Timeline
Sep 18, 2008:
- 11:16 PM Changeset [789] by
- Changed stray double space characters to single tab characters.
- 11:02 PM Changeset [788] by
- Addresses #137. Added documentation.
- 11:02 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
- (In [788]) Addresses #137. Added documentation.
- 11:01 PM Changeset [787] by
- Forgot one copyright line.
- 11:01 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [786]) Addresses #129. Added reference to paper which this plug-in …
- 11:00 PM Changeset [786] by
- Addresses #129. Added reference to paper which this plug-in is based on.
- 10:59 PM Changeset [785] by
- Removed trailing space character.
- 9:53 PM Changeset [784] by
- Addresses #129. Changing to GPL3.
- 9:53 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [784]) Addresses #129. Changing to GPL3.
- 9:28 PM Changeset [783] by
- Addresses #137. Changing to GPL3.
- 9:28 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
- (In [783]) Addresses #137. Changing to GPL3.
- 9:27 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
-
Description changed
- 9:13 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
-
Description changed
- 9:11 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
- (In [782]) Addresses #131. Changing to GPL3.
- 9:11 PM Changeset [782] by
- Addresses #131. Changing to GPL3.
- 9:11 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
-
Description changed
- 8:28 PM Changeset [781] by
- Fixing svn properties.
- 8:25 PM Changeset [780] by
- References #131. Fixing clean up.
- 8:25 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
- (In [780]) References #131. Fixing clean up.
- 8:09 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
- (In [779]) References #137. run should be chmod and fixed class path.
- 8:09 PM Changeset [779] by
- References #137. run should be chmod and fixed class path.
- 7:31 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
-
Description changed
- 7:30 PM Changeset [778] by
- Fixing svn properties.
- 7:27 PM Changeset [777] by
- Addresses #137. README replaces doc/INSTALL.txt
- 7:27 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
- (In [777]) Addresses #137. README replaces doc/INSTALL.txt
- 7:21 PM Changeset [776] by
- Addresses #137.
- 7:21 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
- (In [776]) Addresses #137.
- 7:18 PM Changeset [775] by
- References #131.
- 7:18 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
- (In [775]) References #131.
- 7:16 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [774]) References #129.
- 7:16 PM Changeset [774] by
- References #129.
- 4:37 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [773]) References #129.
- 4:37 PM Changeset [773] by
- References #129.
- 3:39 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) updated by
-
Status changed
- 3:25 PM Changeset [772] by
- References #129.
- 3:25 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [772]) References #129.
- 3:18 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) updated by
-
Status changed
- 2:51 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) closed by
- fixed: (In [771]) Fixes #136. Version is propagated.
- 2:51 PM Changeset [771] by
- Fixes #136. Version is propagated.
- 2:38 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) closed by
- wontfix: The new BASEFile<R,S> construct is undocumented and my Java skills are …
- 2:37 PM Changeset [770] by
- Addresses #131. Added information on how to create a package.
- 2:37 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
- (In [770]) Addresses #131. Added information on how to create a package.
- 2:12 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) updated by
-
Status changed
- 2:01 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
-
Summary changed
- 2:01 PM Ticket #83 (ReplicateError: Error in ReplicateError) updated by
-
Description, Summary changed
- 1:01 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by
-
Owner, Component, Description changed
- 12:58 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) created by
- The onk.lu.se ticket will be split into several stand-alone packages …
- 12:04 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) updated by
-
Status, Owner, Component changed
- 12:04 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) updated by
-
Owner, Component changed
- 12:03 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
-
Component changed
- 12:03 PM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) updated by
-
Owner, Component changed
- 12:03 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
-
Component changed
- 12:02 PM Ticket #83 (ReplicateError: Error in ReplicateError) updated by
-
Component changed
- 12:02 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) updated by
-
Owner, Component changed
- 11:49 AM se.lu.onk.BAFsegmentation edited by
- (diff)
Sep 17, 2008:
- 3:57 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) created by
- configurationfiles should have version updated.
- 1:31 PM se.lu.onk.BAFsegmentation edited by
- (diff)
- 1:29 PM se.lu.onk.BAFsegmentation edited by
- (diff)
- 12:50 PM se.lu.onk.BAFsegmentation edited by
- (diff)
- 12:06 PM se.lu.onk.BAFsegmentation edited by
- (diff)
- 11:40 AM se.lu.onk.BAFsegmentation edited by
- (diff)
- 11:38 AM se.lu.onk.BAFsegmentation edited by
- (diff)
- 11:19 AM se.lu.onk.BAFsegmentation edited by
- (diff)
Sep 16, 2008:
- 9:08 PM Changeset [769] by
- Fixes #133. Read comment made to the ticket.
- 9:08 PM Ticket #133 (ReplicateError: The plug-in adds new entries to the stdout.txt for ...) closed by
- fixed: (In [769]) Fixes #133. Read comment made to the ticket.
