GeWorkbench Release 1.7
From Informatics
geWorkbench 1.7.0
Final URL - the final URL of this page is http://wiki.c2b2.columbia.edu/informatics/index.php/GeWorkbench_Release_1.7. Please check if you were redirected from the old (development) URL and if so update your link.
geWorkbench 1.7.0 was originally slated for the caBIG LSD 1.2 release, which has been delayed.
The geWorkbench release schedule, which carried over from the original LSD plan, is:
- Code freeze: June 22, 2009
- Final release target: July 10, 2009
- Actual release date: July 16, 2009
General notes, feature requests and FAQ page - This page was started with material from the time of release 1.7.0 and will be updated continually.
Final list of major changes in release 1.7.0
List of changes discovered after release!
- Addition of PDB file download from File menu.
- In bug 1897 it mentions an old cabio component, but my records indicate that some versions ago there was a caBIO Pathways component called org.workbench.components.annotations.PathwayPanel. There is code for a caBIO Viewer in the annotations component.
The following new components are included in geWorkbench release 1.7.0
- MarkUs - The MarkUs component assists in the assessment of the biochemical function for a given protein structure. It serves as an interface to the Mark-Us web server at Columbia. Mark-Us identifies related protein structures and sequences, detects protein cavities, and calculates the surface electrostatic potentials and amino acid conservation profile.
- MRA - The Master Regulator Analysis component attempts to identify transcription factors which control the regulation of a set of differentially expressed target genes (TGs). Differential expression is determined using a t-test on microarray gene expression profiles from 2 cellular phenotypes, e.g. experimental and control.
- Pudge - Interface to a protein structure prediction server (Honig lab) which integrates tools used at different stages of the structural prediction process.
- ARACNe2 - upgraded to ARACNe2 distribution from Califano lab, which adds selectable modes (Preprocessing, Discovery, Complete) and a new algorithm (Adaptive Partitioning). Preprocessing allows determination of key parameters from actual input dataset.
- caGrid v1.3 - Upgrading of grid services to caGrid v1.3 + introduction of caTransfer for large data tranfers.
- Component Configuration Manager - allows individual components to be loaded into or unloaded from geWorkbench.
- genSpace collaborative framework - discovery and visualization of workflows. Implemented user registration and preferences.
- SVM 3.0 (GenePattern) - Support Vector machines for classification.
Other changes in release 1.7.0:
- Analysis - Parameter saving implemented in all components. If current settings match a saved set, it is highlighted.
- ARACNe - improved description of DPI in Online Help.
- caArray - query filtering on Array Provider, Organism and Investigator implemented.
- caArray - can now add a local annotation file to caArray data downloads.
- caGrid - caGrid connectivity for supported components is no longer a separate component but is built into ......
- caScript - The caScript editor is no longer supported.
- Color Mosaic - now interactive with the Marker Sets list and Selection set.
- Cytoscape - Upgrade to Cytoscape version 2.4 for network visualization and interaction.
- Cytoscape - Set operations on genes being returned from Cytoscape network visualizations, via right-click menu.
- Cytoscape - Changes to tag-for-visualization - e.g., now only one way, from marker set to Cytoscape, not vice-versa.
- Gene Ontology - the OBO 1.2 file format is supported.
- Marker Annotations - Direct access to the NCI Cancer Gene Index was added. It supplies detailed literature-based annotations on a curated set of cancer-related genes.
- Marker Annotations - add export to CSV file.
- Marker Sets component - a set copy function was added.
- MINDy - many improvements to display and results filtering - including marker set filtering.
- Scatter Plot - Up to 100 overlapping points can be displayed in a single tooltip.
- Various - A number of components were refactored.
- Workspace saving - now works properly for all components.
- moved GeneOntologyTreePopulateComponent.java out of goterms component into framework.
- Bug 1740 - had to use Plastic3DLookAndFeel style on Mac to avoid white-on-white highlight problem in Tabular Microarray Viewer.
