Timeline
Jun 10, 2009:
- 11:58 PM Changeset [1124] by
- Fixes #231.
- 11:58 PM Ticket #231 (Illumina detection P-value fails if no negative controls are available ...) closed by
- fixed: (In [1124]) Fixes #231.
- 11:56 PM Changeset [1123] by
- Fixed CamelCase escape
- 11:41 PM Changeset [1122] by
- Fixes #227.
- 11:41 PM Ticket #227 (Illumina detection P-value plug-in description must be improved) closed by
- fixed: (In [1122]) Fixes #227.
- 10:49 PM Changeset [1121] by
- 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
- 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
- fixed: (In [1120]) Fixes #232.
- 10:42 PM Changeset [1120] by
- Fixes #232.
- 1:36 PM Ticket #218 (Proof-of-concept: run a selected GenePattern module from BASE) updated by
- (In [1119]) References #218: Proof-of-concept: run a selected …
- 1:36 PM Changeset [1119] by
- References #218: Proof-of-concept: run a selected GenePattern module …
- 1:21 PM Changeset [1118] by
- References #229: Implement API for additional GenePattern web services …
- 1:21 PM Ticket #229 (Implement API for additional GenePattern web services) updated by
- (In [1118]) References #229: Implement API for additional GenePattern …
- 1:14 PM Ticket #229 (Implement API for additional GenePattern web services) updated by
-
Priority changed
- 1:13 PM Ticket #221 (Configure GenePattern server) updated by
- (In [1117]) References #221: Configure GenePattern server Changed the …
- 1:13 PM Changeset [1117] by
- References #221: Configure GenePattern server Changed the AJAX calls …
- 12:54 PM Changeset [1116] by
- References #222 and #229. File transfer gateway now uses the new wrappers.
- 12:54 PM Tickets #222,229 batch updated by
- (In [1116]) References #222 and #229. File transfer gateway now uses …
- 12:51 PM Ticket #229 (Implement API for additional GenePattern web services) updated by
- (In [1115]) References #229: Implement API for additional GenePattern …
- 12:51 PM Changeset [1115] by
- References #229: Implement API for additional GenePattern web services …
- 12:15 AM Ticket #232 (Fix deprecation warnings in detection P-value plug-in) updated by
-
Description changed
- 12:14 AM Ticket #232 (Fix deprecation warnings in detection P-value plug-in) updated by
-
Description changed
- 12:13 AM Ticket #232 (Fix deprecation warnings in detection P-value plug-in) created by
- And BackgroundCorrection plug-in
- 12:09 AM Ticket #113 (Add support for more variations of Illumina detection P-value calculations) updated by
- (In [1114]) Addresses #113. The Pvalue calculation is in place. Need …
- 12:09 AM Changeset [1114] by
- Addresses #113. The Pvalue calculation is in place. Need to figure …
- 12:08 AM Ticket #113 (Add support for more variations of Illumina detection P-value calculations) updated by
-
Summary changed
Jun 9, 2009:
- 9:48 PM Ticket #231 (Illumina detection P-value fails if no negative controls are available ...) updated by
-
Status, Owner changed
- 9:48 PM Ticket #231 (Illumina detection P-value fails if no negative controls are available ...) created by
- 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) updated by
-
Status, Owner, Component changed
- 9:39 PM Ticket #230 (Illumina detection P-value Control outlier cut-off parameter cannot be zero) created by
- Setting the parameter to 0 creates an empty control probe set. Change …
- 12:16 AM Ticket #205 (Change link README_PluginDetails to point to tags at next release) updated by
-
Status, Owner changed
- 12:14 AM Ticket #227 (Illumina detection P-value plug-in description must be improved) updated by
- (In [1113]) Addresses #227
- 12:14 AM Changeset [1113] by
- Addresses #227
- 12:08 AM Changeset [1112] by
- Addresses #227
- 12:08 AM Ticket #227 (Illumina detection P-value plug-in description must be improved) updated by
- (In [1112]) Addresses #227
Jun 8, 2009:
- 10:30 PM Changeset [1111] by
- Adding and changing svn properties.
