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ReleaseNotes_1.7.0.txt
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ReleaseNotes_1.7.0.txt
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Release Notes
geWorkbench V1.7.0
(revised)
July 17, 2009
Joint Centers for Systems Biology, Columbia University
New York, NY 10032
http://www.geworkbench.org
================================================================
Contents
================================================================
1.0 geWorkbench Installation Notes
2.0 geWorkbench Introduction and History
3.0 New Features and Updates
4.0 Known Issues/Defects
5.0 Bug Reports and Support
6.0 Documentation and Files
7.0 geWorkbench Web Pages
================================================================
1.0 geWorkbench Installation Notes
================================================================
geWorkbench has been built and tested using Java 1.5.
We recommend running it on your computer under Java 1.5*.
Windows and Linux installer versions of geWorkbench include
the Java JRE 1.5. Current versions of MacOSX by default also
provide the Java JRE 1.5.
A generic version of geWorkbench is also available that can be
run on any platform. For this version, the user must insure
that the Java JRE 1.5 is present and properly configured.
Additional installation details are provided below, and at
geworkbench.org.
Platform-specific release details:
1. Windows (tested on XP/Vista)
Special note for Vista - if you run this installer on Vista,
please install geWorkbench to c:\geWorkbench_1.7.0 rather
than to C:\Program Files\geWorkbench_1.7.0.
File: geWorkbench_v1.7.0_Windows_installer_with_JRE1.5.exe -
Includes Sun Java 1.5 JRE.
2. MacOSX
File: geWorkbench_v1.7.0_MacOSX_installer.zip.
3. Linux
File: geWorkbench_v1.7.0_Linux_installer_with_JRE1.5.bin.
4. Generic - A non-installer-based version of
geWorkbench is supplied in a Zip file which will work on
any platform.
File: geWorkbench_v1.7.0_Generic.zip
Installation:
* Unzip the file. It will create a directory
geWorkbench1.7.0.
Running geWorkbench (generic):
* You must have the Java 1.5 JRE/JDK installed and the
JRE must be in the path for geWorkbench.
* Windows: you can double click on the file
"launch_geWorkbench.bat" to launch geWorkbench, or
run it from a command window.
* Linux/Unix: Execute the script"launch_geworkbench.sh".
* Any: Alternatively, if you have Apache Ant installed,
you can type "ant run" in the geWorkbench directory.
* Note on Java 1.6 - connectivity to caArray 2.1.* and 2.2.* is known not to work
under Java 1.6.
================================================================
2.0 - geWorkbench Introduction and History
================================================================
geWorkBench, an open source bioinformatics platform
written in Java, makes sophisticated tools for data management,
analysis and visualization available to the community in a
convenient fashion.
geWorkbench evolved from a project, caWorkbench, which was originally
sponsored by the National Cancer Institute Center for Bioinformatics
(NCICB). Some of the most fully developed capabilities of the platform
include microarray data analysis, pathway analysis, sequence
analysis, transcription factor binding site analysis,
and pattern discovery.
geWorkbench 1.7.0 is a major release which adds several new components
and contains numerous enhancements and bug fixes.
================================================================
3.0 New Features and Updates
================================================================
Changes included in geWorkbench 1.7.0
New components
1. 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.
2. 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.
3. Pudge - Interface to a protein structure
prediction server (Honig lab) which integrates tools used
at different stages of the structural prediction process.
4. 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.
5. caGrid v1.3 - Upgrading of grid services to caGrid v1.3 +
introduction of caTransfer for large data tranfers.
6. Component Configuration Manager - allows individual components to
be loaded into or unloaded from geWorkbench.
7. genSpace collaborative framework - discovery and visualization
of workflows. Implemented user registration and preferences.
8. SVM 3.0 (GenePattern) - Support Vector machines for classification.
Other changes in release 1.7.0:
1. Analysis - Parameter saving implemented in all components. If
current settings match a saved set, it is highlighted.
2. ARACNe - improved description of DPI in Online Help.
3. caArray - query filtering on Array Provider, Organism and Investigator
implemented.
