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Ticket Summary Owner Type Priority Milestone Component
#571 Update Reggie to new scripting pattern (first step) Nicklas Nordborg enhancement critical Reggie v2.16 net.sf.basedb.reggie
#583 Require 'embedding date' in 'Register paraffin blocks' wizard Nicklas Nordborg defect critical Reggie v2.15 net.sf.basedb.reggie
#630 Start cufflinks Nicklas Nordborg task critical Reggie v2.17 net.sf.basedb.reggie
#641 Import data from cufflinks result files Nicklas Nordborg task critical Reggie v2.17 net.sf.basedb.reggie
#652 New location of BASE JAR files Jari Häkkinen task critical not classified
#656 FASTQ files are not always stored in the expected folder Nicklas Nordborg defect critical Reggie v2.16.1 net.sf.basedb.reggie
#658 Adjust fragment size mean and standard deviation Nicklas Nordborg enhancement critical Reggie v2.16.1 net.sf.basedb.reggie
#662 Race conditions in demux script Nicklas Nordborg defect critical Reggie v2.16.2 net.sf.basedb.reggie
#667 Library registration wizard complains about missing concentration for Stratagene Nicklas Nordborg defect critical Reggie v2.16.3 net.sf.basedb.reggie
#669 RNAQC Caliper well table import wizard should check if values are missing Nicklas Nordborg defect critical Reggie v2.17 net.sf.basedb.reggie
#672 RNA concentration normalization wizard Nicklas Nordborg task critical Reggie v2.18 net.sf.basedb.reggie
#673 Register RNA QC results from BioAnalyzer runs Nicklas Nordborg task critical Reggie v2.18 net.sf.basedb.reggie
#674 Generate document with report of sequencing results Nicklas Nordborg task critical Reggie v2.18 net.sf.basedb.reggie
#697 Can't start alignment if there are libraries without a library plate Nicklas Nordborg defect critical Reggie v2.17.2 net.sf.basedb.reggie
#709 Depend on BASE 3.4 Nicklas Nordborg task critical Reggie v3.0 net.sf.basedb.reggie
#717 Auto-confirmation service Nicklas Nordborg task critical Reggie v3.0 net.sf.basedb.reggie
#719 NullPointerException in extraction registration wizard Nicklas Nordborg defect critical Reggie v2.18.1 net.sf.basedb.reggie
#727 RNAQC importer says "No 'RNA Quality Score' value found....; using -100 instead" for all wells Nicklas Nordborg defect critical Reggie v2.18.2 net.sf.basedb.reggie
#729 Check YubiKey password before user password Nicklas Nordborg enhancement critical YubiKey v1.2 net.sf.basedb.yubikey
#740 Add support for reprocessing specimen Nicklas Nordborg task critical Reggie v3.2 net.sf.basedb.reggie
#753 Case summary breaks if no stained histology has GoodStain Nicklas Nordborg defect critical Reggie v3.2.1 net.sf.basedb.reggie
#757 Some latest RNAQC items are not fetched in the Flagged RNA wizard Nicklas Nordborg defect critical Reggie v3.2.1 net.sf.basedb.reggie
#773 The mRNA wizard must be smarter when auto-selecting pre-normalized RNA Nicklas Nordborg enhancement critical Reggie v3.4 net.sf.basedb.reggie
#775 Histology scoring wizard does not work Nicklas Nordborg defect critical Reggie v3.3.1 net.sf.basedb.reggie
#776 An old storage box position can be re-used for new specimens Nicklas Nordborg defect critical Reggie v3.4 net.sf.basedb.reggie
#778 Can't create manual pool when there is no plate waiting Nicklas Nordborg defect critical Reggie v3.3.2 net.sf.basedb.reggie
#782 Fix compilation error when compiling against BASE 3.6 Nicklas Nordborg task critical Reggie v4.0 net.sf.basedb.reggie
#784 Can't create new histology work list Nicklas Nordborg defect critical Reggie v3.3.3 net.sf.basedb.reggie
#785 Separate project archive folder for external samples Nicklas Nordborg enhancement critical Reggie v4.0 net.sf.basedb.reggie
#793 Implement thumbnails for PNG and JPG images Nicklas Nordborg task critical Thumbnails v1.0 net.sf.basedb.thumbnails
