Timeline



Jun 10, 2009:

11:58 PM Changeset [1124] by Jari Häkkinen
Fixes #231.
11:58 PM Ticket #231 (Illumina detection P-value fails if no negative controls are available ...) closed by Jari Häkkinen
fixed: (In [1124]) Fixes #231.
11:56 PM Changeset [1123] by Jari Häkkinen
Fixed CamelCase escape
11:41 PM Changeset [1122] by Jari Häkkinen
Fixes #227.
11:41 PM Ticket #227 (Illumina detection P-value plug-in description must be improved) closed by Jari Häkkinen
fixed: (In [1122]) Fixes #227.
10:49 PM Changeset [1121] by Jari Häkkinen
Fixes #230. Lower limit is now 1.
10:49 PM Ticket #230 (Illumina detection P-value Control outlier cut-off parameter cannot be zero) closed by Jari Häkkinen
fixed: (In [1121]) Fixes #230. Lower limit is now 1.
10:42 PM Ticket #232 (Fix deprecation warnings in detection P-value plug-in) closed by Jari Häkkinen
fixed: (In [1120]) Fixes #232.
10:42 PM Changeset [1120] by Jari Häkkinen
Fixes #232.
1:36 PM Changeset [1119] by Nicklas Nordborg
References #218: Proof-of-concept: run a selected GenePattern? module …
1:21 PM Changeset [1118] by Nicklas Nordborg
References #229: Implement API for additional GenePattern? web services …
1:13 PM Changeset [1117] by Nicklas Nordborg
References #221: Configure GenePattern? server Changed the AJAX calls …
12:54 PM Changeset [1116] by Nicklas Nordborg
References #222 and #229. File transfer gateway now uses the new wrappers.
12:51 PM Changeset [1115] by Nicklas Nordborg
References #229: Implement API for additional GenePattern? web services …
12:13 AM Ticket #232 (Fix deprecation warnings in detection P-value plug-in) created by Jari Häkkinen
And BackgroundCorrection plug-in
12:09 AM Changeset [1114] by Jari Häkkinen
Addresses #113. The Pvalue calculation is in place. Need to figure …

Jun 9, 2009:

9:48 PM Ticket #231 (Illumina detection P-value fails if no negative controls are available ...) created by Jari Häkkinen
The message is Error -1. Change the message to something more informative.
9:39 PM Ticket #230 (Illumina detection P-value Control outlier cut-off parameter cannot be zero) created by Jari Häkkinen
Setting the parameter to 0 creates an empty control probe set. Change …
12:14 AM Changeset [1113] by Jari Häkkinen
Addresses #227
12:08 AM Changeset [1112] by Jari Häkkinen
Addresses #227

Jun 8, 2009:

10:30 PM Changeset [1111] by Jari Häkkinen
Adding and changing svn properties.
10:26 PM net.sf.basedb.illumina edited by Jari Häkkinen
Updated link. (diff)
10:20 PM net.sf.basedb.illumina edited by Jari Häkkinen
Split listing of todo to sections assigned and others (diff)

Jun 5, 2009:

1:53 PM Changeset [1110] by Nicklas Nordborg
References #218: Proof-of-concept: run a selected GenePattern? module …
8:36 AM Ticket #229 (Implement API for additional GenePattern web services) created by Nicklas Nordborg
The GenePattern? API includes an API for accessing some parts of the …

Jun 4, 2009:

11:35 AM Changeset [1109] by Nicklas Nordborg
References #222: Utility for transfering file between BASE and a …
9:18 AM Changeset [1108] by Nicklas Nordborg
Fixes #221: Configure GenePattern? server The settings are now saved …
9:18 AM Ticket #221 (Configure GenePattern server) closed by Nicklas Nordborg
fixed: (In [1108]) Fixes #221: Configure GenePattern? server The settings are …

Jun 3, 2009:

9:25 PM Ticket #221 (Configure GenePattern server) reopened by Nicklas Nordborg
It will not work to store the GenePattern? options with …
10:48 AM Changeset [1107] by Nicklas Nordborg
References #222: Utility for transfering file between BASE and a …
8:43 AM Ticket #228 (net.sf.basedb.normalizers: Normalizers should use ask BASE whether ...) created by Jari Häkkinen
and use that information appropriately. Either set a proper default …
8:21 AM Ticket #227 (Illumina detection P-value plug-in description must be improved) created by Jari Häkkinen
The current information does not say anything. Look at …

Jun 2, 2009:

9:34 AM Changeset [1106] by Nicklas Nordborg
Fixes #224: Add a "Test" button on the GenePattern? 'edit server' page …
9:34 AM Ticket #224 (Add a "Test" button on the GenePattern 'edit server' page) closed by Nicklas Nordborg
fixed: (In [1106]) Fixes #224: Add a "Test" button on the GenePattern? 'edit …

Jun 1, 2009:

9:36 PM Ticket #226 (Update to MeV 4.4) created by Jari Häkkinen
We should upgrade the MeV package. …
8:45 AM Changeset [1105] by Nicklas Nordborg
Ant 1.7 is needed for zip file extraction with the <mapper> element.

