geWorkbench

geWorkbench 2.0.2

• Alignment Results (BLAST Results Viewer) - Due to recent changes in the NCBI BLAST website (August, 2010), geWorkbench could not retrieve hit sequences to add them to the project. This affected two buttons: "Add Selected Sequences to Project" and "Only Add Aligned Parts". Fixed in release 2.1.0
• Dataset History: the settings used by the following normalizers are not recorded in the Dataset History component: Mean Variance Normalizer, Missing Values Normalizer, Quantile Normalizer, Threshold Normalizer. Fixed in 2.1.0.
• CNKB - not all listed interaction databases are open for querying. See the page CNKB Data for a summary of available databases and interaction types. Fixed in 2.1.0.

geWorkbench 2.0.1

• genSpace - Logging was not working. Fixed in release 2.0.2.

geWorkbench 2.0.0

• Grid Services - No geWorkbench grid services are currently available outside of the Columbia firewall. Fixed in release 2.0.1.
• genSpace - Logging was not working. Fixed in release 2.0.2.

geWorkbench 1.8.0 and earlier

Linux on the desktop

Description of the problem

A problem has been found on the Linux desktop platform (as opposed to a remote Linux server) when running InstallAnywhere-packaged versions of geWorkbench with include the Java Run-Time Environment (JRE) (geWorkbench_v1.8.0_Linux_installer_with_JRE1.5.bin).

The conflict appears to involve the GTK toolkit used to draw components in the geWorkbench graphical user interface. This conflict apparently occurs with earlier versions of both the Java 5 JRE (JRE 1.5) and earlier versions of the Java 6 JRE (JRE 1.6).

The problem does not affect installations where geWorkbench runs on a remote Linux server and a Windows machine running a Cygwin X-windows server is used to view geWorkbench.

Resolution

We provide two versions of geWorkbench 1.8.0 without the packaged JRE. Either should work on Linux desktops if you separately install the latest version of the Java JRE. While formal testing of geWorkbench was performed using the Java 5 JRE (JRE 1.5), geWorkbench has also been shown to work with the latest Java 6 JREs (JRE 1.6).

The two versions for desktop Linux are:

• geWorkbench_v1.8.0_Linux_installer_noJRE.bin - This version includes an installation wizard but no JRE. You must install the latest JRE separately if it is not already on your system.
• geWorkbench_v1.8.0_Generic.zip - This version includes no installer wizard and no JRE. You just unzip the file with the "unzip" command. You must install the latest JRE separately if it is not already on your system.

Macintosh OSX and Java 6 JRE

Description of the problem

The Macintosh installer version of geWorkbench works correctly when Java 5 is used, but does not start when Java 6 is used.

Resolution

The Generic version of geWorkbench has been shown to work on Macintosh OSX 10.5 and the Java 6 JRE.

Windows and caArray downloads

Description of the problem

If a Java 6 JRE is used on Windows, e.g. with the Generic installation of geWorkbench, caArray downloads can lead to crashes.

Resolution

Use the Java 5 JRE, such as included with the Installer version of geWorkbench for Windows.

geWorkbench 1.7.0

• Annotations - The retrieval of annotations using the Marker Annotations component does not work for microarray data downloaded from caArray. Bug 1956.
  • There is an easy work-around. After downloading data from caArray, and optionally setting up any needed groups of arrays or markers (e.g. treatment groups, controls etc), save the dataset as file type "Exp" format. You can then reload that saved dataset and associate the annotation file at that time.
• caArray - Data downloaded from caArray is being stored in a way that uses a large amount of memory, limiting the size of the dataset that can be used. Bug 1930.
  • The first work-around is to increase the amount of memory allocated to geWorkbench.
  • A second work around, if the first is impractical, is to download the data, using the "merge" check-box, in reasonable sized sets of arrays and then save each merged set as a separate "Exp" format file. Once saved, delete the downloaded data set in geWorkbench and then download the next set from caArray until all data has been saved to separate merged "Exp" files.
  • The Exp files can then be all read back in together and merged into a single data object (make sure to check the "merge" check-box).
• caArray - Data downloads from instances of caArray housed at the NCI can be very slow.