#809 Improve performance of demux+merge step Nicklas Nordborg enhancement critical Reggie v3.6 net.sf.basedb.reggie
#812 Pilot report wizard Nicklas Nordborg task critical Reggie v3.7 net.sf.basedb.reggie
#813 IndexOutOfBoundsException when selecting 7 lysates in the Lab Tracking Protocol for Allprep isolation wizard Nicklas Nordborg defect critical Reggie v3.6.1 net.sf.basedb.reggie
#822 Fix character encoding problems with R scripts Nicklas Nordborg enhancement critical Reggie v3.7.1 net.sf.basedb.reggie
#827 Implement support for YellowLabel in the specimen tube registration wizard Nicklas Nordborg enhancement critical Reggie v4.0 net.sf.basedb.reggie
#834 Auto-analyze when sequencing has ended Nicklas Nordborg task critical Reggie v4.1 net.sf.basedb.reggie
#887 Release export wizard Nicklas Nordborg task critical Reggie v4.5 net.sf.basedb.reggie
#891 Report delivery system Nicklas Nordborg task critical Reggie v4.6 net.sf.basedb.reggie
#904 Implement an Open Grid Scheduler service extension Nicklas Nordborg task critical Open Grid Scheduler service v1.0 net.sf.basedb.opengrid
#905 Move Open Grid Scheduler functionality to a separate extension Nicklas Nordborg task critical Reggie v4.9 net.sf.basedb.reggie
#912 Fix report delivery system Nicklas Nordborg defect critical Reggie v4.7.1 net.sf.basedb.reggie
#913 Implement a set of wizards for handling outtakes Nicklas Nordborg task critical Reggie v4.8 net.sf.basedb.reggie
#922 Create an example of a custom extension point Nicklas Nordborg task critical Example code v1.8 net.sf.basedb.examplecode
#938 Release exporter should export files that can be imported on a different server Nicklas Nordborg enhancement critical Reggie v4.10 net.sf.basedb.reggie
#939 Installation wizard for Relax server Nicklas Nordborg task critical Relax v1.0 net.sf.basedb.relax
#940 Release importer Nicklas Nordborg task critical Relax v1.0 net.sf.basedb.relax
#941 Create the Relax extension Nicklas Nordborg task critical Relax v1.0 net.sf.basedb.relax
#947 Demux fails if all barcodes have been used Nicklas Nordborg defect critical Reggie v4.9.2 net.sf.basedb.reggie
#962 Add ReferenceDate annotation to Case Nicklas Nordborg task critical Reggie v4.10 net.sf.basedb.reggie
#972 Fix problems with bad URLs Nicklas Nordborg defect critical Reggie v4.10 net.sf.basedb.reggie
#983 Merge the Tophat alignment and Cufflinks job to a single job Nicklas Nordborg task critical Reggie v4.11 net.sf.basedb.reggie
#984 Remove the raw data import step for Cufflinks data Nicklas Nordborg task critical Reggie v4.11 net.sf.basedb.reggie
#985 Re-design the gene report generator so that it can produce the report using data from the cufflinks file Nicklas Nordborg task critical Reggie v4.11 net.sf.basedb.reggie
#990 Release exporter looks for files in incorrect directory Nicklas Nordborg defect critical Reggie v4.11.2 net.sf.basedb.reggie
#994 Level 3 exporter Nicklas Nordborg task critical Relax v1.1 net.sf.basedb.relax
#995 Project archive files are lacking access permission Nicklas Nordborg defect critical Reggie v4.11.2 net.sf.basedb.reggie
#997 Implement new secondary analysis pipeline Nicklas Nordborg task critical Reggie v4.12 net.sf.basedb.reggie
#999 Release exporter need to match Histology item based on partition date Nicklas Nordborg defect critical Reggie v4.11.3 net.sf.basedb.reggie
#1035 Upgrade SSHj library enhancement critical Open Grid Scheduler service v1.2 net.sf.basedb.opengrid
#1039 Remove BouncyCastle jar files Nicklas Nordborg task critical Reggie v4.19 net.sf.basedb.reggie
#1048 Release importer fails if the export contain integer enumerated annotation types defect critical Relax v1.3 net.sf.basedb.relax
