Timeline



Oct 1, 2009:

2:43 PM Ticket #250 (Add GSEA as an extension) updated by Nicklas Nordborg
Because the GenePattern server doesn't have to be on the same server …
2:19 PM Ticket #250 (Add GSEA as an extension) updated by Peter Johansson
I read the README for GenePattern and understand that the idea is to …
8:00 AM Ticket #250 (Add GSEA as an extension) updated by Nicklas Nordborg
This is the same license as for GenePattern and if GSEA is also a …
7:30 AM Ticket #250 (Add GSEA as an extension) updated by Jari Häkkinen
Maybe the route forward is to create export plug-ins that generate …
2:03 AM Ticket #250 (Add GSEA as an extension) updated by Peter Johansson
I'm not a lawyer, but to me the it seems like the license of GSEA is …

Sep 30, 2009:

2:43 PM Ticket #250 (Add GSEA as an extension) created by Jari Häkkinen
http://www.broadinstitute.org/gsea/ GSEA source is available and …

Sep 29, 2009:

3:07 PM Ticket #249 (net.sf.basedb.illumina: Version should autopropagate from build.xml to ...) updated by Jari Häkkinen
The same should happen for required version in at least …
3:06 PM Changeset [1175] by Jari Häkkinen
Updated release procedure. Fixed BASE version requirement.
2:31 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
2:19 PM Changeset [1174] by Jari Häkkinen
Preparing for future 1.5 release.
2:15 PM Ticket #115 (MeV launch returns a 'jsp' extension not a 'jnlp') updated by Jari Häkkinen
Milestone changed
2:14 PM Ticket #236 (Reporter import of Illumina BGX file fails on section [controls]) updated by Jari Häkkinen
Milestone changed
2:13 PM Milestone Illumina package v1.4 completed
See Illumina plug-ins package for BASE
2:13 PM Ticket #249 (net.sf.basedb.illumina: Version should autopropagate from build.xml to ...) created by Jari Häkkinen
At least when packaging.
2:11 PM net.sf.basedb.illumina edited by Jari Häkkinen
(diff)
2:10 PM illumina-plugins-1.4.tar.gz attached to net.sf.basedb.illumina by Jari Häkkinen
2:10 PM Changeset [1173] by Jari Häkkinen
Tagging Illumina package 1.4 a second time
2:09 PM Changeset [1172] by Jari Häkkinen
Preparing release 1.4 once more
2:08 PM Changeset [1171] by Jari Häkkinen
Missed to change on version number in source code.
2:05 PM Ticket #205 (Change link README_PluginDetails to point to tags at next release) closed by Jari Häkkinen
fixed
2:05 PM net.sf.basedb.illumina edited by Jari Häkkinen
Releasing Illumina package v1.4 (diff)
1:58 PM Changeset [1170] by Jari Häkkinen
Tagging Illumina package 1.4
1:55 PM Changeset [1169] by Jari Häkkinen
Preparing release 1.4
11:53 AM Ticket #204 (Add option to include all available negative controls in detection ...) closed by Jari Häkkinen
fixed: (In [1168]) Fixes #204. Also improved docs.
11:53 AM Changeset [1168] by Jari Häkkinen
Fixes #204. Also improved docs.

Sep 28, 2009:

2:51 PM Changeset [1167] by Jari Häkkinen
Fixes #113. The code change in changeset:1114 is valid, fixed docs.
2:51 PM Ticket #113 (Add support for more variations of Illumina detection P-value calculations) closed by Jari Häkkinen
fixed: (In [1167]) Fixes #113. The code change in changeset:1114 is valid, …
2:51 PM Ticket #113 (Add support for more variations of Illumina detection P-value calculations) updated by Jari Häkkinen
Description changed
1:59 PM Ticket #160 (wenni and the underlying super class should be abortable (se.lu.thep.WeNNI)) updated by Jari Häkkinen
Milestone changed
1:58 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Jari Häkkinen
Milestone changed
1:58 PM Ticket #248 (net.sf.basedb.illumina: The background correction plug-in should store ...) updated by Jari Häkkinen
Milestone changed
1:57 PM Ticket #245 (net.sf.basedb.illumina: Detection P-value fails if there is no ...) updated by Jari Häkkinen
Milestone changed
1:56 PM Ticket #204 (Add option to include all available negative controls in detection ...) updated by Jari Häkkinen
Status, Owner, Milestone changed
1:31 PM Changeset [1166] by Jari Häkkinen
Fixes #235 and spelling.
1:31 PM Ticket #235 (Illumina package: Add instructions on how to remove 'Illumina' raw ...) closed by Jari Häkkinen
fixed: (In [1166]) Fixes #235 and spelling.
10:36 AM net.sf.basedb.illumina edited by Jari Häkkinen
Added link to trunk source tree. (diff)
10:30 AM Ticket #235 (Illumina package: Add instructions on how to remove 'Illumina' raw ...) updated by Jari Häkkinen
Status, Owner, Milestone changed

Sep 25, 2009:

