Timeline


and

May 28, 2009:

2:33 PM PluginDownload edited by jari
Added link to core plugins. (diff)
11:49 AM Ticket #222 (Utility for transfering file between BASE and a GenePattern server) created by nicklas
It is not possible to send URL:s to the GenePattern? server in the same …
11:42 AM Ticket #221 (Configure GenePattern server) created by nicklas
Each user must be able to configure which GenePattern? server to use …
11:16 AM Milestone MEV Launcher v1.3 completed
See MEV Launcher extension page for more …
11:16 AM Milestone Extension examples v1.1 completed
BASE 2.12 is adding more extension points to the web client. We should …
11:15 AM PluginDownload edited by nicklas
(diff)
11:14 AM Changeset [1101] by nicklas
Preparing for future release 1.4
11:14 AM net.sf.basedb.mev edited by nicklas
Releasing MeV Launcher 1.3 (diff)
11:12 AM mev-launcher-1.3.tar.gz attached to net.sf.basedb.mev by nicklas
MeV Launcher 1.3
11:11 AM Changeset [1100] by nicklas
Tagging version 1.3
11:10 AM Changeset [1099] by nicklas
Preparing for release 1.3
11:10 AM Changeset [1098] by nicklas
Fixes #220: MeV doesn't download files correctly Added the file id …
11:10 AM Ticket #220 (MeV doesn't download files correctly) closed by nicklas
fixed: (In [1098]) Fixes #220: MeV doesn't download files correctly Added …
9:52 AM Ticket #220 (MeV doesn't download files correctly) created by nicklas
There is a strange behaviour with MeV. It has some kind of cache for …
9:37 AM Changeset [1097] by martin
References #180. The plot-extension is almost done. How the spot data …
9:12 AM PluginDownload edited by nicklas
(diff)
9:10 AM PluginDownload edited by nicklas
(diff)
9:09 AM Changeset [1096] by nicklas
Preparing for future release 1.2
9:08 AM net.sf.basedb.examplecode edited by nicklas
Releasing extensions examples 1.1 (diff)
9:05 AM extension-examples-1.1.tar.gz attached to net.sf.basedb.examplecode by nicklas
Example extensions v1.1
9:04 AM Changeset [1095] by nicklas
Tagging version 1.1
9:03 AM Changeset [1094] by nicklas
Preparing for release 1.1

May 27, 2009:

4:20 PM PluginDownload edited by jari
Removed non-working link. (diff)
4:14 PM PluginDownload edited by jari
Added references to papers for some plug-ins (diff)
4:06 PM PluginDownload edited by jari
(diff)
3:56 PM PluginDownload edited by jari
Fixed BASE 1.2 plug-in list (diff)
2:37 PM PluginDownload edited by jari
Restructured BASE 1.2 plug-in table list. (diff)
2:33 PM PluginDownload edited by jari
Added link to WeNNI publication (diff)
2:16 PM Changeset [1093] by martin
References #182 The information is now inserted in the README file, in …
2:04 PM WikiStart edited by jari
Made download link more visible. (diff)
10:00 AM Changeset [1092] by nicklas
References #217: GCT exporter Make sure assay names are unique in the …
9:51 AM Changeset [1091] by nicklas
Fixes #217: GCT exporter
9:51 AM Ticket #217 (GCT exporter) closed by nicklas
fixed: (In [1091]) Fixes #217: GCT exporter
8:22 AM Ticket #216 (Setup source code repository for GenePattern integration) closed by nicklas
fixed: (In [1090]) Fixes #216: Setup source code repository for GenePattern?
8:22 AM Changeset [1090] by nicklas
Fixes #216: Setup source code repository for GenePattern? integration

May 26, 2009:

