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Ticket Summary Owner Type Priority Milestone Component
#89 Installation program and documentation Johan Enell task critical Illumina package v1.0 net.sf.basedb.illumina
#90 Create array design from a bgx-file Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#91 Import Illumina Bead Summary(IBS) files as raw data Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#93 Illumina SNP validator and meta-data extractor Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#94 Import reporter annotations from bgx files Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#98 Implement validator and metadata extractor plug-in for BGX files Martin Svensson task major Illumina package v1.0 net.sf.basedb.illumina
#100 Add Illumina SNP platform to the installation program Martin Svensson enhancement critical Illumina package v1.0 net.sf.basedb.illumina
#101 Import plug-in for SNP raw data Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#102 Intensity calculator for Illumina SNP data Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#105 Complete the move of the example code from BASE. Nicklas Nordborg task blocker Plugin examples v2.6 net.sf.basedb.examples.plugins
#106 Move the example web services code from the BASE server Nicklas Nordborg task major Web services examples v2.6 net.sf.basedb.examples.webservices
#103 Create example extensions Nicklas Nordborg task blocker Extension examples v1.0 net.sf.basedb.examples.extensions
#107 Move the MEV specific code from BASE Nicklas Nordborg task blocker MEV Launcher v1.0 net.sf.basedb.mev
#108 Update information about MEV on the BASE-hacks site Nicklas Nordborg task major MEV Launcher v1.0 net.sf.basedb.mev
#95 Intensity calculator for Illumina expression data Jari Häkkinen task major Illumina package v1.1 net.sf.basedb.illumina
#104 Add information that BASE2WSClient.jar is needed to compile the plug-ins Jari Häkkinen defect major Illumina package v1.1 net.sf.basedb.illumina
#109 Add information to the wiki page on how to give feedback on the Illumina package Nicklas Nordborg task major Illumina package v1.1 net.sf.basedb.illumina
#110 Illumina detection P-value plug-in Jari Häkkinen enhancement major Illumina package v1.1 net.sf.basedb.illumina
#111 Update Illumina wiki pages and related documentation before release Jari Häkkinen task major Illumina package v1.1 net.sf.basedb.illumina
#112 Illumina plug-in installer script fails (in some cases) Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#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
#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
#142 Illumina installer plugin cannot be installed in some cases Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#143 Illumina plug-in package installer requests wrong permissions Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#150 Fix layout of DetectionPValue.java Nicklas Nordborg task minor Illumina package v1.2 net.sf.basedb.illumina
#151 Use two queries instead of one in DetectionPValue.run() method Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#117 Create average nomralization plug-in Martin Svensson task major Normalization package v1.0 net.sf.basedb.normalizers
#122 Add wiki-page for Normalization-package Martin Svensson task major Normalization package v1.0 net.sf.basedb.normalizers
#124 files in Normalization package state they're are part of Illumina package Martin Svensson defect trivial Normalization package v1.0 net.sf.basedb.normalizers
#141 Rank invariant should not support configurations Martin Svensson defect critical Normalization package v1.0 net.sf.basedb.normalizers
#163 Rank invariant normalization has a sorting bug Martin Svensson defect critical Normalization package v1.0 net.sf.basedb.normalizers
#165 Create quantile normalizer Jari Häkkinen task major Normalization package v1.0 net.sf.basedb.normalizers
#167 (net.sf.basedb.normalizers) Average normalizer should use geometric mean Jari Häkkinen enhancement major Normalization package v1.0 net.sf.basedb.normalizers
#164 Improve documentation on how to upgrade the illumina plug-in package Martin Svensson task major Illumina package v1.3 net.sf.basedb.illumina
#170 Result dialouge after batch importing several raw bioassays is somewhat confusing Martin Svensson defect major Illumina package v1.3 net.sf.basedb.illumina
#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
#173 Remove the float to integer conversions in beadstudio2ibs.pl when ticket:171 is fixed and 1.3 is released Martin Svensson defect 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
#127 Update to final release of Apache Mina FTP server Nicklas Nordborg task critical FTP Server v1.0 net.sf.basedb.ftp
#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
#162 Upgrade to MeV 4.3 Nicklas Nordborg enhancement critical MEV Launcher v1.1 net.sf.basedb.mev
#178 The MeV launcher should use attached file instead of running BioAssaySetExporter Nicklas Nordborg enhancement critical MEV Launcher v1.1 net.sf.basedb.mev
#179 Add user-configurable option for JVM max memory Nicklas Nordborg task major MEV Launcher v1.1 net.sf.basedb.mev
#193 Use one JNLP file for each pre-signed JAR file Nicklas Nordborg defect major MEV Launcher v1.2 net.sf.basedb.mev
#189 Add toolbar extension examples Nicklas Nordborg task major Extension examples v1.1 net.sf.basedb.examples.extensions
#198 Change source files to UTF-8 Nicklas Nordborg task minor Extension examples v1.1 net.sf.basedb.examples.extensions