Online Help/ Tutorials
Added new or updated existing tutorials and online help for the following components:
- ARACNe - updated
- Cytoscape -added - however note that it does not appear in the Online Help. Reason unknown. (Reported as bug 2012).
- CCM - added
- Master Regulator Analysis (MRA) - added
- Mark-Us - added
- Pudge - added
Documentation changes needed
Cytoscape
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1743
A new right-click menu-option was added. If in Cytoscape multiple nodes are selected, for example by using SHIFT-left-click, then the intersection or union of all the nodes connected to the selected nodes can be determined. Right-click on a selected node and choose "Add to set", then from the submenu choose either "Intersection" or "Union". The markers which result from the chosen action will be placed in the Markers component in the set "Cytoscape selection". Note that the node selection in Cytoscape is done at the level of genes. In the markers component, multiple markers can correspond to a single gene.
(Resolution - Explained in Cytoscape tutorial on Wiki).
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1749
In reference to bug 1749, it was learned (from Mark) that the Node gene names in Cytoscape are mapped to a Swissprot ID using a facility that was originally implemented for GeneWays. The Swissprot ID is what is used to search for matching markers in the Markers component. No string search on actual gene names is done against the markers component. So a gene which does not for some reason have a Swissprot ID will not map back from Cytoscape to the Markers component.
The "tag for visualization" function however uses gene names, not Swissprot IDs, to select markers in Cytoscape.
(Resolution - Copied this to the geWorkbench general notes page).
CNKB
Only genes that are present in the microarray dataset will be displayed in the network displayed in Cytoscape.
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1724
(resolution - added description of this to the CNKB wiki tutorial. Online help needs to be synched, it is older).
Sequence Alignment
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1746
Columbia removed as a Service, leaving only NCBI.
(resolution - Sequence alignment/BLAST wiki tutorial completely revamped, online help was synched with tutorial for release 1.8.)
ARACNE
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1750
Added ability to select marker from Sets, and changed "list" entry to now only read from file ("From File").
Added MODE and ALGORITHM options. Upgraded to ARACNe2 jar from Califano lab.
(Done - all included in tutorials and online help for release 1.7)
Project Folders
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1722
File types are now listed alphabetically in File Open dialog, will need to recreate any screenshots in tutorials or manual to match.
(resolution - transfered to release 1.8 list)
Analysis
If all parameters currently set in an analysis component match a saved parameter setting, it will be highlighted. See e.g. bug 1300.
(resolution - described in Analysis tutorial - no such Online Help section currently exists. Transfer to release 1.8.0 list)
Scatter Plot
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1782
A feature had been added to Scatter Plot to allow overlapping points to each display a tooltip. This did not work if many points were overlapping, or if there were too many points in the dataset being compared. If more than 100 points are being compared in the plot, the enhanced tooltip feature is turned off, and only one point will show a tooltip for a given location.
(resolution - transfered to release 1.8 list)
MINDy
The way marker filtering is done has changed to use a built in set selection feature in the MINDy viewer, rather than using activated marker sets. See bug 1673.
(resolution - transfered to release 1.8 list)
Tips
Color Mosaic
In the color mosaic component, e.g. when displaying a t-test result, you can click on individual cells, and the corresponding marker will be selected in the Markers component. If you then double click on it there, it will be transfered to the Selection set. So one can transfer a subset of the signficant genes into a new set.
Of Note
Cancer Gene Index
Mantis bug entry #1757 has a lengthy use case description for the CGI component.
Grid jobs
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1771
Notes on control of grid jobs: (1) once a grid job is running, there is no way to cancel the actual execution on the back end, and (2) if you right-click on the pending node indication in Project folders, you can remove the job from geWorkbench. This effectively cancels the grid job from the user's point of view. The results will then not be posted into geWorkbench when the remote node completes.
ANOVA
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1732
TIGR's MeV code executes the permutations twice when Westfall-Young is selected: "The code that outputs the matrix numbers for two rounds is in org.tigr.microarray.mev.cluster.algorithm.impl.OneWayANOVA - not geWorkbench's source code."
