From Informatics

Contents 1 Role Assignments 2 Final Release Date 3 Fixed in this release 4 List of Included Components 4.1 New Modules 4.2 Data Managmenent: 4.3 File input filters: 4.4 Data filters: 4.5 Normalization: 4.6 Experiment Information: 4.7 Analyis/Visualization 5 Excluded Components 5.1 Dropped components 6 Externally supplied components 6.1 MatrixReduce 6.1.1 Source 6.1.2 Compiling 6.1.3 Notes 6.2 Aracne.jar for MINDY 6.3 Cytoscape 6.4 Any other components? 7 Other Mysteries 8 Functionality Modifications 9 CVS Tag Info 10 Building the Application 10.1 For Testing 10.2 For Release 11 System Testing 12 Release 12.1 Date 13 Other post-release Notes/Suggestions

Role Assignments

• Release Manager – Kenneth Smith
• Release Engineer – Xiaoqing Zhang
• Tech Lead – Kiran Keshav
• Tester – Bernd Jagla
• Test Manager – Bernd Jagla
• Technical Writer – Mary VanGinhoven

Final Release Date

geWorkbench v1.5.1 was released on September 23, 2008. Builds for Windows, Linux and MacOSX were created using InstallAnywhere2008. In addition, a generic ZIP file was created which can be used on any platform. The installation packages are available at:

https://gforge.nci.nih.gov/frs/?group_id=78

Fixed in this release

geWorkbench 1.5.1 is purely a maintenance release. It fixes two problems with connectivity to outside services, and fixes file handling problems.

• For the geWorkbench caArray v2.0 component, the NCI server-side API changed with release 2.1 of caArray. The following files were changed in geWorkbench to allow caArray 2.1 connectivity:
  • list files here....
• For the Marker Annotations component, there was a change in the API of the NCI server-side component. The situation is this: caBIO is currently at release 4.1, whereas geWorkbench is using Jar files from caBIO 4.0. However, though this should be updated, this is not the problem. Subsequent to caBIO 4.1, NCI propagated a further update to their caBIO server, to the file: filename.... . Replacing this file with the NCI's current version restored geWorkbench connectivity. The change from 4.0 to 4.1 must still be dealt with.
• Fixed code to correctly handle annotation files when data is being merged. In release 1.5 annotation was lost if a merge occured.
• Updated annotation parser to handle new Affymetrix release 26 files.
• Fixed a problem with GenSpace configuration.
• Started using InstallAnywhere2008, which removed problems with Vista and Linux release builds under older InstallAnywhere version used for geWorkbench release 1.5.

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:GeWorkbench1.5-component status.xls showing detailed release status is available here and on Sharepoint under Release Process. This spreadsheet was not updated for release 1.5.1.

For modules dependencies, please see Additional necessary files included in distribution.

New Modules

None

Data Managmenent:

• Arrays/Phenotypes
• Markers
• preferences
• Project Panel
• Session Mgr

File input filters:

• Affy File Format (MAS5/GCOS)
• Tab Delimited Format(GEO/RMA Express)
• CEL File Loader
• Exp. Format
• FASTA Format
• Genepix File 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

• ANOVA
• ARACNE
• MatrixREDUCE
• Cellular Networks Knowledge Base
• GenePattern components
  • PCA
  • Weighted Voting
  • K-nearest neighbors
• Alignment Results
• Analysis
• caBIO Pathways (this has been integrated in the Marker Annotations component)
• 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

Excluded 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.

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.

• Cancer-GEMS (awaiting further development from NCI)
• Cytoscape_V2_4 (still some problems)
• NetBoost
• EdgeListFileFormat (NetBoost)
• MEDUSA
• Mindy
• SkyLine
• GeneWays
• Evidence Integration
• GCRMA Via R CEL Loader (in \geworkbench\src\org\geworkbench\components\parsers)
• 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).
• Network Browser (was part of Reverse Engineering - would require major rewrite to revive. PathwayDecoder is module name)
• SVM Format (in \geworkbench\src\org\geworkbench\components\parsers)
• Synteny (in \geworkbench\components\alignment\src\org\geworkbench\components\alignment\client)
• t-profiler
• Simulation (a student project)

In addition, the following are excluded:

• \geworkbench\lib\Simulation_libs
• \geworkbench\lib\caArrayMageom

Dropped components

These components are not expected to be used again.

• Pattern Discovery Algorithm (association analysis)
• Reverse Engineering (non-ARACNE, unpublished algorithm. PathwayDecoder is module name)
• Genotypic File Format (in \geworkbench\src\org\geworkbench\components\parsers\genotype)
• 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)
• Interactions (early version of CNKB)

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?

Other Mysteries

Functionality Modifications

CVS Tag Info

Tag = geWorkbench-v1_5_1

Building the Application

Check out the new geWorkbench1_5_1 tag 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

Full system tests will not be executed for this release as it only affects two components...

Release

Date

geWorkbench 1.5.1 was released on September 23, 2008.

Other post-release Notes/Suggestions