- 10:26 PM net.sf.basedb.illumina edited by
- Updated link. (diff)
- 10:20 PM net.sf.basedb.illumina edited by
- Split listing of todo to sections assigned and others (diff)
- 10:14 PM Ticket #227 (Illumina detection P-value plug-in description must be improved) updated by
-
Status, Owner changed
- 10:13 PM Ticket #113 (Add support for more variations of Illumina detection P-value calculations) updated by
-
Status, Owner, Milestone, Description, Summary changed
Jun 5, 2009:
- 1:55 PM Ticket #229 (Implement API for additional GenePattern web services) updated by
-
Status changed
- 1:53 PM Changeset [1110] by
- References #218: Proof-of-concept: run a selected GenePattern module …
- 1:53 PM Ticket #218 (Proof-of-concept: run a selected GenePattern module from BASE) updated by
- (In [1110]) References #218: Proof-of-concept: run a selected …
- 9:36 AM Ticket #229 (Implement API for additional GenePattern web services) updated by
- It seems like this doesn't need to be very complicated at all. There …
- 8:36 AM Ticket #229 (Implement API for additional GenePattern web services) created by
- The GenePattern API includes an API for accessing some parts of the …
Jun 4, 2009:
- 11:35 AM Changeset [1109] by
- References #222: Utility for transfering file between BASE and a …
- 11:35 AM Ticket #222 (Utility for transfering file between BASE and a GenePattern server) updated by
- (In [1109]) References #222: Utility for transfering file between BASE …
- 9:18 AM Changeset [1108] by
- Fixes #221: Configure GenePattern server The settings are now saved …
- 9:18 AM Ticket #221 (Configure GenePattern server) closed by
- fixed: (In [1108]) Fixes #221: Configure GenePattern server The settings are …
Jun 3, 2009:
- 9:25 PM Ticket #221 (Configure GenePattern server) reopened by
- It will not work to store the GenePattern options with …
- 10:49 AM Ticket #218 (Proof-of-concept: run a selected GenePattern module from BASE) updated by
-
Status changed
- 10:48 AM Changeset [1107] by
- References #222: Utility for transfering file between BASE and a …
- 10:48 AM Ticket #222 (Utility for transfering file between BASE and a GenePattern server) updated by
- (In [1107]) References #222: Utility for transfering file between BASE …
- 8:43 AM Ticket #228 (net.sf.basedb.normalizers: Normalizers should use ask BASE whether ...) created by
- and use that information appropriately. Either set a proper default …
- 8:28 AM Ticket #227 (Illumina detection P-value plug-in description must be improved) updated by
-
Description changed
- 8:21 AM Ticket #227 (Illumina detection P-value plug-in description must be improved) created by
- The current information does not say anything. Look at …
Jun 2, 2009:
- 11:41 AM Ticket #222 (Utility for transfering file between BASE and a GenePattern server) updated by
-
Status changed
- 9:34 AM Changeset [1106] by
- 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
- 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
- We should upgrade the MeV package. …
- 8:45 AM Changeset [1105] by
- Ant 1.7 is needed for zip file extraction with the <mapper> element.