Scatter Plot
http://wiki.c2b2.columbia.edu/mantis/view.php?id=1186
Extensive changes were made to scatter plot code to allow overlapping values to be displayed on mouse-over. Pretty neat but complicated code!
Other Changes
The following changes have been made subsequent to geWorkbench release 1.6.2(?):
Documentation
The ARACNE Online Help was updated to include the correct interpretation of the "DPI Target List" option, based on the email exchange between Aris and Kai Wang. Many other sections were edited/polished. The finished text was ported to the Wiki-based tutorial for ARACNE.
The Mindy Online Help is being revised to be consistent with changes to the ARACNE Online Help and tutorial. In addition, the description of exactly which parameters apply to each stage of the MINDy calculation has been revised.
Refactoring:
- genetegrate was removed from the cagrid component and made into a separate component.
- The cagrid component was removed, including its redundant caScript editor.
- Hierarchical Clustering and SOM Clustering were previously intermingled. They are now completely separate:
- The hierarchicalclustering component had all SOM clustering code removed. The SOM code was incorporated into the existing "clustering" component.
- The clustering component was renamed to be the SOMClustering component.
The following files were removed on 12/8/2008:
- CLink.java
- HierClustAnalysis.java
- JniHierClustAnalysis.java
- SLink.java.
Files
Updated Java Help jar file to that found in release 2.0_05. The manifest file inside of jhall.jar gives the version as "2.0_03". The previous version, used in geWorkbench releases up through geWorkbench 1.6.2, was "2.0_01"
Role Assignments
- Release Manager – Kenneth Smith
- Release Engineer – Zhou Ji, Yih-Shien (Mark) Chiang
- Tech Lead – Kiran Keshav
- Tester – Udo Tobben, and the rest of the bunch
- Test Manager – Udo Tobben
- Technical Writer – Mary VanGinhoven
Final Release Date
The actual final release date was July 17, 2009.
The target final release date was July 10, 2009.
geWorkbench v1.7 was scheduled to meet the original Life Sciences Distribution 1.2 schedule, which had a release date of July 10th. LSD 1.2 has now been delayed to September.
Builds for Windows, Linux and MacOSX will be created using InstallAnywhere2008. In addition, a generic ZIP file will be created which can be used on any platform. The installation packages will be available at:
https://gforge.nci.nih.gov/frs/?group_id=78
Subsequent point releases
Subsequent releases in the 1.7 series:
Fixed in this release
Major outstanding issues
- How to handle log-normalization of data for volcano plot [outstanding].
- t-test p-value/t statistic display in color mosaic component???
- getting rid of caBIO jar dependencies??? [must be done but need to check????]
- Documentation/Tutorials outstanding for existing modules...
- caArray download needs annotation file....[done]
- Sequence ambiguity codes [outstanding]
- caGrid 1.2 migration of grid services [done - moved to cagGrid 1.3]
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>
A spreadsheet File:GeWorkbench1.6-component status.xls (A new file must be created for release 1.7) showing detailed release status as of version 1.7 will be available here and on Sharepoint under Release Process.
For modules dependencies, please see Additional necessary files included in distribution.
New/Updated components in release 1.7.0
- MarkUs
- MRA - Master Regulator Analysis - include, we need to develop online help and tutorial (Aris). (Done).
- Pudge - if this is working (Kiran?) we should include. We can create a very simple online help file, essentially pointing to the Pudge documentation at the Honig site (Aris). (Done).
- GeneWays (need for Cytoscape viewer for ARACNe) exclude, last I heard this component was not working; plus, we do
not have end-user documentation materials (Aris). (Included only by way of Cutenet/Cytoscape entanglement. However, it cannot be seen in the geWorkbench GUI nor CCM).
- ARACNe2 - adds Adaptive Partitioning algorithm and Preprocessing mode.
- caGrid v1.3 - Upgrading of grid services to caGrid v1.3 + introduction of caTransfer for large data tranfers.
- Cancer Gene Index integration in the Marker Annotations component.
