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Ticket Summary Owner Type Priority Milestone Component
#227 Illumina detection P-value plug-in description must be improved Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#228 net.sf.basedb.normalizers: Normalizers should use ask BASE whether data is logged or not olle Request major Normalization package v1.1 net.sf.basedb.normalizers
#230 Illumina detection P-value Control outlier cut-off parameter cannot be zero Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#231 Illumina detection P-value fails if no negative controls are available in the bio assayset Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#237 Add support for MicroRNA BGX files to reporter importer Nicklas Nordborg Request major Illumina package v1.4 net.sf.basedb.illumina
#240 Bead summary importer should have an option to fail if the number of skipped data lines get too high Nicklas Nordborg Request major Illumina package v1.4 net.sf.basedb.illumina
#252 net.sf.basedb.illumina: The background correction plug-in should store the reporters used for background calculations Jari Häkkinen Request major Illumina package v1.5 net.sf.basedb.illumina
#259 Apply patch provided in the BASE dev list to Tab2MageExporter Jari Häkkinen Request major ZZ Other tickets not classified
#303 Automatic attachment of files to sample (Case) items Nicklas Nordborg Request major Reggie v1.2 net.sf.basedb.reggie
#322 Select multiple "not asked" sub-options Nicklas Nordborg Request major Reggie v1.5 net.sf.basedb.reggie
#326 Updates required for BASE 3 support Nicklas Nordborg Request blocker Reggie v2.0 net.sf.basedb.reggie
#353 The No and Not asked biosources should have their own Types Nicklas Nordborg Request major Reggie v2.2 net.sf.basedb.reggie
#394 Change weight table order in Partition wizard Jari Häkkinen Request major Reggie v2.7 not classified
#541 net.sf.basedb.normalizers: Normalizers should store normalized data in proper base olle Request major Normalization package v1.1 net.sf.basedb.normalizers
#607 Date /time format is different in configuration file and GUI olle Request trivial LabEnv v1.2 net.sf.basedb.labenv
#1072 Introduce Lysate item between RNA and Specimen Nicklas Nordborg Request major Relax v1.4 net.sf.basedb.relax
#1177 Remove <add-read-groups-options> from reggie-config.xml Nicklas Nordborg Request trivial Reggie v4.23.1 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
#17 Export RMA bioassayset as a tab delimited file Jari Häkkinen enhancement minor se.lu.thep.affymetrix
#26 Print result table as Output txt Johan Enell enhancement trivial se.lu.onk.ztest
#28 Create plot observed/expected Johan Enell enhancement minor se.lu.onk.ztest
#29 Create plot FDR vs rank Johan Enell enhancement minor se.lu.onk.ztest
#30 Create combination plot Johan Enell enhancement minor se.lu.onk.ztest
#31 More reporter info Johan Enell enhancement trivial se.lu.onk.ztest
#32 Create histogram plot Johan Enell enhancement minor se.lu.onk.ztest
#33 Change normsdist calculations Johan Enell enhancement major se.lu.onk.ztest
#37 Add box-plot output Johan Enell enhancement major se.lu.onk.smooth
#40 Create virtual bioassay containing analysis results Johan Enell enhancement major se.lu.onk.ztest
#42 Add sample extended-properties.xml and configuration files needed for BASE plug-ins. Jari Häkkinen enhancement minor se.lu.thep.affymetrix
#44 Add information on how to compile RMAExpressConsole to the RMAExpress plug-in page Jari Häkkinen enhancement major se.lu.thep.affymetrix
#63 make distcheck should work Jari Häkkinen enhancement major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#65 version number in BASE1 plugin is not updated automatically Peter Johansson enhancement minor se.lu.thep.wenni
#84 Change parameter in ReplicateError (se.lu.onk.ReplicateError) olle enhancement major ZZ Other tickets se.lu.onk series plug-ins
#99 The tagging system of the repository should be changed Jari Häkkinen enhancement major tracpages
#100 Add Illumina SNP platform to the installation program Martin Svensson enhancement critical Illumina package v1.0 net.sf.basedb.illumina
#110 Illumina detection P-value plug-in Jari Häkkinen enhancement major Illumina package v1.1 net.sf.basedb.illumina