- 9:07 PM Ticket #133 (ReplicateError: The plug-in adds new entries to the stdout.txt for ...) updated by
-
Status, Owner, Description changed
Now I have a better understanding of the issue. The problem is that in … - 9:01 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) closed by
- fixed
- 9:00 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) updated by
- This was fixed in changeset:768
- 8:59 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) reopened by
- This is not done yet. changeset:768 fixes ticket:134
- 6:36 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) created by
- […]
- 4:24 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) closed by
- fixed: (In [768]) Fixes #131.
- 4:24 PM Changeset [768] by
- Fixes #131.
- 4:15 PM Changeset [767] by
- Addresses #56. Making sure that this tree does not compile.
- 4:15 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by
- (In [767]) Addresses #56. Making sure that this tree does not compile.
- 3:53 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) updated by
-
Status, Owner changed
- 3:53 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) created by
- After the call to the function the file pointer will be position to …
- 2:11 PM se.lu.onk.BAFsegmentation edited by
- (diff)
- 11:22 AM Changeset [766] by
- Addresses #129. Updated configuration files, reworked html result …
- 11:22 AM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [766]) Addresses #129. Updated configuration files, reworked html …
- 11:20 AM Changeset [765] by
- Addresses #131.
- 11:20 AM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
- (In [765]) Addresses #131.
- 11:16 AM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 11:11 AM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [764]) Addresses #129. Added version info, not distributing …
- 11:11 AM Changeset [764] by
- Addresses #129. Added version info, not distributing source, …
- 11:07 AM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 11:07 AM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 10:30 AM se.lu.onk.BAFsegmentation edited by
- (diff)
- 10:28 AM se.lu.onk.BAFsegmentation edited by
- (diff)
- 10:06 AM Ticket #133 (ReplicateError: The plug-in adds new entries to the stdout.txt for ...) created by
- This causes Base1PluginExecurter to import these reporters with null …
Sep 15, 2008:
- 7:36 PM Changeset [763] by
- Moved README.old to lib.
- 7:34 PM Changeset [762] by
- Moved Concept.ps to lib and added a PDF version of the file.
- 6:59 PM Changeset [761] by
- Addresses #129. Added license and moved README to README.old
- 6:59 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
- (In [761]) Addresses #129. Added license and moved README to README.old
- 6:31 PM Changeset [760] by
- Fixed spelling.
- 3:53 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) created by
- See Johans Test Expression 2 experiment on the production server.
- 3:19 PM PluginDownload edited by
- Addresses ticket:129 (diff)
- 3:17 PM PluginDownload edited by
- Addresses ticket:131 (diff)
- 2:35 PM se.lu.onk.ReplicateError created by
- Addresses ticket:129
- 2:30 PM Changeset [759] by
- Addresses #131. Added version info.
- 2:30 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
- (In [759]) Addresses #131. Added version info.
- 2:27 PM se.lu.onk.BaseFile created by
- Addresses ticket:131
- 1:45 PM Changeset [758] by
- Addresses #56, #129, #131. Created se.lu.onk.BaseFile and moved …
- 1:45 PM Tickets #129,131,56 batch updated by
- (In [758]) Addresses #56, #129, #131. Created se.lu.onk.BaseFile and …
- 1:43 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) updated by
-
Status, Owner changed
- 1:42 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by
-
Description changed
- 1:41 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by
-
Summary changed
- 1:40 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by
-
Description changed
- 1:40 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) created by
- Relates to ticket:56 BaseFile should be its own packages. This will …
- 10:00 AM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) created by
- If the plug-in fails the job reports done! There is information …
Sep 14, 2008:
- 7:12 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) updated by
-
Status, Owner changed
- 7:12 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by
-
Description, Summary changed
- 7:11 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) created by
- The onk.lu.se ticket will be split into several stand-alone packages …
- 7:05 PM Ticket #83 (ReplicateError: Error in ReplicateError) updated by
-
Status, Owner changed
Sep 11, 2008:
- 8:50 AM Ticket #128 (Warning when ftp-config.xml is missing) created by
- There should perhaps be a warning when trying to start the BASE …
Sep 8, 2008:
- 1:32 PM PluginDownload edited by
- Releasing FTP Server 1.0beta (diff)
- 1:27 PM Ticket #127 (Update to final release of Apache Mina FTP server) created by