- Component Configuration Manager.
- Cytoscape_V2_4
- GenePattern SVM component.
- genSpace collaborative framework - improvements.
- SVM 3.0 (GenePattern) - include, we need to develop online help and tutorial (Aris). (No online help tutorial yet developed as of release).
Data Managmenent:
- Arrays/Phenotypes
- Markers
- preferences
- Project Panel
- Session manager - no one knows what this is - probably a SOAP interface. But it is definitely needed!
File input filters:
- Affy File Format
- CEL File Loader
- Exp. Format
- FASTA Format
- Genepix File Format
- PDB Structure Format
- Tab-delimited (RMA Express Format)
Connectivity
- caArray2 - supports caArray 2.2.1 (released May 2009), and the caArray client jar is backwards compatible to caArray 2.1.0 (released August, 2008) See caArray 2.2.1 Release Notes for further details.
- caGrid v1.3 - Upgrading of grid services to caGrid v1.3 + introduction of caTransfer for large data tranfers.
Data filters:
- Filtering
- Affy Detection Call Filter
- Deviation Filter
- Expression Threshold Filter
- Genepix Filter (Two channel filter)
- Genepix Flag Filter
- Missing Values Filter
Normalization:
- HouseKeeping Genes Normalizer
- Normalization
- Log2 Tranformation
- Marker Centering Normalizer
- Mean Variance Normalizer
- Missing Values (Normalizer)
- Microarray Centering Normalizer
- Quantile Normalizer
- Threshold Normalizer
Experiment Information:
- Dataset Annotation
- Dataset History
- Experiment Info
- Version Information
Analyis/Visualization
- Alignment Results
- Analysis
- ANOVA
- ARACNe2 - adds Adaptive Partitioning algorithm and Preprocessing mode.
- caBIO Pathways (this has been integrated in the Marker Annotations component)
- Cancer Gene Index integration in the Marker Annotations component.
- CELImageViewer
- Cellular Networks Knowledge Base
- Color Mosaic
- Component Configuration Manager.
- Cytoscape_V2_4 - updated version of Cytoscape.
- Dendrogram
- Expression Profiles
- Expression Value Distribution
- Hierarchical Clustering Analysis
- genSpace collaborative framework - improvements.
- Image Viewer
- Jmol
- Marker Annotations
- MarkUs - Analysis and Viewer
- MRA - Master Regulator Analysis - Analysis and Viewer - include, we need to develop online help and tutorial (Aris).
- MatrixREDUCE
- Microarray Viewer
- Mindy - Analysis and Viewer
- Pattern Discovery
- Position Histogram
- Pudge - Analysis and Viewer (Browser) - if this is working (Kiran?) we should include. We can create a very simple online help file, essentially pointing to the Pudge documentation at the Honig site (Aris).
- Promoter
- Scatter Plot
- Sequence
- Sequence Alignment
- Sequence Retriever
- SOM Analysis
- SOM Clusters
- t Test Analysis
- Tabular Microarray Viewer
- Volcano Plot
- GenePattern components
- PCA (GenePattern) - Analysis and Viewer
- K-nearest neighbors (GenePattern)
- SVM 3.0 (GenePattern) - Analysis and Viewer - include, we need to develop online help and tutorial (Aris).
- WV - Weighted Voting (GenePattern)
- GeneWays (need for Cytoscape viewer for ARACNe) exclude, last I heard this component was not working; plus, we do
not have end-user documentation materials (Aris). However, Geneways must be included for Cytoscape interaction to function, but Geneways itself cannot be chosen as a component nor used directly.
Legacy directories needing cleanup
These directories arose for specific projects that are no longer active or have been redesigned. But some files within these directories are still being used by unknown components. These dependencies should be worked out and any needed files moved to more appropriate locations.
- \geworkbench\lib\Simulation_libs
- \geworkbench\lib\caArrayMageom
Also, the "lib" directory has a number of files that are probably no longer needed.