4. caArray - can now add a local annotation file to caArray data downloads.
5. caGrid - caGrid connectivity is now built directly in to supported
components rather than being a separate component itself.
6. caScript - The caScript editor is no longer supported.
7. Color Mosaic - now interactive with the Marker Sets list and Selection set.
8. Cytoscape - Upgrade to Cytoscape version 2.4 for network visualization
and interaction.
9. Cytoscape - Set operations on genes being returned from
Cytoscape network visualizations, via right-click menu.
10. Cytoscape - Changes to tag-for-visualization - e.g., now only
one way, from marker set to Cytoscape, not vice-versa.
11. Gene Ontology file - the OBO 1.2 file format is supported.
12. 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.
13. Marker Annotations - add export to CSV file.
14. Marker Sets component - a set copy function was added.
15. MINDy - many improvements to display and results filtering - including
marker set filtering.
16. Scatter Plot - Up to 100 overlapping points can be displayed in a single
tooltip.
17. Various - A number of components were refactored.
18. Workspace saving - now works properly for all components.
***Changes in previous versions***
Changes included in geWorkbench 1.6.3
* geWorkbench 1.6.3 fixes several caArray related issues:
- connection issue that may cause a time-out on some machines.
- incorrect caching of caArray query results.
- duplicate query process removed.
Changes included in geWorkbench 1.6.2
* geWorkbench 1.6.2 provides improved proxy communication with its grid
service dispatcher component (see Mantis bug 1631).
* A problem was fixed in the server-side grid implementation of
hierarchical clustering (Mantis bug 1598).
Changes included in geWorkbench 1.6.1
* A Java servlet now provides connectivity to the Cellular Networks
Knowledge Base database through the firewall.
* Online help for the Sequence Retriever component was added.
* The GenePix annotation parser was augmented to include more data fields.
* Added a missing GenSpace component.
* The GenSpace component was moved from the visual area to the command area.
* Volcano plot scaling was fixed to display extreme P-values (E-45).
Changes included in geWorkbench 1.6.0
* Adds Mindy component
* The GO Terms component is not included in this release. It will
return in a future release.
* Fixed a problem (caused by a change in a server-side URL) with
retrieving annotations for genes in Biocarta pathway diagrams (bug 1577).
* The default caArray server was set to the production server at NCI
(array.nci.nih.gov, port 8080) (bug 1602). The URL for the staging
array was updated to array-stage.nci.nih.gov.
* An incorrect argument was being sent to NCBI's BLAST server. Due to
recent changes there implementing stricter checking, blastn would no
longer run. (bug 1597).
* Corrected a problem where, when using the adjusted Bonferroni correction,
or the Westphal-Young with MaxT, only values with positive fold-changes
were returned and displayed (bug 1603).
* Added a feature whereby the user is warned before any operation that
will alter the dataset, e.g. before filtering out markers, or before
a log2 transformation.
* Added a feature to allow adding a new empty marker set. This can then
be used to receive markers selected interactively in Cytoscape (bug 1541).
* Fixed a problem displaying patterns in the sequence viewer after running
Pattern Discovery (SPLASH) (bug 1415).
* Fixed a problem with displaying adjacency matrices generated by ARACNE
in the Cytoscape component (bug 1449).
* Numerous changes were made to improve responsiveness, including when
- selecting a marker in a large dataset (bug 1346),
- right-clicking on Project with a large dataset (bug 1337),
- saving a workspace (bug 1525), and
- starting an analysis (bug 1544).
* Remaining changes, not listed here in detail, included
- internal issues within geWorkbench,
- improved verification of parameters and set selections before
beginning a calculation,
- improvements to the graphical user interfaces of many components, and
- corrections to the grid implementations of analytical services
(Hierarchical Clustering, SOM, ANOVA etc).
Changes included in geWorkbench 1.5.1:
.
* It addresses changes in the APIs for the caArray and caBIO
data services since geWorkbench 1.5 was released. geWorkbench 1.5.1
can currently connect with caArray 2.1 and caBIO 4.0/4.1.
* It also includes an update to parse the new release 26 of Affymetrix
annotation files.
