What's new in geWorkbench 2.6.0.2
Feb 21, 2015
- BLAST:
- 3799 - Fix tool email in BLAST job submission
- 3975 - Change frequency of result polling
New in geWorkbench 2.6.0.1 (Jan 30, 2015)
- GenomeSpace:
- 3958 - fix exception on upload
New in geWorkbench 2.6.0 (Jan 30, 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
New in geWorkbench 2.5.0 (Oct 17, 2013)
- New features and changes:
- Analysis:
- 3146 - Removal of “All Markers / All Arrays” checkboxes from analysis
- controls.
- BLAST:
- 3404, 3505, 3508, 3526, 3527, 3529 - Full parsing and display of
- results from XML
- ARACNe:
- 3098 - Write out adjacency matrix using hub-targets convention per line
- ceRNA/Hermes:
- 3503 - Implement data query browser for HERMES/ceRNA data
- Consensus Clustering:
- 3502 - Implement interface to GenePattern 3.0 Consensus Clustering
- Gene Ontology:
- 3540 - new PURL and file name for gene ontology file download
- LINCS Query:
- 3382, 3389, 3495 - Implement LINCS Query and Display component
- MARINa/MRA:
- 3086, 3511 - separate MRA and MARINa components, add bar code display
- for MARINa
- 3020, 3212 - implement save image of bar code graph
- Online Help:
- 3498 - Remove from geWorkbench
- Skybase:
- 2619 - Implement saving of image of histogram, and export of results to
- CSV file.
- Workspace:
- 3310, 3379 - Remove “Project” level from Workspace data hierarchy
- Enhancements and bug fixes:
- Analysis:
- 2062 - cyclic events in parameter saving mechanism
- BLAST:
- 3180 - when no result returned, previous result displayed
- ARACNe:
- 3037 - Preprocessing repeated if complete mode chosen with boostrapping
- 3040 - resampling during bootstrapping not allowing "with replacement".
- 3265 - Change DPI default value to zero
- 3535 - ARACNe hub markers pulldown not populated (CCM loading order)
- 3566 - bootstrap count is not printed to Dataset History
- 3568 - unique names for grid result nodes
- CNKB:
- 3499 - improper handling of affy “///” separator
- Color Mosaic:
- 3200 - Changes to activated sets changing displayed heatmap.
- CCM:
- 3545 - remove state dependence from CCM links
- Cytoscape:
- 3184 - disable Cytoscape control panel floating windows (incompatible
- with geWorkbench)
- File Parsers:
- 3006 - problem in parsing Affymetrix 1.0 ST files.
- 3203 - exception can occur when reloading workspace file
- 3288 - update parser menu label to reflect Gene 2.0 ST also supported
- 3364 - "exp" format reader skips empty cells
- 3492 - Simplify annotation type selection to avoid exception
- Filtering:
- 1847 - improve labels for filtering criteria
- 3484 - filtering introduces discrepancy in data views involving
- Cytoscape (looking up marker names from gene names).
- Gene Ontology Analysis:
- 3563 - fixed problem with saving parameters involving "changed gene"
- marker set.
- GenomeSpace:
- 3273 - Implement large file data upload from geWorkbench for
- GenomeSpace
- genSpace:
- 2999 - Registration issue
- Jmol:
- 3284 - update to Jmol 13.0.18
- Marker Sets/Array sets:
- 3185 - exception on unselecting all sets (is this related to 3146?)
- 3486 - clarify labeling of set context pulldown lists
- MARINa/MRA:
- 3291, 3157 - remove unsupported computational options, make consistent
- response to set activation (MARINa)
- 3159 - parameter validation (MARINa).
- 3292 - Change default setting (min number of samples)
- 3501, 3536 - network file pulldown not populated (CCM loading order)
- 3512 - Add absNES column to main MARINa results table
- 3517 - MARINa Viewer - remember the array sets that were activated, and
- the case/control status for each run
- MINDy:
- 3287 - dataset history falsely indicates only activated marker set used
- Normalization:
- 3214 - Change "Cancel" action on warning to return to panel
- 3483 - cyclic event on parameter saving
- Promoter:
- 3474 - 13K sequence set not downloading; added to source
- SAM:
- 3383 - Incorrect path handling on Mac
- Skybase:
- 3564 - correctly handle unexpected (null/invalid) data
- SVM:
- 3163 - fixed problem with saving workspace with SVM results; Test tab
- should reflect any changes in workspace
- 3164 - exception if no “Test” array selected
- 3523 - improve consistency of threshold filter action
- 3562 - save info on markers/arrays used to dataset history.
- 3570 Exception based on order of component loading (CCM).
- 877 - fix range checking on inputs
- 1061 - add dataset history
New in geWorkbench 2.4.1 (Sep 2, 2013)
- BLAST - Due to changes in the HTML output format of BLAST result pages from NCBI, results from an NCBI BLAST search could no longer be parsed into geWorkbench. geWorkbench will now rely primarily on NCBI's XML result format, which should remain more stable.
- ANOVA - A problem with activated marker sets has been corrected. Incorrect markers may have been used.
- Installation - The installer will now install geWorkbench to the user's home directory on all platforms.
New in geWorkbench 2.2.2 (Feb 1, 2012)
- #2705 - caArray array list searchability
- #2710 - GO tree browser returns additional markers
- #2711 - Gene Ontology analysis fails after reloading workspace
- #2713 - Marker set from GO does not appear in ARACNe Hub Markers box when selected
New in geWorkbench 2.2.1 (Aug 13, 2011)
- ANOVA
- #2618 - Control buttons repositioned for easier use.
- #2694 - The simple range check as a test of whether data was
- log-normalized was removed.
- ARACNe
- #2494 - Bonferroni correction option added.
- The "Choose edges with hightest MI" option was renamed to "Merge
- multiple probesets".
- #2648 - The adjacency matrix is no longer made symmetric. Each line now
- starts with a hub gene.
- Similarily, the adjacency matrix, when saved to file, is not made
- symmetric.
- #2679 - The "merge multiple probesets" option was not recorded in
- the dataset history.
- Merging of multiple probesets is now just within a hub gene, not global.
- #2684 - When a subset of markers was activated, the grid service
- version used an incorrect offset into the marker list.