In geWorkbench 1.7, the following files were removed from lib\caArrayMageom:
- caarray-client.jar
- commons-collections.jar
- log4j.1.2.5.jar
- mageom-client.jar
The following components were removed from lib but then replaced:
- lib/mageom.jar - put back in, needed by Bison.
- lib/arrayexpressWithoutDoc.jar - put back in , needed by GenSpace!
- lib/mageom-client.jar - put back in.
- lib/ArrayExpress.jar - put back in.
- lib/caBIO.jar - put back in.
The following files could be removed from lib (probably belonged to old reverse engineering component):
- GenesAtWork.dll
- mutualinfo.dll
- MutualInfoDLL.dll
Excluded and Dropped Components
The release creation script in build.xml now explicitly includes components by name (previously it excluded components by name) The following is a list of modules known to be excluded.
Excluded components
The following components are excluded for a variety of reasons, most often due to lack of formal requirements documentation or/and associated system test scripts. Some of them should be scheduled for inclusion in the next production release. For modules not found in the current all.xml a path to the component is shown.
Still under development:
- Cancer-GEMS (awaiting further development from NCI)
- NetBoost
- EdgeListFileFormat (NetBoost)
- Evidence Integration
- MEDUSA
- Skyline - awaiting documentation to be developed in cooperation with the Murray lab.
- Skybase- awaiting documentation to be developed in cooperation with the Murray lab.
Not actively being developed:
- GCRMA Via R CEL Loader (in \geworkbench\src\org\geworkbench\components\parsers)
- GSEA
- Multi-t-test (OK, but need to understand when it would be used, e.g. after ANOVA, and if it is what we really want).
- SMLR - Sparse Multinomial Logistic Regression - implementation by John Watkinson.
- SVM Format (in \geworkbench\src\org\geworkbench\components\parsers) (left over from a John Watkinson project).
- Synteny (in \geworkbench\components\alignment\src\org\geworkbench\components\alignment\client)
- t-profiler
Dropped components
These components are not expected to be used again.
- Column Major Format (in \geworkbench\src\org\geworkbench\components\parsers)
- Frequency Threshold Filter (There is a class called AllelicFrequencyThresholdFilter in \geworkbench\components\filtering\src\org\geworkbench\components\filtering)
- GeneOntology
- Genotypic File Format (in \geworkbench\src\org\geworkbench\components\parsers\genotype)
- Network Browser (was part of Reverse Engineering - would require major rewrite to revive. PathwayDecoder is module name)
- Pattern Discovery Algorithm (association analysis)
- Patterns (Pattern Panel) - Omit from release - Appears to have been superseded by the Sequence component.
- Reverse Engineering (non-ARACNE, unpublished algorithm. PathwayDecoder is module name)
- Simulation (a student project)
Note - the original "interactions" component was dropped and reimplemented as the Cellular Networks Knowledge Base. It took a brief detour as being called component "interactions2".
Externally supplied components
The following components originate external to the geWorkbench source tree:
MatrixReduce
Source
MatrixReduce source code was obtained from the Bussemaker lab and a modified copy saved under: adcvs.cu-genome.org:/cvs/magnet/matrixreduce_distribution. This modified copy contains Java API changes made to integrate with geWorkbench.
Compiling
MatrixReduce is compiled using the following commands:
- FitModel binary is compiled manually as follows
- gcc -c -O2 -mno-cygwin -funroll-loops *.c
- gcc -mno-cygwin -static nrutil.o fncs_cmns.o fncs_seqs.o fncs_tdat.o fncs_seed.o fncs_app1.o fncs_app2.o fncs_nrcs.o fncs_topo.o fncs_mylm.o fncs_bits.o FitModel.o -o FitModel –lm (for windows and linux)
- gcc -mno-cygwin nrutil.o fncs_cmns.o fncs_seqs.o fncs_tdat.o fncs_seed.o fncs_app1.o fncs_app2.o fncs_nrcs.o fncs_topo.o fncs_mylm.o fncs_bits.o FitModel.o -o FitModelMac –lm (for Mac)
- API jar: The Java API jar is created with the makefile, command "make jar".
