GeWorkbench Release 1.0.5
From Informatics
Contents |
Role Assignments
- Release Manager – Kenneth Smith
- Release Engineer – Xiaoqing Zhang
- Tech Lead – Matt Hall
- Tester – Bernd Jagla
- Test Manager – Bernd Jagla
- Technical Writer – Eileen Daly
List of Included Components
<Comment>Every included component should have a dependency sheet listing any external files, executables etc. that are required for it to function, and their expected location (geWorkbench root, data etc).</Comment>
For modules dependencies, please see Additional necessary files included in distribution.
Data Managmenent:
- Arrays/Phenotypes
- Markers
- preferences
- Project Panel
- Session Mgr
File input filters:
- Affy File Format
- CEL File Loader
- Exp. Format
- FASTA Format
- Genepix File Format
- RMA Express Format
Data filters:
- Filtering
- Affy Detection Call Filter
- Deviation Filter
- Expression Threshold Filter
- Genepix Filter (Two channel filter)
- Genepix Flag Filter
- Missing Values Filter
- PDB Structure Format
Normalization:
- HouseKeeping Genes Normalizer
- Normalization
- Log2 Tranformation
- Marker Centering Normalizer
- Mean Variance Normalizer
- Missing Values
- Microarray Centering Normalizer
- Quantile Normalizer
- Threshold Normalizer
Experiment Information:
- Dataset Annotation
- Dataset History
- Experiment Info
- Version Infomation
Analyis/Visualization
- Alignment Results
- Analysis
- caBIO Pathways
- CELImageViewer
- Color Mosaic
- Dendrogram
- Expression Profiles
- Expression Value Distribution
- Fast Hierachical Clustering Analysis
- Gene Ontology
- Image Viewer
- Jmol
- Marker Annotations
- Microarray Viewer
- Pattern Discovery
- Patterns (Pattern Panel)
- Position Histogram
- Promoter
- Scatter Plot
- Sequence
- Sequence Alignment
- Sequence Retriever
- SOM Analysis
- SOM Clusters
- SPLASH Patterns
- t Test Analysis
- Tabular Microarray Viewer
- Volcano Plot
Exluded Components
The following components, present in version 1.0.4, were removed from the 1.0.5 distribution:
- ARACNE
- Column Major Format
- Cytoscape
- Frequency Threshold Filter
- GCRMA Via R CEL Loader
- Genotypic File Format
- Interactions
- Network Browser
- Pattern Discovery Algorithm (association analysis?)
- Reverse Engineering
- SVM Format
- Synteny
Functionality Modifications
Annotations Panel
- Integration with new version of caCORE API, v3.1. As part of integrating with the new caBIO API, we have also made a number of changes in how the API is used. In the past, we were retrieving gene annotations using as a search term the Affy probeset id (e.g., 31335_at). Unfortunately, the caBIO servers contain probe-based information only for the HU133 chip. To alleviate this problem, we now use the following search approach:
- If the input dataset was associated with an annotations file when it was opened, then we retrieve the HUGO gene symbol associated with a marker (e.g., for marker 31335_at the HUGO symbol is IGF1R) and search caBIO using this gene symbol as a query.
- If the input dataset does not have an associated annotation file, then we do the caBIO search using the marker name. In this case we are restricted, as the only markers for which we will be able to retrieve information are the ones in the HU133 chip.
- Browser access to CGAP gene annotations. In the past, clicking on a gene name hyperlink would directly bring up the corresponding CGAP page. Now, the users are provided with an option; namely then are asked which of the supported CGAP organisms (human or mouse) they want to retrieve info for. In the (near) future we plan to provide additional options here, such as searching Entrez Gene instead of CGAP.
- Extract markers/genes from pathways. In the past, the only operation available for BioCarta pathways was the ability to visualize the pathway image in the caBIO Pathways component. Now, 2 more options are avaible:
- Add pathway genes to set. Selecting this option results in retrieving the HUGO sysmbols of all genes that comprise the pathway. For each such symbol XXX the application will try to find if the currently selected microarray set has a marker whose associated gene is XXX (obviously this will work only if the mocroarray set has been associated with an annotations file). If one (or more) such markers exist, then they will be placed in a marker set which will be named after the pathway and will be added in the Markers panel.
- Export genes to CVS: Information about all genes in the pathway is exported to a text file. The file contains as many rows as the genes extracted and each row contains 2 comma separated values: (1) a gene symbol, and (2) the description associated with that gene.
CVS Tag Info
geWorkbench-v1_0_5
Building the Application
Check out the new geWorkbench1_0_5 branch to a new directory.
For Testing
- Go to the new directory and run `ant createDist`. This step will create a folder named "cleanFolder" at the same level as the directory where the CVS code was extracted into. It will put into cleanFolder a new (simple) build.xml designed for running the application in test mode. Only the all_release.xml configuration file will be included in cleanFolder/conf/.
- Go to the cleanFolder directory and run "ant" to start the application; the application will use the all_release.xml to load components.
For Release
- To create a final distribution folder go to the new directory where the CVS code was extracted and run "ant createCleanDist". This task will clean and rebuild the application into cleanFolder.
System Testing
Table with assigned system tests. The name of the file (word document), the assigned tester, the relative location on share point and the names of the data files are given.
For results, see http://afdev/systemtest/BrowseLogs.php