#113 Add support for more variations of Illumina detection P-value calculations Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#116 Make the MEV launcher extension aware of bioassaysets that store data in file Nicklas Nordborg enhancement major MEV Launcher v1.1 net.sf.basedb.mev
#121 BGX-importer should 0-pad Array_Address_ID if the BGX-file doesn't have done that already Martin Svensson enhancement major Illumina package v1.2 net.sf.basedb.illumina
#133 ReplicateError: The plug-in adds new entries to the stdout.txt for reporters that had null values in stdin.txt Jari Häkkinen enhancement major onk.lu.se
#138 Importing data for multiple raw bioassays in one step Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#140 Add support in build.xml for automatic download of BASE jar files Nicklas Nordborg enhancement minor Illumina package v1.2 net.sf.basedb.illumina
#148 BASE1 configuration: execname should be set automatically during build Jari Häkkinen enhancement major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#151 Use two queries instead of one in DetectionPValue.run() method Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#161 (net.sf.basedb.normalizers) Automatic download of BASE API Martin Svensson enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#162 Upgrade to MeV 4.3 Nicklas Nordborg enhancement critical MEV Launcher v1.1 net.sf.basedb.mev
#167 (net.sf.basedb.normalizers) Average normalizer should use geometric mean Jari Häkkinen enhancement major Normalization package v1.0 net.sf.basedb.normalizers
#171 IBS raw data importer should be able to handle floats in some columns Martin Svensson enhancement major Illumina package v1.3 net.sf.basedb.illumina
#174 Change license to GPL 3 for the illumina package? Martin Svensson enhancement major Illumina package v1.3 net.sf.basedb.illumina
#175 Update the ant script to include contrib directory when creating package. Nicklas Nordborg enhancement major Illumina package v1.3 net.sf.basedb.illumina
#178 The MeV launcher should use attached file instead of running BioAssaySetExporter Nicklas Nordborg enhancement critical MEV Launcher v1.1 net.sf.basedb.mev
#184 qQuantileNormalizer should update progress bar Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#186 qQuantileNormalizer method storeResult must be reimplemented Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#187 qQuantileNormalizer should allow user to select the normaliztion reference assay set Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#191 net.sf.basedb.normalizers: qQN should support standard options ... Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#194 Default export file names should be more unique Nicklas Nordborg enhancement major MEV Launcher v1.3 net.sf.basedb.mev
#195 net.sf.basedb.normalizers: Normalizers should ask user for how to calculate averages Martin Svensson enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#204 Add option to include all available negative controls in detection P-value calculation Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#206 net.sf.basedb.normalizers: Make qQuantileNormalization handle missing values Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#224 Add a "Test" button on the GenePattern 'edit server' page Nicklas Nordborg enhancement major ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#233 Add example that uses the alternate approach for invoking servlets Nicklas Nordborg enhancement major Extension examples v1.2 net.sf.basedb.examples.extensions
#235 Illumina package: Add instructions on how to remove 'Illumina' raw data type from the server Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#238 Supply plug-in configuration files for MicroRNA files Nicklas Nordborg enhancement major Illumina package v1.4 net.sf.basedb.illumina
#246 Add MeV Analysis file to list of MIME types Nicklas Nordborg enhancement major MeV Launcher v1.5 net.sf.basedb.mev
#248 net.sf.basedb.illumina: The background correction plug-in should store the background intensity Jari Häkkinen enhancement major Illumina package v1.5 net.sf.basedb.illumina
#272 Handle CWD . commands correctly Nicklas Nordborg enhancement minor FTP Server v1.1 net.sf.basedb.ftp
