
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(http://helpdesk.cu-genome.org/informatics/)
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          2.14 Promoter Analysis
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ICTVdb
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http://wiki.c2b2.columbia.edu/ictvdb/
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nonpublic documents:
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adcvs.cu-genome.org:/cvs/magnet

Latest revision as of 13:11, 6 August 2013

Resources:

http://geworkbench.org = http://wiki.c2b2.columbia.edu/workbench

http://wiki.c2b2.columbia.edu/workbook/index.php/Genomics_Workbook

https://sharepoint.c2b2.columbia.edu/c2b2/default.aspx

http://wiki.c2b2.columbia.edu/mantis/

http://wiki.c2b2.columbia.edu/mantis/view_all_bug_page.php

http://wiki.c2b2.columbia.edu/mantis/login_page.php

http://wiki.c2b2.columbia.edu/isrce/index.php/MARINa,_IDEA,_CUPID_Grid_Service_Implementation


http://gforge.nci.nih.gov

http://gforge.nci.nih.gov/projects/geworkbench

http://wiki.c2b2.columbia.edu/informatics/ same as (http://helpdesk.cu-genome.org/informatics/)


ICTVdb


http://wiki.c2b2.columbia.edu/ictvdb/

nonpublic documents:

adcvs.cu-genome.org:/cvs/magnet

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