Changes in geWorkbench 2.6.0.3 Released December 21, 2016 BLAST - 4703 - Update BLAST API URLs to use HTTPS as required by NCBI. Sequence Retriever - 3987 - Handle missing genome description strings in remote online source database. This problem prevented Sequence Retriever from running. Update mysql-connector library to mysql-connector-java-5.1.39-bin.jar. GenomeSpace - Turn GenomeSpace component off by default. Updates to library/data files - obo-basic.obo - Update to latest version (12/20/2016) - mysql-connector-java-5.1.39-bin.jar in Sequence Retriever. Changes in geWorkbench 2.6.0.2 Released February 20, 2015 BLAST - 3799 - Fix tool email in BLAST job submission - 3975 - Change frequency of result polling Changes in geWorkbench 2.6.0.1 Released January 28, 2015 GenomeSpace - 3958 - fix exception on upload Changes in geWorkbench 2.6.0 Released January 22, 2015 Analysis - 3077 - Document special behaviour of components that ignore marker or array set activation - 3955 - Fix synchronization problem ARACNe - 3590 - Add true Bonferroni correction - 3622 - Make using DPI the default - 3869 - Move preprocessing files from system to temp folder - 3914 - only one array seen if array set activated (Java 7) BLAST (Alignment results ) - 3799 - Add client name and email contact to all BLAST queries (new NCBI req't). - 3198 - Update BLAST DB names to match changes at NCBI - 3760 - Clarify BLAST result sequence buttons and code - 3915 - No hit found if sequence is in an activated set (Java 7) CaArray - 3874 - Filtering on "PI" produces casting error (Java 7) CART - Added ceRNA - 3901 - Change button label in Export dialog from "Open" to "Save" CNKB - 3588 - Change "export to project" to "export to workspace" - 3953 - Allow server-side control of which interactomes can be exported. Color mosaic - 3626 - Update "sort" button hover text Component Configuration Manager - 3614 - Updates to CCM entries - 3770 - Update all Broad Institute author URLS in CCM Cupid - 3902 - Change button label in Export dialog from "Open" to "Save" Cytoscape - 3763 - Networks did not draw if displayed on second video screen under Java 7 DeMAND - 3718 - DeMAND web service shows local R install message - 3632 - Change labels to use "DeMAND" Expression profiles - 3896 - If component loaded after data, failure to plot - 3767 - Require a marker set to be activated to draw plot (safety feature) Expression Value Distribution - 3546 - EVD range incorrect when an array set is activated (Java 7) - 3947 - Fix synchronization problem that was causing exceptions. GenomeSpace - 3703 - Allow user to see shared and public GenomeSpace folders - 3651 - Local file conversion in GenomeSpace is destructive - 3698 - Change right-click option to "Download to geWorkbench" - 3699 - Correct GenomeSpace spelling in CCM - 3700 - Increase size of GenomeSpace login window - 3652 - Change "Project Folders" to "Workspace", update description GenSpace - 3818 - genSpace-related exception on LINCS query (Java 8) - 3654 - Exception when run GSEA without array sets Help files - 3909 - Remove unused help files Installation / Release Files - 3903 - Add clickable command files for various Java heap memory sizes - 3904 - Changes to build.xml and build_runDirect.xml for #3903 LINCS - 3802 - Sort score from highest to lowest value - 3766 - Do not show FMOA network nodes which have no differential expression data - 3690 - Add concentration units to the titration curves - 3863 - "Add to Set" in Cytoscape throws exception for LINCS data Marker sets/arrays phenotypes - 3490 - Only first gene name on marker set read in from file is matched to annotation list MarkUs - 3721 - fix MarkUs local service URL and update tutorial for stricter Java applet req'ts. MARINa (Master Regulator Analysis) - 3719 - One-sample analysis leads to exception on bar-code graphing - 3610 - Restore paired-sample analysis mode MRA-FET (Master Regulator Analysis) - 2793, 3077 - Prevent MRA-FET from running if any marker sets are activated. MatrixReduce - 3910 - Move file writes out of install directory - 3661 - Exception on running MatrixReduce (EDT) Menu items - 3601 - Add "How to Cite" MINDy - 3882 - Cannot load marker files if data loaded before component Other - 3748 - Remove all file writes to installation directory - 3907 - Remove unused lib files - 3908 - Update to lib/jfreechart-1.0.19.jar and lib/jcommon-1.0.23.jar files - 3918 - Update lib/xalan.jar, lib/xml-apis.jar, add lib/serializer.jar (all from xalan 2.7.2). Pattern Discovery - 3918 - No patterns uploaded if a marker set (sequences) is activated (Java 7) - 3930 - Did not display result if searched on activated marker (sequence) set. - 3952 - Correct tooltip sequence position numbers on pattern viewer display. Position histogram - 2344 - Correct binning of values Preferences - 3894 - Removing trailing slash from R package path - 3589 - Spelling correction Project Folders - 3866 - Do not include file names in dataset name after merge Pudge - 3796 - Pudge does not run, error with getParameters() SAM - 3593 - SAM (R) does not run on Java 6 update 45 and above: Runtime.exec command string decoding error - 3388 - Table sorting compares digits, not numbers - 3875 - Update SAM analysis to use geWorkbench Preference "R package directory" Scatter plot - 3762, 3870, 3931 - Fix problems with how component responds to activated Array and Marker sets. - 3923, 3944 - Fix feature allowing reassignment of x-axis marker/array. Sequence Panel - 3919 - no sequences displayed if marker set activated (Java 7) SkyBase - 3664 - Rename ATP button to ATW (due to previous dropping old "Project Folders" in Workspace) T-test - 3544 - Sorting removed the whole heat map Viper - 3723 - VIPER notifies that it needs an R installation even for the remote web version - 3547 - Update web service - 3603 - Remove warning label