12:55 PM Changeset [1089] by nicklas
References #216: Setup source code repository for GenePattern?
12:53 PM Changeset [1088] by nicklas
References #216: Setup source code repository for GenePattern? integration
12:50 PM Ticket #219 (Setup a GenePattern server for testing) created by nicklas
I didn't manage to setup a server on my development machine. I got it …
12:46 PM Ticket #218 (Proof-of-concept: run a selected GenePattern module from BASE) created by nicklas
It doesn't matter much which module that we choose, but it is …
11:14 AM Ticket #217 (GCT exporter) created by nicklas
Create an exporter that can export a bioassay set to GCT format. This …
11:06 AM Ticket #216 (Setup source code repository for GenePattern integration) created by nicklas
The usual standard directories, build.xml, readme, etc. that we need …
10:59 AM net.sf.basedb.genepattern edited by nicklas
(diff)
10:57 AM net.sf.basedb.genepattern created by nicklas
Created GenePattern? wiki page

May 19, 2009:

2:30 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by martin
fixed: (In [1087]) Fixes #195 net.sf.basedb.normalizers: Normalizers should …
2:30 PM Changeset [1087] by martin
Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for …
2:25 PM net.sf.basedb.normalizers edited by martin
(diff)
2:24 PM net.sf.basedb.normalizers edited by martin
INSTALL and README links now points to the current stable version of … (diff)
11:43 AM Changeset [1086] by nicklas
References #212: Add support for exporting CGH data to MeV Fixed a …
9:46 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) closed by nicklas
fixed: (In [1085]) Fixes #215: BGX reporter importer hangs if the [Controls] …
9:46 AM Changeset [1085] by nicklas
Fixes #215: BGX reporter importer hangs if the [Controls] section has …

May 18, 2009:

2:59 PM Changeset [1084] by martin
References #195 Updates everything except documentation/wiki, cause …
2:52 PM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) created by jari
The BGX file for microRNA arrays is not exactly the same as for the …
2:51 PM Ticket #212 (Add support for exporting CGH data to MeV) closed by nicklas
fixed
2:19 PM Changeset [1083] by nicklas
References #212: Add support for exporting CGH data to MeV I have …
11:22 AM Changeset [1082] by nicklas
References #212: Add support for exporting CGH data to MeV The …
10:45 AM Changeset [1081] by nicklas
References #214: Move TDMS export to this extension Logged values can …

May 15, 2009:

7:48 PM Changeset [1080] by jari
Changes for future release 0.3
7:38 PM Changeset [1079] by jari
Fixes #118. qQuantiler will only show up in proper context and …
7:38 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) closed by jari
fixed: (In [1079]) Fixes #118. qQuantiler will only show up in proper context …
7:34 PM PluginUtilities-0.2.tgz.MD5 attached to net.sf.basedb.pluginutilties by jari
7:34 PM PluginUtilities-0.2.tgz attached to net.sf.basedb.pluginutilties by jari
7:32 PM Changeset [1078] by jari
Tagging version 0.2 of PluginUtilities?.
5:29 PM Changeset [1077] by jari
Releasing version 0.2 of PluginUtilities?.
5:27 PM Changeset [1076] by jari
Adding context checks for number of channels.
4:41 PM Changeset [1075] by jari
Cleaner code, removed unused imports.
2:38 PM Changeset [1074] by jari
Addresses #118. Added documentation for qQuantiler.
2:11 PM Changeset [1073] by jari
Addresses #118. q=max(10,min(100,target_size/10))
1:28 PM Ticket #77 (Update information about webservice) closed by nicklas
fixed: Everything on that page was more than 18 months old. Even the …
1:26 PM Changeset [1072] by jari
Fixing cut&paste typo. Thanks Peter.
1:13 PM net.sf.basedb.mev edited by nicklas
Added links to changelog to download table (diff)
11:53 AM Changeset [1071] by nicklas
References #214: Move TDMS export to this extension Removed …
11:06 AM Changeset [1070] by nicklas
Fixes #194: Default export file names should be more unique
11:06 AM Ticket #194 (Default export file names should be more unique) closed by nicklas
fixed: (In [1070]) Fixes #194: Default export file names should be more unique
11:03 AM Changeset [1069] by nicklas
References #214: Move TDMS export to this extension Removed some …
11:01 AM Changeset [1068] by nicklas
Fixes #214: Move TDMS export to this extension
11:01 AM Ticket #214 (Move TDMS export to this extension) closed by nicklas
fixed: (In [1068]) Fixes #214: Move TDMS export to this extension