May 29, 2009:
- 4:12 PM Ticket #225 (qQuantiler should select all assays as reference by default) updated by
-
Summary changed
- 4:11 PM Ticket #225 (qQuantiler should select all assays as reference by default) created by
- 2:54 PM Ticket #219 (Setup a GenePattern server for testing) updated by
- One important thing to know when setting up a server is that the …
- 2:53 PM Changeset [1104] by
- References #224: Add a "Test" button on the GenePattern 'edit server' …
- 2:53 PM Ticket #224 (Add a "Test" button on the GenePattern 'edit server' page) updated by
- (In [1104]) References #224: Add a "Test" button on the GenePattern …
- 2:46 PM Ticket #224 (Add a "Test" button on the GenePattern 'edit server' page) updated by
-
Status changed
- 2:46 PM Ticket #223 (Add target in build.xml for downloading required GenePattern jar files) updated by
-
Status changed
- 8:45 AM Ticket #223 (Add target in build.xml for downloading required GenePattern jar files) updated by
- (In [1103]) References #223: Add target in build.xml for downloading …
- 8:45 AM Changeset [1103] by
- 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
- A user can click on the test button to check that the server url, …
- 8:14 AM Ticket #221 (Configure GenePattern server) closed by
- fixed: (In [1102]) Fixes #221: Configure GenePattern server
- 8:14 AM Changeset [1102] by
- Fixes #221: Configure GenePattern server
- 7:54 AM Ticket #223 (Add target in build.xml for downloading required GenePattern jar files) created by
- The GenePattern license doesn't allow us to distribute their jar …
May 28, 2009:
- 2:33 PM PluginDownload edited by
- Added link to core plugins. (diff)
- 11:49 AM Ticket #222 (Utility for transfering file between BASE and a GenePattern server) created by
- 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
- 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
- (diff)
- 11:14 AM Changeset [1101] by
- Preparing for future release 1.4
- 11:14 AM net.sf.basedb.mev edited by
- Releasing MeV Launcher 1.3 (diff)
- 11:11 AM Changeset [1100] by
- Tagging version 1.3
- 11:10 AM Changeset [1099] by
- Preparing for release 1.3
- 11:10 AM Changeset [1098] by
- 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
- 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
- There is a strange behaviour with MeV. It has some kind of cache for …
- 9:37 AM Changeset [1097] by
- References #180. The plot-extension is almost done. How the spot data …
- 9:37 AM Ticket #180 (Overview plot extensions for Illumina expression) updated by
- (In [1097]) References #180. The plot-extension is almost done. How …
- 9:12 AM PluginDownload edited by
- (diff)
- 9:10 AM PluginDownload edited by
- (diff)
- 9:09 AM Changeset [1096] by
- Preparing for future release 1.2
- 9:08 AM net.sf.basedb.examplecode edited by
- Releasing extensions examples 1.1 (diff)
- 9:04 AM Changeset [1095] by
- Tagging version 1.1
- 9:03 AM Changeset [1094] by
- Preparing for release 1.1
May 27, 2009:
- 4:20 PM PluginDownload edited by
- Removed non-working link. (diff)
- 4:14 PM PluginDownload edited by
- Added references to papers for some plug-ins (diff)
- 4:06 PM PluginDownload edited by
- (diff)
- 3:56 PM PluginDownload edited by
- Fixed BASE 1.2 plug-in list (diff)
- 2:37 PM PluginDownload edited by
- Restructured BASE 1.2 plug-in table list. (diff)
- 2:33 PM PluginDownload edited by
- Added link to WeNNI publication (diff)
- 2:16 PM Changeset [1093] by
- References #182 The information is now inserted in the README file, in …
- 2:16 PM Ticket #182 (Illumina probes not found message should be documented) updated by
- (In [1093]) References #182 The information is now inserted in the …
- 2:04 PM WikiStart edited by
- Made download link more visible. (diff)
- 11:09 AM Ticket #182 (Illumina probes not found message should be documented) updated by
-
Status, Owner changed
- 10:00 AM Changeset [1092] by
- References #217: GCT exporter Make sure assay names are unique in the …
- 10:00 AM Ticket #217 (GCT exporter) updated by
- (In [1092]) References #217: GCT exporter Make sure assay names are …
- 9:51 AM Changeset [1091] by
- Fixes #217: GCT exporter
- 9:51 AM Ticket #217 (GCT exporter) closed by
- fixed: (In [1091]) Fixes #217: GCT exporter
- 8:23 AM Ticket #217 (GCT exporter) updated by
-
Status changed
- 8:22 AM Ticket #216 (Setup source code repository for GenePattern integration) closed by