2:44 PM Ticket #248 (net.sf.basedb.illumina: The background correction plug-in should store ...) created by Jari Häkkinen
Now the assays are background corrected but it would be nice to easily …
2:10 PM Changeset [1165] by Nicklas Nordborg
References #242: Implement "Save to BASE" function in the MeV gui The …
2:10 PM Ticket #242 (Implement "Save to BASE" function in the MeV gui) updated by Nicklas Nordborg
(In [1165]) References #242: Implement "Save to BASE" function in the …

Sep 23, 2009:

11:38 AM PluginDownload edited by Jari Häkkinen
Updated BASE 1 download link. (diff)
11:08 AM Changeset [1164] by Jari Häkkinen
Fixes #247. A work around for the erroneous export from exportPlainMatrix.
11:08 AM Ticket #247 (net.sf.basedb.normalizers: qQuantileNormalization crashes when ...) closed by Jari Häkkinen
fixed: (In [1164]) Fixes #247. A work around for the erroneous export from …
11:03 AM Ticket #247 (net.sf.basedb.normalizers: qQuantileNormalization crashes when ...) updated by Jari Häkkinen
Status changed
11:03 AM Ticket #183 (Change result storage of qQuantilNormalizer when BASE bioassay set ...) updated by Jari Häkkinen
Description changed
11:02 AM Ticket #247 (net.sf.basedb.normalizers: qQuantileNormalization crashes when ...) created by Jari Häkkinen
When qQuantiler normalizes bioassay sets where assays have been …

Sep 22, 2009:

1:52 PM Ticket #242 (Implement "Save to BASE" function in the MeV gui) updated by Nicklas Nordborg
(In [1163]) References #242: Implement "Save to BASE" function in the …
1:52 PM Changeset [1163] by Nicklas Nordborg
References #242: Implement "Save to BASE" function in the MeV gui The …
9:05 AM Ticket #246 (Add MeV Analysis file to list of MIME types) closed by Nicklas Nordborg
fixed: (In [1162]) Fixes #246: Add MeV Analysis file to list of MIME types
9:05 AM Changeset [1162] by Nicklas Nordborg
Fixes #246: Add MeV Analysis file to list of MIME types
8:16 AM Ticket #246 (Add MeV Analysis file to list of MIME types) created by Nicklas Nordborg
The analysis file is actually a zip file with a .anl extension.

Sep 18, 2009:

4:19 PM Ticket #204 (Add option to include all available negative controls in detection ...) updated by Jari Häkkinen
Description changed
4:18 PM Ticket #245 (net.sf.basedb.illumina: Detection P-value fails if there is no ...) created by Jari Häkkinen
The plug-in returns with Status: Error: -1 The plug-in should return …
9:56 AM Ticket #242 (Implement "Save to BASE" function in the MeV gui) updated by Nicklas Nordborg
I just found out one potential issue that limits the usability of this …

Sep 16, 2009:

9:00 AM Ticket #242 (Implement "Save to BASE" function in the MeV gui) updated by Nicklas Nordborg
Status changed
8:57 AM Changeset [1161] by Nicklas Nordborg
Fixes #241: Add MeV Analysis file as a file type for bioassay sets …
8:57 AM Ticket #241 (Add MeV Analysis file as a file type for bioassay sets) closed by Nicklas Nordborg
fixed: (In [1161]) Fixes #241: Add MeV Analysis file as a file type for …

Sep 15, 2009:

2:37 PM Ticket #243 (Create a sample MeV analysis file for testing purposes) closed by Nicklas Nordborg
fixed: The test files (one tdms file and one analysis file) can be found in …
2:28 PM Changeset [1160] by Nicklas Nordborg
References #241: Add MeV Analysis file as a file type for bioassay …
2:28 PM Ticket #241 (Add MeV Analysis file as a file type for bioassay sets) updated by Nicklas Nordborg
(In [1160]) References #241: Add MeV Analysis file as a file type for …
1:22 PM Ticket #241 (Add MeV Analysis file as a file type for bioassay sets) updated by Nicklas Nordborg
(In [1159]) References #241: Add MeV Analysis file as a file type for …
1:22 PM Changeset [1159] by Nicklas Nordborg
References #241: Add MeV Analysis file as a file type for bioassay …
12:51 PM Changeset [1158] by Nicklas Nordborg
Checking in the .classpath file for Eclipse since it is so boring to …
12:46 PM Ticket #241 (Add MeV Analysis file as a file type for bioassay sets) updated by Nicklas Nordborg
(In [1157]) References #241: Add MeV Analysis file as a file type for …
12:46 PM Changeset [1157] by Nicklas Nordborg
References #241: Add MeV Analysis file as a file type for bioassay …

Sep 14, 2009:

1:44 PM Changeset [1156] by Nicklas Nordborg
References #241: Add MeV Analysis file as a file type for bioassay …
1:44 PM Ticket #241 (Add MeV Analysis file as a file type for bioassay sets) updated by Nicklas Nordborg
(In [1156]) References #241: Add MeV Analysis file as a file type for …

Sep 11, 2009:

2:02 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)

Sep 9, 2009:

10:51 AM Ticket #209 (Export of data to data repositories such as GEO and ArrayExpress) updated by Jari Häkkinen
A GEO export should probably be a two step process. One step to export …
10:48 AM Ticket #244 (Create a SAM plug-in) created by Jari Häkkinen
SAM is available in MeV but it would be nice to have it as an …
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