May 14, 2009:

7:05 PM Changeset [1067] by jari
Addresses #118. Forcing negative and 0 intensities to be NaNs? with 0 …
5:09 PM Changeset [1066] by jari
Preparing for next milestone.
1:22 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) reopened by martin
BASE 2.12 is required. Build.xml, base-plugins.xml and …
12:28 PM Changeset [1065] by jari
Reverting changes commit by mistake to README.
12:26 PM Changeset [1064] by jari
Addresses #118. Calculate target with median instead of mean.
12:01 PM Changeset [1063] by jari
Add qQuantiler to autodetection list.
7:39 AM Ticket #207 (Illumina DASL arrays) closed by jari
invalid

May 13, 2009:

8:09 AM Changeset [1062] by jari
Addresses #118. Added support to use either mean or median in target …

May 11, 2009:

1:23 PM Changeset [1061] by nicklas
References #214: Move TDMS export to this extension The new exporter …
1:06 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by martin
fixed: (In [1060]) Fixes #195 Normalizers should ask user for how to …
1:06 PM Changeset [1060] by martin
Fixes #195 Normalizers should ask user for how to calculate averages
12:36 PM Ticket #214 (Move TDMS export to this extension) created by nicklas
The BioAssaySetExporter is going through refactoring as described by …

May 8, 2009:

3:02 PM Changeset [1059] by jari
Use functionality already in yat.
12:24 PM Changeset [1058] by jari
The normalizer package now depends in PluginUtilites? version 0.1
12:18 PM PluginUtilities-0.1.tgz.MD5 attached to net.sf.basedb.pluginutilties by jari
12:18 PM PluginUtilities-0.1.tgz attached to net.sf.basedb.pluginutilties by jari
12:17 PM Changeset [1057] by jari
Tagging version 0.1 of PluginUtilities?
12:15 PM Changeset [1056] by jari
Preparing release 0.1 of PluginUtilities? package.

May 7, 2009:

12:43 AM Changeset [1055] by jari
Reverting previuos commit on configure.ac, still requiring 0.5.3
12:41 AM Changeset [1054] by jari
Cleaned up iterator usage in qQN.cc
12:30 AM Changeset [1053] by jari
Addresses #208. Fixing typos.
12:28 AM Changeset [1052] by jari
Fixes #208. Reverted changeset:1045 and added requirement on yat 0.5.3.
12:28 AM Ticket #208 (Revert changeset:1045 when yat bug ...) closed by jari
fixed: (In [1052]) Fixes #208. Reverted changeset:1045 and added requirement …

May 6, 2009:

1:15 PM Changeset [1051] by jari
Updated documentation on QuantileNormalization?.
11:11 AM Changeset [1050] by jari
Addresses #118. Non-logged input values are expected, geometric mean …
9:20 AM Changeset [1049] by jari
Addresses #206. Last commit destroyed nan fixing in changeset:1045 for …

May 4, 2009:

11:46 AM Changeset [1048] by nicklas
Fixes #213: Cannot save MeV options It was caused by #203 and never …
11:46 AM Ticket #213 (Cannot save MeV options) closed by nicklas
fixed: (In [1048]) Fixes #213: Cannot save MeV options It was caused by #203

Apr 30, 2009:

11:47 AM Ticket #213 (Cannot save MeV options) created by nicklas
It is not possible to save options for MeV. The options dialog is …

Apr 28, 2009:

8:12 AM Ticket #212 (Add support for exporting CGH data to MeV) created by nicklas
This is supposed to be straightforward the format is well-defined.
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