- fixed: (In [1090]) Fixes #216: Setup source code repository for GenePattern …
- 8:22 AM Changeset [1090] by
- Fixes #216: Setup source code repository for GenePattern integration
May 26, 2009:
- 12:55 PM Changeset [1089] by
- References #216: Setup source code repository for GenePattern …
- 12:55 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
- (In [1089]) References #216: Setup source code repository for …
- 12:53 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
-
Summary changed
- 12:53 PM Changeset [1088] by
- References #216: Setup source code repository for GenePattern integration
- 12:53 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
- (In [1088]) References #216: Setup source code repository for …
- 12:51 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
-
Status changed
- 12:50 PM Ticket #219 (Setup a GenePattern server for testing) created by
- 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
- It doesn't matter much which module that we choose, but it is …
- 11:14 AM Ticket #217 (GCT exporter) created by
- 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
- The usual standard directories, build.xml, readme, etc. that we need …
- 10:59 AM net.sf.basedb.genepattern edited by
- (diff)
- 10:57 AM net.sf.basedb.genepattern created by
- Created GenePattern wiki page
May 20, 2009:
- 1:08 PM Ticket #180 (Overview plot extensions for Illumina expression) updated by
-
Status, Owner, Milestone changed
May 19, 2009:
- 2:30 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by
- fixed: (In [1087]) Fixes #195 net.sf.basedb.normalizers: Normalizers should …
- 2:30 PM Changeset [1087] by
- Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for …
- 2:25 PM net.sf.basedb.normalizers edited by
- (diff)
- 2:24 PM net.sf.basedb.normalizers edited by
- INSTALL and README links now points to the current stable version of … (diff)
- 11:43 AM Changeset [1086] by
- References #212: Add support for exporting CGH data to MeV Fixed a …
- 11:43 AM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- (In [1086]) References #212: Add support for exporting CGH data to MeV …
- 9:46 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) closed by
- fixed: (In [1085]) Fixes #215: BGX reporter importer hangs if the [Controls] …
- 9:46 AM Changeset [1085] by
- Fixes #215: BGX reporter importer hangs if the [Controls] section has …
- 9:12 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) updated by
-
Summary changed
- 9:08 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) updated by
-
Status changed
I know what is causing this. The problem is with the [Controls] …
May 18, 2009:
- 3:09 PM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) updated by
- On a freshly rebooted server I reach another status message with the …
- 2:59 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) updated by
- (In [1084]) References #195 Updates everything except …
- 2:59 PM Changeset [1084] by
- 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
- 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
- fixed
- 2:19 PM Changeset [1083] by
- References #212: Add support for exporting CGH data to MeV I have …
- 2:19 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- (In [1083]) References #212: Add support for exporting CGH data to MeV …
- 11:22 AM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- (In [1082]) References #212: Add support for exporting CGH data to MeV …
- 11:22 AM Changeset [1082] by
- References #212: Add support for exporting CGH data to MeV The …
- 10:45 AM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1081]) References #214: Move TDMS export to this extension …
- 10:45 AM Changeset [1081] by
- References #214: Move TDMS export to this extension Logged values can …
May 15, 2009:
- 7:48 PM Changeset [1080] by
- Changes for future release 0.3
- 7:38 PM Changeset [1079] by
- 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
- fixed: (In [1079]) Fixes #118. qQuantiler will only show up in proper context …
- 7:32 PM Changeset [1078] by
- Tagging version 0.2 of PluginUtilities.
- 5:29 PM Changeset [1077] by
- Releasing version 0.2 of PluginUtilities.
- 5:27 PM Changeset [1076] by
- Adding context checks for number of channels.
- 4:41 PM Changeset [1075] by
- Cleaner code, removed unused imports.
- 2:38 PM Changeset [1074] by
- Addresses #118. Added documentation for qQuantiler.