* Fixes a problem where annotation information was not associated with
arrays that were merged.
Changes included in geWorkbench 1.5:
New Modules:
* ARACNE gene network reverse engineering (from Andrea
Califano's lab at Columbia University,
http://wiki.c2b2.columbia.edu/califanolab/index.php/Software).
* ANOVA Analysis of variance, ported from TIGR's MEV,
http://www.tm4.org/mev.html).
* caArray2.0 connectivity query for and download data from
caArray 2.0 directly into geWorkbench.
* Cellular Networks Knowledge Base database of molecular
interactions. (from Andrea Califano's lab at Columbia University,
http://amdec-bioinfo.cu-genome.org/html/BCellInteractome.html).
* GenSpace - provide social networking capabilities and
allow you to connect with other geWorkbench users.
* MatrixReduce transcription factor binding site prediction
(from Harmen Bussemaker's lab at Columbia University,
http://bussemaker.bio.columbia.edu/software/MatrixREDUCE/).
* Analysis components ported from GenePattern (http://www.genepattern.org)
- Principle Component Analysis (PCA)
- K-nearest neighbors (KNN)
- Weighted Voting (WV)
New File types supported
* The NCBI GEO series matrix file for microarray data (tab-delimited)
New server side architecture
* Invocation of caGrid services is now delagated to an independent
component (the Dispatcher). This makes it possible to exit geWorkbench
after submitting a long-running job and then automatically pick up any
results next time the application starts.
Other changes
* The Marker and Array/Phenotypes components now support algebraic operations
(union, intersection, xor) on marker and array groups.
* Upon exiting the application, the user is prompted to store their workspace.
* Workspace persistence problems have been resolved.
* The Marker Annotations component has been enhanced in several ways:
** The integration with caBIO has been updated to use API Version 4.0
** The caBIO Pathway component (previously an independent geWorkbench
component that would display BioCarta pathway images) has been
integrated into the Marker Annotations component.
** Markers can be returned from BioCarta pathway diagrams.
** A new option is provided to choose between human or mouse CGAP
annotation pages.
================================================================
4.0 Known Issues/Defects
================================================================
Affymetrix Annotation files:
Due to licensing restrictions, Affymetrix annotation files cannot be
included in this distribution. geWorkbench users who are working
with Affymetrix chip data should retrieve the latest version of the
appropriate annotation file for the chip type they using directly from
https://www.affymetrix.com/site/login/login.affx
A free account at Affymetrix.com is required.
Current annotation files in CSV format are listed there.
If you need an annotation file for an older file you can use
its name in the search field on the web page, e.g. "HG_U95Av2".
An example file from the Affymetrix site is
"HG_U95Av2.na28.annot.csv.zip". This file would need to be
unzipped before use. You can place the file in any convenient
directory. When you load a new data file, you will be asked
for the location of the annotation file and can browse to it.
Grid Computations
The reference implementations of the server-side grid-enabled algorithms
currently are running on a single front-end server not meant for
heavy computational use. That server is not configured for computing on large
datasets or for long-running jobs.
================================================================
5.0 Bug Reports and Support
================================================================
Support is provided via online forums at the NCI's Molecular Analysis Tools
Knowledge Center.
See https://cabig-kc.nci.nih.gov/Molecular/forums/
FAQs and other articles are also available at
https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page#geWorkbench
Finally, please see the geWorkbench project page for additional known issues and FAQs.
www.geworkbench.org.
================================================================
6.0 Documentation and Files
================================================================
The documents and support files in this distribution include:
geWorkbench Release Notes:
ReleaseNotes-v1.7.0.txt (this file)
geWorkbench License:
geWorkbenchLicense.txt
Online Help:
Within geWorkbench, users can access "Help Topics" by clicking the
top menu. It has detailed information about each module.
For other documentation not directly included as part of the
distribution, see the following section (7.0) Web Resources.
================================================================
7.0 geWorkbench Web Resources
================================================================
The geWorkbench team maintains a Wiki containing extensive documentation,
a User Manual, tutorials and training slides. It is available at:
http://www.geworkbench.org