#278 Plug-in should suggest better job names Nicklas Nordborg enhancement major Illumina package v1.7 net.sf.basedb.illumina
#279 Plug-in should suggest better job names Nicklas Nordborg enhancement major MeV Launcher v1.8 net.sf.basedb.mev
#280 Plug-in should suggest better job names Nicklas Nordborg enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#281 Plug-in should suggest better job names Nicklas Nordborg enhancement major Example code v1.3 net.sf.basedb.examples.plugins
#289 Add 'download-lib' target to ant buildfile and remove checked in BASE jar file Nicklas Nordborg enhancement minor Plugin examples v2.x net.sf.basedb.examples.plugins
#290 Add 'download-lib' target to ant buildfile and remove checked in BASE jar file Nicklas Nordborg enhancement minor Web services examples v3.0 net.sf.basedb.examples.webservices
#293 Remove workaround for for BASE ticket 1583 when 2.17.1 has been released Martin Svensson enhancement major Reggie v1.4 net.sf.basedb.reggie
#298 VirtualArray can work with 1-channel data Jari Häkkinen enhancement minor VirtualArray 1.2 se.lu.onk series plug-ins
#299 Add field for PAD when no specimen tubes exists for a case Nicklas Nordborg enhancement major Reggie v1.1 net.sf.basedb.reggie
#300 Allow non-standard personal numbers Nicklas Nordborg enhancement major Reggie v1.1 net.sf.basedb.reggie
#302 Update functionality in the Personal information registration Nicklas Nordborg enhancement major Reggie v1.2 net.sf.basedb.reggie
#316 Add support for 'YYYYMMDD' date format in the 'Consent form registration wizard' Martin Svensson enhancement major Reggie v1.4 net.sf.basedb.reggie
#330 Partition registration wizard Martin Svensson enhancement major Reggie v1.6 net.sf.basedb.reggie
#337 Specimen tube wizard: Automatically restart Martin Svensson enhancement major Reggie v2.1 net.sf.basedb.reggie
#339 New entry: Report generator Martin Svensson enhancement major Reggie v2.1 net.sf.basedb.reggie
#341 Specimen tube registration wizard should check name format Martin Svensson enhancement major Reggie v2.1 net.sf.basedb.reggie
#342 reggie partition manager should not list deleted specimen tubes in 'Select specimen tubes' dialouge Nicklas Nordborg enhancement major Reggie v2.0.1 net.sf.basedb.reggie
#345 Add header line to csv file that can be downloaded from the partition wizard Nicklas Nordborg enhancement major Reggie v2.1 net.sf.basedb.reggie
#346 Create virtual patient for cases with consent=no or not asked Nicklas Nordborg enhancement major Reggie v2.1 net.sf.basedb.reggie
#348 Consent form registration wizard should allow 'Yes' in all cases Nicklas Nordborg enhancement critical Reggie v2.2 net.sf.basedb.reggie
#349 Copy consent information to multiple cases Nicklas Nordborg enhancement critical Reggie v2.2 net.sf.basedb.reggie
#351 Check case name in all wizards Nicklas Nordborg enhancement minor Reggie v2.2 net.sf.basedb.reggie
#354 Changes related to new GUI in BASE 3.1 Nicklas Nordborg enhancement major Reggie v2.4 net.sf.basedb.reggie
#355 Partition wizard should use local storage to save form Nicklas Nordborg enhancement major Reggie v2.3 net.sf.basedb.reggie
#357 Some barcoded personal numbers is using 2-digit years instead of 4 Nicklas Nordborg enhancement major Reggie v2.3 net.sf.basedb.reggie
#359 Changes related to new GUI in BASE 3.1 Nicklas Nordborg enhancement minor Example code v1.4 net.sf.basedb.examplecode
#360 Changes related to new GUI in BASE 3.1 Nicklas Nordborg enhancement major MeV Launcher v1.9 net.sf.basedb.mev
#363 Add 'install' target to ant build script Nicklas Nordborg enhancement minor Illumina package v1.8 net.sf.basedb.illumina
#368 Clearing the PAD field in the registration wizard should clear the PAD on specimen Nicklas Nordborg enhancement major Reggie v2.4 net.sf.basedb.reggie
#369 Update names for an existing patient Nicklas Nordborg enhancement major Reggie v2.4 net.sf.basedb.reggie
#374 Store operation date on case items Nicklas Nordborg enhancement major Reggie v2.4 net.sf.basedb.reggie
#380 Refactor annotation type handling in Reggie Nicklas Nordborg enhancement major Reggie v2.5 net.sf.basedb.reggie
#384 RNAQC subtype should set the 'Push annotations to parent' option Nicklas Nordborg enhancement minor Reggie v2.5 net.sf.basedb.reggie
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