Timeline



Oct 4, 2008:

12:28 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)

Oct 3, 2008:

8:03 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)

Oct 1, 2008:

4:57 PM PluginDownload edited by Jari Häkkinen
(diff)
4:55 PM PluginDownload edited by Jari Häkkinen
Releasing MergeBioAssay? 2.1 (diff)
4:51 PM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
(diff)
4:51 PM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
Releasing MergeBioAssay? 2.1 (diff)
4:47 PM MergeBioAssay-2.1.tgz.MD5 attached to se.lu.onk.MergeBioAssay by Jari Häkkinen
4:46 PM MergeBioAssay-2.1.tgz attached to se.lu.onk.MergeBioAssay by Jari Häkkinen
4:46 PM Changeset [806] by Jari Häkkinen
Setting pre tag to trunk version of MergeBioAssay?.
4:45 PM Changeset [805] by Jari Häkkinen
Fixes #137. Releasing MergeBioAssay? 2.1
4:45 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) closed by Jari Häkkinen
fixed: (In [805]) Fixes #137. Releasing MergeBioAssay? 2.1
4:44 PM Changeset [804] by Jari Häkkinen
Addresses #137. Preparing release 2.1 of MergeBioAssay? package.
4:39 PM Changeset [803] by Jari Häkkinen
Setting pre tag to trunk version of ReplicateError?.
4:35 PM PluginDownload edited by Jari Häkkinen
Releasing ReplicateError? 1.3 (diff)
4:31 PM se.lu.onk.ReplicateError edited by Jari Häkkinen
Releasing ReplicateError? 1.3 (diff)
4:28 PM ReplicateError-1.3.tgz.MD5 attached to se.lu.onk.ReplicateError by Jari Häkkinen
4:28 PM ReplicateError-1.3.tgz attached to se.lu.onk.ReplicateError by Jari Häkkinen
4:27 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) closed by Jari Häkkinen
fixed: (In [802]) Fixes #129. Releasing ReplicateError? 1.3
4:27 PM Changeset [802] by Jari Häkkinen
Fixes #129. Releasing ReplicateError? 1.3
4:25 PM Changeset [801] by Jari Häkkinen
Addresses #129. Preparing release of ReplicateError? 1.3
4:16 PM Changeset [800] by Jari Häkkinen
References #129
4:09 PM Changeset [799] by Jari Häkkinen
Setting pre tag to trunk version of BaseFile?.
4:06 PM PluginDownload edited by Jari Häkkinen
Added link to BaseFile? 1.0 package (diff)
4:02 PM se.lu.onk.BaseFile edited by Jari Häkkinen
Uploaded BaseFile? 1.0 package. (diff)
3:54 PM BaseFile-1.0.tgz.MD5 attached to se.lu.onk.BaseFile by Jari Häkkinen
3:54 PM BaseFile-1.0.tgz attached to se.lu.onk.BaseFile by Jari Häkkinen
3:53 PM PluginDownload edited by Jari Häkkinen
Added BaseFile? version information. (diff)
3:44 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) closed by Jari Häkkinen
fixed: (In [798]) Fixes #131. Releasing BaseFile? 1.0
3:44 PM Changeset [798] by Jari Häkkinen
Fixes #131. Releasing BaseFile? 1.0
3:41 PM Changeset [797] by Jari Häkkinen
Addresses #131. Preparing release BaseFile? 1.0
3:09 PM Changeset [796] by Jari Häkkinen
References #129. Improved table footnote.
2:41 PM Changeset [795] by Jari Häkkinen
Fixes #83. Also shifted code lines to align the WA and AA class …
2:41 PM Ticket #83 (ReplicateError: Error in ReplicateError) closed by Jari Häkkinen
fixed: (In [795]) Fixes #83. Also shifted code lines to align the WA and AA …

Sep 28, 2008:

10:44 AM Changeset [794] by Jari Häkkinen
References #129. Added note about different numbers in table and …

Sep 25, 2008:

10:37 AM Changeset [793] by Jari Häkkinen
References #129. No need to generate group information for within …

Sep 24, 2008:

9:52 PM Changeset [792] by Jari Häkkinen
Fixes #132. Spot object seems to never get more than one position, but …
9:52 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) closed by Jari Häkkinen
fixed: (In [792]) Fixes #132. Spot object seems to never get more than one …
9:16 PM Changeset [791] by Jari Häkkinen
References #129. Removed unused code, moved common code to super …

Sep 23, 2008:

11:12 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)

Sep 21, 2008:

10:42 AM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) closed by Jari Häkkinen
invalid
10:42 AM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) reopened by Jari Häkkinen
10:34 AM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) closed by Jari Häkkinen
wontfix

Sep 19, 2008:

2:31 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
1:37 PM Ticket #139 (ReplciateError: A few data files are created that are always deleted ...) created by Jari Häkkinen
We should maybe stop creating these files.
11:24 AM Changeset [790] by Jari Häkkinen
Addresses #129. Added proper publication figure references for the algos.
10:22 AM Ticket #138 (Importing data for multiple raw bioassays in one step) created by Jari Häkkinen
See http://base.thep.lu.se/ticket/1135 and …

Sep 18, 2008:

11:16 PM Changeset [789] by Jari Häkkinen
Changed stray double space characters to single tab characters.
11:02 PM Changeset [788] by Jari Häkkinen
Addresses #137. Added documentation.
11:01 PM Changeset [787] by Jari Häkkinen
Forgot one copyright line.
11:00 PM Changeset [786] by Jari Häkkinen
Addresses #129. Added reference to paper which this plug-in is based on.
10:59 PM Changeset [785] by Jari Häkkinen
Removed trailing space character.
9:53 PM Changeset [784] by Jari Häkkinen
Addresses #129. Changing to GPL3.
9:28 PM Changeset [783] by Jari Häkkinen
Addresses #137. Changing to GPL3.
9:11 PM Changeset [782] by Jari Häkkinen
Addresses #131. Changing to GPL3.
8:28 PM Changeset [781] by Jari Häkkinen
Fixing svn properties.
8:25 PM Changeset [780] by Jari Häkkinen
References #131. Fixing clean up.
8:09 PM Changeset [779] by Jari Häkkinen
References #137. run should be chmod and fixed class path.
7:30 PM Changeset [778] by Jari Häkkinen
Fixing svn properties.
7:27 PM Changeset [777] by Jari Häkkinen
Addresses #137. README replaces doc/INSTALL.txt
7:21 PM Changeset [776] by Jari Häkkinen
Addresses #137.
7:18 PM Changeset [775] by Jari Häkkinen
References #131.
7:16 PM Changeset [774] by Jari Häkkinen
References #129.
4:37 PM Changeset [773] by Jari Häkkinen
References #129.
3:25 PM Changeset [772] by Jari Häkkinen
References #129.
2:51 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) closed by Jari Häkkinen
fixed: (In [771]) Fixes #136. Version is propagated.
2:51 PM Changeset [771] by Jari Häkkinen
Fixes #136. Version is propagated.
2:38 PM Ticket #135 (ReplicateError: deprecated functionality is used, get rid of it) closed by Jari Häkkinen
wontfix: The new BASEFile<R,S> construct is undocumented and my Java skills are …
2:37 PM Changeset [770] by Jari Häkkinen
Addresses #131. Added information on how to create a package.
12:58 PM Ticket #137 (Create a se.lu.onk.MergeBioAssay module) created by Jari Häkkinen
The onk.lu.se ticket will be split into several stand-alone packages …
11:49 AM se.lu.onk.BAFsegmentation edited by markus
(diff)

Sep 17, 2008:

3:57 PM Ticket #136 (ReplicateError: Make version info to propagate automatically during ...) created by Jari Häkkinen
configurationfiles should have version updated.
1:31 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
1:29 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
12:50 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
12:06 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:40 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:38 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:19 AM se.lu.onk.BAFsegmentation edited by markus
(diff)

Sep 16, 2008:

9:08 PM Changeset [769] by Jari Häkkinen
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 Jari Häkkinen
fixed: (In [769]) Fixes #133. Read comment made to the ticket.
9:01 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) closed by Jari Häkkinen
fixed
8:59 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) reopened by Jari Häkkinen
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 Jari Häkkinen
[…]
4:24 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) closed by Jari Häkkinen
fixed: (In [768]) Fixes #131.
4:24 PM Changeset [768] by Jari Häkkinen
Fixes #131.
4:15 PM Changeset [767] by Jari Häkkinen
Addresses #56. Making sure that this tree does not compile.
3:53 PM Ticket #134 (BaseFile: public void resetDataPosition(BASEFileSection section) ...) created by Jari Häkkinen
After the call to the function the file pointer will be position to …
2:11 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
11:22 AM Changeset [766] by Jari Häkkinen
Addresses #129. Updated configuration files, reworked html result …
11:20 AM Changeset [765] by Jari Häkkinen
Addresses #131.
11:16 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
11:11 AM Changeset [764] by Jari Häkkinen
Addresses #129. Added version info, not distributing source, …
11:07 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
11:07 AM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
10:30 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
10:28 AM se.lu.onk.BAFsegmentation edited by markus
(diff)
10:06 AM Ticket #133 (ReplicateError: The plug-in adds new entries to the stdout.txt for ...) created by Jari Häkkinen
This causes Base1PluginExecurter to import these reporters with null …

Sep 15, 2008:

7:36 PM Changeset [763] by Jari Häkkinen
Moved README.old to lib.
7:34 PM Changeset [762] by Jari Häkkinen
Moved Concept.ps to lib and added a PDF version of the file.
6:59 PM Changeset [761] by Jari Häkkinen
Addresses #129. Added license and moved README to README.old
6:31 PM Changeset [760] by Jari Häkkinen
Fixed spelling.
3:53 PM Ticket #132 (ReplicateError: In witihn assays only one position of accepted ...) created by Jari Häkkinen
See Johans Test Expression 2 experiment on the production server.
3:19 PM PluginDownload edited by Jari Häkkinen
Addresses ticket:129 (diff)
3:17 PM PluginDownload edited by Jari Häkkinen
Addresses ticket:131 (diff)
2:35 PM se.lu.onk.ReplicateError created by Jari Häkkinen
Addresses ticket:129
2:30 PM Changeset [759] by Jari Häkkinen
Addresses #131. Added version info.
2:27 PM se.lu.onk.BaseFile created by Jari Häkkinen
Addresses ticket:131
1:45 PM Changeset [758] by Jari Häkkinen
Addresses #56, #129, #131. Created se.lu.onk.BaseFile? and moved …
1:40 PM Ticket #131 (se.lu.onk.BaseFile should be its own package) created by Jari Häkkinen
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 Jari Häkkinen
If the plug-in fails the job reports done! There is information …

Sep 14, 2008:

7:11 PM Ticket #129 (ReplicateError: Create a se.lu.onk.ReplicateError module) created by Jari Häkkinen
The onk.lu.se ticket will be split into several stand-alone packages …

Sep 11, 2008:

8:50 AM Ticket #128 (Warning when ftp-config.xml is missing) created by Martin Svensson
There should perhaps be a warning when trying to start the BASE …

Sep 8, 2008:

1:32 PM PluginDownload edited by Nicklas Nordborg
Releasing FTP Server 1.0beta (diff)
1:27 PM Ticket #127 (Update to final release of Apache Mina FTP server) created by Nicklas Nordborg
The current beta-release relies on the 1.0-M2 (milestone 2) release of …
1:24 PM Changeset [757] by Nicklas Nordborg
Preparing for future release 1.0
1:19 PM net.sf.basedb.ftp edited by Nicklas Nordborg
Releasing FTP Server 1.0beta (diff)
1:14 PM Ticket #114 (Implement FTP Server) closed by Nicklas Nordborg
fixed
1:14 PM Changeset [756] by Nicklas Nordborg
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 Jari Häkkinen
The Illumina package can be improved to utilize the support of storing …
11:41 AM Ticket #125 (MeV ... files are now supported (by the BASEcore) in the BASE analysis tree) created by Jari Häkkinen
The MeV extension can be improved to utilize the support of storing …
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