#1053 The "High HET" filter in the "Flagged alignments" wizard should load more alignments Nicklas Nordborg defect critical Reggie v4.18 net.sf.basedb.reggie
#1063 Specimen tube registration tries to register a new item with the same name as an existing item Nicklas Nordborg defect critical Reggie v4.19.1 net.sf.basedb.reggie
#1064 The temporary case used for holding consent information blocks registration of the real case Nicklas Nordborg defect critical Reggie v4.19.1 net.sf.basedb.reggie
#1086 Changes needed for supporting multiple authentication managers Nicklas Nordborg enhancement critical YubiKey v1.5 net.sf.basedb.yubikey
#1087 Changes needed for supporting multiple authentication managers Nicklas Nordborg enhancement critical OTP login v1.2 net.sf.basedb.otp
#1091 New annotation types in multiple new release version defect critical Relax v1.4 net.sf.basedb.relax
#1103 Add permission check for downloading INCA report files Nicklas Nordborg defect critical Reggie v4.21 net.sf.basedb.reggie
#1133 Re-organize the Reggie front page Nicklas Nordborg enhancement critical Reggie v4.23 net.sf.basedb.reggie
#1160 Investigate changes in Picard since our last modified version Nicklas Nordborg task critical Reggie v4.23 net.sf.basedb.reggie
#2 enhance group/sort command in ReplicateErrorWA Johan Enell enhancement major onk.lu.se
#3 Create replicates with more then 2 spots Johan Enell enhancement major onk.lu.se
#4 Spike Lowess Johan Enell task major onk.lu.se
#5 Center on assay Johan Enell task major onk.lu.se
#6 QQPlot Johan Enell task major onk.lu.se
#7 Merge on genesymbol Johan Enell task major onk.lu.se
#8 COPA Johan Enell task major onk.lu.se
#12 RMAExpress plug-n on mac does not free temporary files when throwing an IOException Jari Häkkinen defect major se.lu.thep.affymetrix
#13 RMAExpress does not exit gracefully if no configuration was available Jari Häkkinen defect major se.lu.thep.affymetrix
#14 RMAExpress: make 'make dist' to set the proper VERSION Jari Häkkinen defect major se.lu.thep.affymetrix
#15 RMAExpress: Instructions on how to update Jari Häkkinen defect major se.lu.thep.affymetrix
#18 AnnotationFiletr Johan Enell defect major onk.lu.se
#19 RMA plugin should check that cel files are assigned to correct cdf. Jari Häkkinen defect major se.lu.thep.affymetrix
#20 extra values pass through Johan Enell enhancement major onk.lu.se
#21 Make installation from the packaged source distribution work Jari Häkkinen defect major se.lu.thep.affymetrix
#22 vrungel Johan Enell enhancement major onk.lu.se
#23 nonsoloamore Jari Häkkinen defect major se.lu.thep.affymetrix
#33 Change normsdist calculations Johan Enell enhancement major se.lu.onk.ztest
#35 free sex pics Jari Häkkinen defect major se.lu.thep.affymetrix
#37 Add box-plot output Johan Enell enhancement major se.lu.onk.smooth
#38 Parameterparser splits the annotations values parameter incorrect Johan Enell defect major onk.lu.se
#40 Create virtual bioassay containing analysis results Johan Enell enhancement major se.lu.onk.ztest
#44 Add information on how to compile RMAExpressConsole to the RMAExpress plug-in page Jari Häkkinen enhancement major se.lu.thep.affymetrix
#45 PLIER - Probe Logaritmic Intensity ERror Peter Johansson task major se.lu.thep.affymetrix
#47 A new release of RMAExpress was released 25 March 2007. Jari Häkkinen defect major se.lu.thep.affymetrix
#48 Rename wiki:WeNNI to wiki:se.lu.thep.wenni Jari Häkkinen task major tracpages
#49 Rename wiki:onk.lu.se.ZTest to wiki:se.lu.onk.ZTest Jari Häkkinen task major tracpages
#51 add configure options to WeNNI Peter Johansson task major se.lu.thep.wenni
#53 update INSTALL Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#54 update README Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
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