- 2:38 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1074]) Addresses #118. Added documentation for qQuantiler.
- 2:14 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- It seems like the information in the documentation is incorrect. In …
- 2:11 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1073]) Addresses #118. q=max(10,min(100,target_size/10))
- 2:11 PM Changeset [1073] by
- Addresses #118. q=max(10,min(100,target_size/10))
- 1:28 PM Ticket #77 (Update information about webservice) closed by
- fixed: Everything on that page was more than 18 months old. Even the …
- 1:26 PM Changeset [1072] by
- Fixing cut&paste typo. Thanks Peter.
- 1:13 PM net.sf.basedb.mev edited by
- Added links to changelog to download table (diff)
- 11:53 AM Changeset [1071] by
- References #214: Move TDMS export to this extension Removed …
- 11:53 AM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1071]) References #214: Move TDMS export to this extension …
- 11:06 AM Changeset [1070] by
- 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
- fixed: (In [1070]) Fixes #194: Default export file names should be more unique
- 11:05 AM Ticket #194 (Default export file names should be more unique) updated by
-
Status, Summary changed
- 11:03 AM Changeset [1069] by
- References #214: Move TDMS export to this extension Removed some …
- 11:03 AM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1069]) References #214: Move TDMS export to this extension …
- 11:01 AM Changeset [1068] by
- Fixes #214: Move TDMS export to this extension
- 11:01 AM Ticket #214 (Move TDMS export to this extension) closed by
- fixed: (In [1068]) Fixes #214: Move TDMS export to this extension
May 14, 2009:
- 7:05 PM Changeset [1067] by
- Addresses #118. Forcing negative and 0 intensities to be NaNs with 0 …
- 7:05 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1067]) Addresses #118. Forcing negative and 0 intensities to be …
- 5:09 PM Changeset [1066] by
- Preparing for next milestone.
- 1:41 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) updated by
- Replying to martin: > BASE 2.12 is required. > …
- 1:23 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- My best idea so far is to not complicate things too much. I prefer not …
- 1:22 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) reopened by
- BASE 2.12 is required. Build.xml, base-plugins.xml and …
- 12:28 PM Changeset [1065] by
- Reverting changes commit by mistake to README.
- 12:26 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1064]) Addresses #118. Calculate target with median instead of mean.
- 12:26 PM Changeset [1064] by
- Addresses #118. Calculate target with median instead of mean.
- 12:01 PM Changeset [1063] by
- Add qQuantiler to autodetection list.
- 7:39 AM Ticket #207 (Illumina DASL arrays) closed by
- invalid
- 7:26 AM Ticket #210 (net.sf.basedb.normalizers: Add proper 2-channel support to ...) updated by
-
Status, Milestone changed
- 7:26 AM Ticket #183 (Change result storage of qQuantilNormalizer when BASE bioassay set ...) updated by
-
Milestone changed
May 13, 2009:
- 8:09 AM Changeset [1062] by
- Addresses #118. Added support to use either mean or median in target …
- 8:09 AM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1062]) Addresses #118. Added support to use either mean or median …
May 11, 2009:
- 1:23 PM Changeset [1061] by
- References #214: Move TDMS export to this extension The new exporter …
- 1:23 PM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1061]) References #214: Move TDMS export to this extension The …
- 1:06 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by
- fixed: (In [1060]) Fixes #195 Normalizers should ask user for how to …
- 1:06 PM Changeset [1060] by
- Fixes #195 Normalizers should ask user for how to calculate averages
- 12:56 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- Some more questions: 1. Are the columns tab-separated? 2. Can …
- 12:55 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- The text below is from the MeV documentation …
- 12:37 PM Ticket #214 (Move TDMS export to this extension) updated by
-
Status changed
- 12:36 PM Ticket #214 (Move TDMS export to this extension) created by
-
The
BioAssaySetExporteris going through refactoring as described by …
Note:
See TracTimeline
for information about the timeline view.