#194 Default export file names should be more unique Nicklas Nordborg enhancement major MEV Launcher v1.3 net.sf.basedb.mev
#203 Change source files to UTF-8 Nicklas Nordborg task minor MEV Launcher v1.3 net.sf.basedb.mev
#212 Add support for exporting CGH data to MeV Nicklas Nordborg task major MEV Launcher v1.3 net.sf.basedb.mev
#213 Cannot save MeV options Nicklas Nordborg defect critical MEV Launcher v1.3 net.sf.basedb.mev
#214 Move TDMS export to this extension Nicklas Nordborg task critical MEV Launcher v1.3 net.sf.basedb.mev
#220 MeV doesn't download files correctly Nicklas Nordborg defect blocker MEV Launcher v1.3 net.sf.basedb.mev
#233 Add example that uses the alternate approach for invoking servlets Nicklas Nordborg enhancement major Extension examples v1.2 net.sf.basedb.examples.extensions
#226 Update to MeV 4.4 Nicklas Nordborg task major MeV Launcher v1.4 net.sf.basedb.mev
#113 Add support for more variations of Illumina detection P-value calculations Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#180 Overview plot extensions for Illumina expression Martin Svensson task major Illumina package v1.4 net.sf.basedb.illumina
#182 Illumina probes not found message should be documented Martin Svensson task major Illumina package v1.4 net.sf.basedb.illumina
#202 Change source files to UTF-8 Nicklas Nordborg task minor Illumina package v1.4 net.sf.basedb.illumina
#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
#205 Change link README_PluginDetails to point to tags at next release Jari Häkkinen defect major Illumina package v1.4 net.sf.basedb.illumina
#215 BGX reporter importer hangs if the [Controls] section has less than 6 columns Nicklas Nordborg task major Illumina package v1.4 net.sf.basedb.illumina
#227 Illumina detection P-value plug-in description must be improved Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#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
#232 Fix deprecation warnings in detection P-value plug-in Nicklas Nordborg task major Illumina package v1.4 net.sf.basedb.illumina
#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
#237 Add support for MicroRNA BGX files to reporter importer Nicklas Nordborg Request 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
#239 BGX reporter/feature importer auto-detection matches any files with at least two sections Nicklas Nordborg defect 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
#241 Add MeV Analysis file as a file type for bioassay sets Nicklas Nordborg task critical MeV Launcher v1.5 net.sf.basedb.mev
#242 Implement "Save to BASE" function in the MeV gui Nicklas Nordborg task critical MeV Launcher v1.5 net.sf.basedb.mev
#243 Create a sample MeV analysis file for testing purposes Nicklas Nordborg task critical MeV Launcher v1.5 net.sf.basedb.mev
#246 Add MeV Analysis file to list of MIME types Nicklas Nordborg enhancement major MeV Launcher v1.5 net.sf.basedb.mev
#258 Update to MeV 4.5.1 Nicklas Nordborg task major MeV Launcher v1.6 net.sf.basedb.mev
#263 Release version 1.0 of the Agilent plug-in package Jari Häkkinen task critical Agilent package 1.0 net.sf.basedb.agilent
#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
#251 net.sf.basedb.illumina: Describe the overview plots in README_PluginDetails Jari Häkkinen task major Illumina package v1.5 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
#257 Fix issues with the BGX reporter importer due to changes in the core api of BASE 2.15 Nicklas Nordborg task blocker Illumina package v1.5 net.sf.basedb.illumina
#273 Bug in detection p-value Jari Häkkinen defect major Illumina package v1.5.1 net.sf.basedb.illumina
#201 Change source files to UTF-8 Nicklas Nordborg task minor FTP Server v1.1 net.sf.basedb.ftp
#264 Investigate and fix issues with external files introduced in BASE 2.16 Nicklas Nordborg task critical FTP Server v1.1 net.sf.basedb.ftp
#269 Update ftp server library version Nicklas Nordborg task major FTP Server v1.1 net.sf.basedb.ftp
#272 Handle CWD . commands correctly Nicklas Nordborg enhancement minor FTP Server v1.1 net.sf.basedb.ftp
#276 Version should autopropagate from build.xml Nicklas Nordborg task minor FTP Server v1.1 net.sf.basedb.ftp
#266 Investigate and fix issues with external files introduced in BASE 2.16 Nicklas Nordborg task critical MeV Launcher v1.7 net.sf.basedb.mev
#271 Update to MeV 4.6.1 Nicklas Nordborg task major MeV Launcher v1.7 net.sf.basedb.mev
#275 Version should autopropagate from build.xml Nicklas Nordborg task minor MeV Launcher v1.7 net.sf.basedb.mev
#249 net.sf.basedb.illumina: Version should autopropagate from build.xml to Illumina.java Nicklas Nordborg task major Illumina package v1.6 net.sf.basedb.illumina
#265 Investigate and fix issues with external files introduced in BASE 2.16 Nicklas Nordborg task critical Illumina package v1.6 net.sf.basedb.illumina
#274 Upgrading the Illumina package does not update the validator path fo BGX files Nicklas Nordborg defect major Illumina package v1.6 net.sf.basedb.illumina
#291 Personal information registration Nicklas Nordborg task critical Reggie v1.0 net.sf.basedb.reggie
#292 Check/create annotation types, etc. required by reggie Nicklas Nordborg task major Reggie v1.0 net.sf.basedb.reggie
#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
#303 Automatic attachment of files to sample (Case) items Nicklas Nordborg Request major Reggie v1.2 net.sf.basedb.reggie
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