- The current beta-release relies on the 1.0-M2 (milestone 2) release of …
- 1:24 PM Changeset [757] by
- Preparing for future release 1.0
- 1:19 PM net.sf.basedb.ftp edited by
- Releasing FTP Server 1.0beta (diff)
- 1:14 PM Ticket #114 (Implement FTP Server) closed by
- fixed
- 1:14 PM Changeset [756] by
- Tagging 1.0beta
Sep 5, 2008:
- 11:46 AM Ticket #126 (Illumina SNP ... files are now supported (by the BASEcore) in the BASE ...) created by
- The Illumina package can be improved to utilize the support of storing …
- 11:43 AM Ticket #125 (MeV ... files are now supported (by the BASEcore) in the BASE analysis tree) updated by
-
Summary changed
- 11:41 AM Ticket #125 (MeV ... files are now supported (by the BASEcore) in the BASE analysis tree) created by
- The MeV extension can be improved to utilize the support of storing …
Sep 4, 2008:
- 11:38 AM Changeset [755] by
- Fixed weaknesses discovered with FindBugs-eclipse plug-in
- 8:30 AM PluginDownload edited by
- (diff)
Sep 3, 2008:
- 2:48 PM Ticket #123 (Update BasePlug-ins' firstpage) closed by
- fixed
- 2:25 PM PluginSubmitReq edited by
- (diff)
- 2:16 PM WikiStart edited by
- Changed obsolete contact information (diff)
- 1:28 PM Ticket #119 (Create rank invariant normalizer) updated by
- (In [754]) References #119 Change to only create a row summary array …
- 1:28 PM Changeset [754] by
- References #119 Change to only create a row summary array if it has …
- 12:59 PM Changeset [753] by
- The SpotData2Ch objects are now compared by their ratio-value and not …
- 11:09 AM Ticket #119 (Create rank invariant normalizer) closed by
- fixed: (In [752]) Fixes #119 Create Rank Invariant normalization
- 11:09 AM Changeset [752] by
- Fixes #119 Create Rank Invariant normalization
- 8:07 AM net.sf.basedb.normalizers edited by
- (diff)
Sep 2, 2008:
- 4:38 PM Changeset [751] by
- References #119 Bug-fixing
- 4:38 PM Ticket #119 (Create rank invariant normalizer) updated by
- (In [751]) References #119 Bug-fixing
- 3:17 PM se.lu.onk.BAFsegmentation edited by
- (diff)
- 3:16 PM se.lu.onk.BAFsegmentation edited by
- (diff)
Sep 1, 2008:
- 4:15 PM Changeset [750] by
- References # 119 The normalization algorithm is almost done. Some …
- 2:08 PM se.lu.onk.popLowess edited by
- (diff)
- 2:07 PM se.lu.onk.popLowess edited by
- (diff)
- 2:03 PM se.lu.onk.BAFsegmentation edited by
- (diff)
Aug 27, 2008:
- 4:41 PM Changeset [749] by
- References # 119 Started with the development of this plug-in. No …
- 2:41 PM PluginDownload edited by
- Moved Illumina package to new plug-in category 'Additional array … (diff)
- 11:26 AM Ticket #119 (Create rank invariant normalizer) updated by
-
Status changed
- 11:07 AM Changeset [748] by
- Fixes #117 Create average nomralization plug-in.
- 11:07 AM Ticket #117 (Create average nomralization plug-in) closed by
- fixed: (In [748]) Fixes #117 Create average nomralization plug-in.
- 8:17 AM Changeset [747] by
- References #124 Corrected a few more copy-paste mistake.
- 8:17 AM Ticket #124 (files in Normalization package state they're are part of Illumina package) updated by
- (In [747]) References #124 Corrected a few more copy-paste mistake.
- 8:02 AM Changeset [746] by
- Fixes #124 Corrected a copy-paste mistake. Also added …
- 8:02 AM Ticket #124 (files in Normalization package state they're are part of Illumina package) closed by
- fixed: (In [746]) Fixes #124 Corrected a copy-paste mistake. Also added …
Aug 26, 2008:
- 4:37 PM Changeset [745] by
- References #117 Bug-fixing
- 4:37 PM Ticket #117 (Create average nomralization plug-in) updated by
- (In [745]) References #117 Bug-fixing
- 1:43 PM Ticket #124 (files in Normalization package state they're are part of Illumina package) created by
-
For instance the
READMEbut I'd grep to check other files. - 9:54 AM Ticket #117 (Create average nomralization plug-in) updated by
- (In [744]) References #117 Corrected a package name. Also changed the …
- 9:54 AM Changeset [744] by
- References #117 Corrected a package name. Also changed the way global …
Aug 25, 2008:
- 4:39 PM Changeset [743] by
- References #117 The normalization is now done. Nothing has been tested …
- 4:39 PM Ticket #117 (Create average nomralization plug-in) updated by
- (In [743]) References #117 The normalization is now done. Nothing has …
- 8:29 AM Ticket #117 (Create average nomralization plug-in) updated by
- (In [742]) References #117 Cleaned up and refactored the classes. The …
- 8:29 AM Changeset [742] by
- References #117 Cleaned up and refactored the classes. The Avg.norm. …
Aug 20, 2008:
- 1:06 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
-
Description changed
- 1:05 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
-
Status changed
- 1:05 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
-
Owner, Status changed
This normalizer is based on the work of Workman et al., …
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