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| − | Design and outline of tutorials for geWorkbench
| + | ==Resources:== |
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| − | Tutorial Design considerations -
| + | http://geworkbench.org = |
| − | 1. Probably best not to use detailed section numbers, since we cannot autoupdate them in this wiki. Instead, rely on links?
| + | http://wiki.c2b2.columbia.edu/workbench |
| − | 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
| + | https://sharepoint.c2b2.columbia.edu/c2b2/default.aspx |
| − | 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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| − | - if no panels are activated, the "Activated Arrays" and "Activated Markers" check boxes should have no effect.
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| − | - if gene or phenotype panels are activated, then these check boxes should control what is used or displayed-
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| − | -- if one of the boxes is checked, only activated markers or arrays will be used.
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| − | -- if the box is not checked, then ('''in most cases - are there any exceptions?''') the gene or phenotype panels will be ignored and all arrays or markers will be used.
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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
| + | http://wiki.c2b2.columbia.edu/mantis/ |
| − | 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
| + | http://wiki.c2b2.columbia.edu/mantis/view_all_bug_page.php |
| − | 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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| − |
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| − | [ These examples not really needed.....
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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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| − | ]
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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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| − | 2.6 Visualize Gene Expression
| + | http://wiki.c2b2.columbia.edu/mantis/login_page.php |
| − | Microarray Panel
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| − | Point out intensity and array sliders, color key and array name.
| + | http://wiki.c2b2.columbia.edu/isrce/index.php/MARINa,_IDEA,_CUPID_Grid_Service_Implementation |
| − | Color Mosaic
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| − | Point out only displays when "Display" button pushed.
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| − | Point out intensity, accession, gene height and width controls.
| + | http://gforge.nci.nih.gov |
| − | ??Explain whether remaining controls work or not: Pat,Abs,Ratio.???
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| − | Expression Profiles
| + | http://gforge.nci.nih.gov/projects/geworkbench |
| − | - displays expression level against array number. Each marker is a separate color line.
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| − | Expression Value Distribution
| + | http://wiki.c2b2.columbia.edu/informatics/ |
| − | - for a single array, plots expression value against marker number.
| + | same as |
| − | 2.6 Filter and Normalize Data
| + | (http://helpdesk.cu-genome.org/informatics/) |
| − | 2.6.1 Normalize
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| − | 2.6.2 Filter
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| − | 2.7 Clustering Gene Expression Data
| + | ICTVdb |
| − | 2.8 Differential Expression
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| − | 2.8.1 T Test
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| − | 2.9 Regulatory Network
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| − | 2.10 Integrated Annotation Information
| + | http://wiki.c2b2.columbia.edu/ictvdb/ |
| − | 2.11 Enrichment Analysis
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| − | 2.12 Sequence Analysis
| + | nonpublic documents: |
| − | 2.13 Pattern Discovery
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| − | 2.14 Promoter Analysis
| + | adcvs.cu-genome.org:/cvs/magnet |