- FitModel binary is compiled manually with gcc, with extra flags to tell it to not use Cygwin, to optimize and to unroll loops
- FitModel.exe bundles both the NR (Numerical Recipies) and GNU libraries.
- The API jar is created with the makefile under MatrixREDUCE's top directory.
Notes
See comment on white spaces in file names/paths in Mantis : http://mantis.cu-genome.org/view.php?id=1316
Aracne.jar for MINDY
Although ARACNE is a geWorkbench component, the MINDY component uses a version of ARACNE that is externally maintained. The file aracne.jar is copied directly into the geWorkbench CVS tree.
The location of the external ARACNE code is:
The version of the external ARACNE code is:
Cytoscape
Any other components?
Functionality Modifications
CVS Tag Info
- geworkbench_1_7_0
Building the Application
Check out the new geworkbench_1_7_0 branch to a new directory.
For Testing
The following steps should be followed to set up geWorkbench for testing.
Release Engineer:
- The file conf\all_release.xml needs to be updated to include the components that are part of the release.
- The target createDist within the file build.xml needs to be updated so that only components that are part of the release are copied into the file ..\cleanFolder.
- Each component now contains a *.ccm.xml file which contains information displayed in the top-level CCM manager. For example, the default state of being automatically loaded or not can be set here.
deprecated with new CCM framework
- Verify that the components are listed in the correct order in all_release.xml. Remember that there is a conflict between Genspace and another component whose resolution depends on the correct order. (Include details here....)
Testers
After the release engineer has properly configured the two files all_release.xml and build.xml (above), the testers should do the following:
- Check out the release branch/tag from CVS into a new directory.
- Change 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 (in case of doubt perform "ant clean" before the "ant createDist").
- Change directory to ..\cleanFolder and start the app there by running “ant run”.
Release-specific versions of system tests are stored in Sharepoint: https://sharepoint.c2b2.columbia.edu/c2b2/Testing/
Procedures for running the system tests are found on the Wiki: http://wiki.c2b2.columbia.edu/informatics/index.php/System_tests#Best_practices_for_System_tests
Also, if a script fails and you believe it is a defect in geWorkbench, please check if the defect is already described in Mantis
- if not in Mantis file a new bug in Mantis
- enter the bug number in the status page for the system tests (http://afdev/systemtest/BrowseLogs.php)
If you believe there is a defect in the System Test please send e-mail to the test lead for further investigation.
Some of the System Tests may need to be updated due to changes in the GUI of geWorkbench since the previous release. Please make note of such cases and send an e-mail to the System Test lead.
For Release
- The Release Engineer should update the date in the "version info" to the actual build date, and make sure the version number is correct.
- 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
The instructions and testing assignments were delivered via this file.
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.
| System test | Assigned tester | location (relative to link | estimated date of completion |
|---|---|---|---|
| 2 channel threshold filter | Min | \microarrays\filtering\2 channel threshold filter | |
| Affy detection filter | Min | microarrays\filtering\Affy detection call filter | |
| Anova | Min | microarrays\Analysis\anova | |
| Aracne | Ken | microarrays\Analysis\aracne | |
| Array based centering | Mark | microarrays\Normalization\array based centering | |
| BLAST | Ken | sequences\analysis area\alignment\BLAST | |
| caArray | not assigned | General\menu\File\caarray | |
| Cell imager | Kiran | microarrays\CEL imager | |
| Cellular Network Knowledge base | Michael | microarrays\Cellular Network KB | |
| Color mosaic | Thomas | microarrays\color mosaic | |
| Dataset annotations | Udo | General\Dataset annotations | |
| deviation filter | Thomas | microarrays\filtering\deviation filter | |