May 29, 2009:

4:11 PM Ticket #225 (qQuantiler should select all assays as reference by default) created by Jari Häkkinen
2:53 PM Changeset [1104] by Nicklas Nordborg
References #224: Add a "Test" button on the GenePattern? 'edit server' …
8:45 AM Changeset [1103] by Nicklas Nordborg
References #223: Add target in build.xml for downloading required …
8:16 AM Ticket #224 (Add a "Test" button on the GenePattern 'edit server' page) created by Nicklas Nordborg
A user can click on the test button to check that the server url, …
8:14 AM Ticket #221 (Configure GenePattern server) closed by Nicklas Nordborg
fixed: (In [1102]) Fixes #221: Configure GenePattern? server
8:14 AM Changeset [1102] by Nicklas Nordborg
Fixes #221: Configure GenePattern? server
7:54 AM Ticket #223 (Add target in build.xml for downloading required GenePattern jar files) created by Nicklas Nordborg
The GenePattern? license doesn't allow us to distribute their jar …

May 28, 2009:

2:33 PM PluginDownload edited by Jari Häkkinen
Added link to core plugins. (diff)
11:49 AM Ticket #222 (Utility for transfering file between BASE and a GenePattern server) created by Nicklas Nordborg
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 Nordborg
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 Nordborg
(diff)
11:14 AM Changeset [1101] by Nicklas Nordborg
Preparing for future release 1.4
11:14 AM net.sf.basedb.mev edited by Nicklas Nordborg
Releasing MeV Launcher 1.3 (diff)
11:12 AM mev-launcher-1.3.tar.gz attached to net.sf.basedb.mev by Nicklas Nordborg
MeV Launcher 1.3
11:11 AM Changeset [1100] by Nicklas Nordborg
Tagging version 1.3
11:10 AM Changeset [1099] by Nicklas Nordborg
Preparing for release 1.3
11:10 AM Changeset [1098] by Nicklas Nordborg
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 Nordborg
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 Nordborg
There is a strange behaviour with MeV. It has some kind of cache for …
9:37 AM Changeset [1097] by Martin Svensson
References #180. The plot-extension is almost done. How the spot data …
9:12 AM PluginDownload edited by Nicklas Nordborg
(diff)
9:10 AM PluginDownload edited by Nicklas Nordborg
(diff)
9:09 AM Changeset [1096] by Nicklas Nordborg
Preparing for future release 1.2
9:08 AM net.sf.basedb.examplecode edited by Nicklas Nordborg
Releasing extensions examples 1.1 (diff)
9:05 AM extension-examples-1.1.tar.gz attached to net.sf.basedb.examplecode by Nicklas Nordborg
Example extensions v1.1
9:04 AM Changeset [1095] by Nicklas Nordborg
Tagging version 1.1
9:03 AM Changeset [1094] by Nicklas Nordborg
Preparing for release 1.1

May 27, 2009:

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

May 26, 2009:

12:55 PM Changeset [1089] by Nicklas Nordborg
References #216: Setup source code repository for GenePattern?
12:53 PM Changeset [1088] by Nicklas Nordborg
References #216: Setup source code repository for GenePattern? integration
12:50 PM Ticket #219 (Setup a GenePattern server for testing) created by Nicklas Nordborg
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 Nordborg
It doesn't matter much which module that we choose, but it is …
11:14 AM Ticket #217 (GCT exporter) created by Nicklas Nordborg
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 Nordborg
The usual standard directories, build.xml, readme, etc. that we need …
10:59 AM net.sf.basedb.genepattern edited by Nicklas Nordborg
(diff)
10:57 AM net.sf.basedb.genepattern created by Nicklas Nordborg
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 Svensson
fixed: (In [1087]) Fixes #195 net.sf.basedb.normalizers: Normalizers should …
2:30 PM Changeset [1087] by Martin Svensson
Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for …
2:25 PM net.sf.basedb.normalizers edited by Martin Svensson
(diff)
2:24 PM net.sf.basedb.normalizers edited by Martin Svensson
INSTALL and README links now points to the current stable version of … (diff)
11:43 AM Changeset [1086] by Nicklas Nordborg
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 Nordborg
fixed: (In [1085]) Fixes #215: BGX reporter importer hangs if the [Controls] …
9:46 AM Changeset [1085] by Nicklas Nordborg
Fixes #215: BGX reporter importer hangs if the [Controls] section has …

May 18, 2009:

2:59 PM Changeset [1084] by Martin Svensson
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 Häkkinen
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 Nordborg
fixed
2:19 PM Changeset [1083] by Nicklas Nordborg
References #212: Add support for exporting CGH data to MeV I have …
11:22 AM Changeset [1082] by Nicklas Nordborg
References #212: Add support for exporting CGH data to MeV The …
10:45 AM Changeset [1081] by Nicklas Nordborg
References #214: Move TDMS export to this extension Logged values can …

May 15, 2009:

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