| expression profiles | Thomas | microarrays\expression profiles | |
| Expression theshold filter | Thomas | microarrays\filtering\Expression threshold filter | |
| Expression Value Distribution | Michael | microarrays/EVD | |
| File formats | Mark | General\menu\File | |
| Gene ontology | not assigned | microarrays\Gene Ontology | |
| Genepix flags filter | Oleg | microarrays\filtering\Genepix flags filter | |
| genSpace | Kiran | General\genspace | |
| Hierarchical clustering | Udo | microarrays\Analysis\Hierarchical clustering | |
| House keeping gene normalizer | Oleg | microarrays\Normalization\house keeping gene normalizer | |
| Log2 transform | Oleg | microarrays\Normalization\Log2 transformation | |
| Marker Annotations | Oleg | microarrays\marker annotations | |
| Marker based centering | Oleg | microarrays\Normalization\Marker based centering | |
| Marker sets (Selection) | Udo | General\Selection | |
| MatrixReduce | Min | microarrays\Analysis\matrix reduce | |
| Mean Variance normalizer | Mark | microarrays\Normalization\mean variance normalizer | |
| Microarray viewer | Mark | microarrays\Microarray Viewer | |
| Mindy | Ken | microarrays\Analysis\MINDY | |
| missing value | Mark | microarrays\Normalization\missing value computations | |
| Online Help | Ken | general/Help | |
| pattern discovery | not assigned | pattern discovery | |
| PCA | Udo | microarrays\Analysis\PCA | |
| Preferences | Udo | General\Preferences | |
| Promoter panel | Kiran | sequences\visual area\Promoter | |
| Quantile normalizer | Kiran | microarrays\Normalization\quantile normalization | |
| scatter plot | Ken | microarrays\scatter plot | |
| Sequence Panel | Udo | sequences/visual area/Sequence | |
| sequence retriever | Kiran | microarrays\sequence retriever | |
| SOM | Min | microarrays\Analysis\SOM | |
| T-test | Thomas | microarrays\Analysis\t-test | |
| Tabular microarray viewer | Michael | microarrays\Tabular Microarray Viewer |
For results, see http://afdev/systemtest/BrowseLogs.php
Release
Date
Lessons Learned
Please review the 1.6 lessons learned while preparing this release.
System Test Scripts
- caArray - There is no current system test for caArray, and no testing of caArray was assigned, due to problems Udo had in trying to update the script. Ken will test caArray.
- There seems to be no system test for the Pattern Discovery (Splash) components:Pattern Discovery, Patterns, and Position Histogram.
- The following components do not have their own system tests but are assumed to be tested as part of other components:
- Cytoscape 2.4 (ARACNe, CNKB?)
- Dendrogram (Hierarchical Clustering?)
- Volcano Plot (t-test?)
System Test Process
Release Build Process
For Windows and Macintosh, only distributions including the JRE 1.5 were distributed. There are observed problems with Java 1.6.
- caArray connectivity via the Java API does not work under JRE 1.6.
- geWorkbench occasionally freezes up at apparently random moments under JRE 1.6.
GUI/Functionality changes
Grid Server and URLs corresponding to release 1.7.0
The form of the Index and Dispatcher service URLs changed.
- Index Service URL: http://geworkbench17grid.c2b2.columbia.edu:8080/wsrf/services/DefaultIndexService
- Dispatcher URL: http://geworkbench17grid.c2b2.columbia.edu:8080/wsrf/services/cagrid/Dispatcher
- Server: cagridnode.c2b2.columbia.edu
An example grid service URL is http://cagridnode.c2b2.columbia.edu:8080/v1.7.0/wsrf/services/cagrid/Aracne
General notes
Notes on release process
- Make sure version date is updated before release.
- Make sure geWorkbench splash screen has been updated.
- Try out actual installer release build versions well before the final release, to catch anything to do with file location or installer incompatibilities etc.
- The Promoter component has two Jaspar data files in the source directory. The Jaspar website needs to be checked for new data file releases.
Kiran's Follow-up Notes
See here.
Post-release updates to other Wiki pages
- Updated Bcell-100.exp (as Bcell-100.zip) on the Wiki. This version corrects the naming of the final arrays so that they are part of the "non-GC Tumor" group. Previously, a slight variation on the name put them into a separate group.
