Timeline



Jan 7, 2009:

9:50 AM Ticket #169 (Running two "New root bioassay set" jobs at the same time makes the ...) created by Nicklas Nordborg
Moved from http://base.thep.lu.se/ticket/1224. This is at least true …

Dec 21, 2008:

5:01 PM Changeset [935] by Jari Häkkinen
Removing braches.
4:59 PM se.lu.thep.affymetrix edited by Jari Häkkinen
Added link to repository. (diff)

Dec 18, 2008:

5:05 PM se.lu.onk.CGHDataDumper edited by Jari Häkkinen
(diff)
5:03 PM PluginDownload edited by Jari Häkkinen
(diff)
4:07 PM PluginDownload edited by Jari Häkkinen
Update normalization package information (diff)
12:57 PM Ticket #120 (Create a normalization plug-in package.) closed by Jari Häkkinen
fixed: Released working plugins in 1.0. The remaining tickets moved to 1.1
12:56 PM Milestone Normalization package v1.0 completed
For more information see the [wiki:net.sf.basedb.normalizers
12:55 PM net.sf.basedb.normalizers edited by Jari Häkkinen
(diff)
12:54 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Added raw download tag to package link. (diff)
12:53 PM normalization-plugins-1.0.tar.gz.MD5 attached to net.sf.basedb.normalizers by Jari Häkkinen
12:53 PM normalization-plugins-1.0.tar.gz attached to net.sf.basedb.normalizers by Jari Häkkinen
12:52 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Preparing 1.0 release of net.sf.basedb.normalizers package. (diff)
12:48 PM Ticket #168 (MD5 sum should be automatically generated for a package) created by Jari Häkkinen
12:44 PM Changeset [934] by Jari Häkkinen
Tagging version 1.0 of the net.sf.basedb.normalizers.
12:41 PM Changeset [933] by Jari Häkkinen
Corrected spelling
12:40 PM Changeset [932] by Jari Häkkinen
Addresses #120.
12:30 PM Changeset [931] by Jari Häkkinen
Addresses #120. Preparing 1.0 release.
12:29 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Preparing 1.0 release of net.sf.basedb.normalizers package. (diff)
12:18 PM Changeset [930] by Jari Häkkinen
Typo
12:15 PM Changeset [929] by Jari Häkkinen
Removing CubicSplineNormalization? stub.
12:12 PM Changeset [928] by Jari Häkkinen
Fixes #167. Now using geometric mean
12:12 PM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) closed by Jari Häkkinen
fixed: (In [928]) Fixes #167. Now using geometric mean
12:11 PM Changeset [927] by Jari Häkkinen
Refs #165.
11:13 AM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) created by Jari Häkkinen
The current version uses the arithmetic mean.

Dec 17, 2008:

11:24 PM Ticket #166 ((net.sf.basedb.normalizers) Automatic progression of version to source ...) created by Jari Häkkinen
The version of the plug-in is hard coded in the java source
11:22 PM Ticket #163 (Rank invariant normalization has a sorting bug) closed by Jari Häkkinen
fixed: The fix passes my test now (I found another issue in my own test code).
11:20 PM Ticket #165 (Create quantile normalizer) closed by Jari Häkkinen
fixed: (In [926]) Fixes #165. Simply renamed rank invariant to quantile and …
11:20 PM Changeset [926] by Jari Häkkinen
Fixes #165. Simply renamed rank invariant to quantile and made …
10:37 PM Ticket #119 (Create rank invariant normalizer) reopened by Jari Häkkinen
The normalizer is not the rank invariant normalizer but rather …
10:15 PM Ticket #165 (Create quantile normalizer) created by Jari Häkkinen
9:06 PM Changeset [925] by Jari Häkkinen
Improved README.
9:05 PM Changeset [924] by Jari Häkkinen

Dec 16, 2008:

11:45 PM Ticket #164 (Improve documentation on how to upgrade the illumina plug-in package) created by Jari Häkkinen
As the INSTALL doc now stands it is hard to know how an upgrade of the …
4:55 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
4:52 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
4:51 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
2:23 PM Changeset [923] by Martin Svensson
References #163 Disregard the last commit. This will do instead.
1:52 PM Changeset [922] by Martin Svensson
References #163 The sorting of spotdata should be stable now. Please …
9:11 AM Changeset [921] by Nicklas Nordborg
Preparing for future release 1.0
9:10 AM net.sf.basedb.ftp edited by Nicklas Nordborg
Releasing FTP Server 1.0beta2 (diff)
9:05 AM Changeset [920] by Nicklas Nordborg
Tagging release of FTP Server 1.0beta2
9:04 AM Changeset [919] by Nicklas Nordborg
Preparing release of FTP Server 1.0beta2

Dec 15, 2008:

2:43 PM Changeset [918] by Jari Häkkinen
Removed stray lines.
2:41 PM Ticket #163 (Rank invariant normalization has a sorting bug) created by Jari Häkkinen
I think the sorting is not stable for cases when there is a tie …

Dec 12, 2008:

9:35 AM Changeset [917] by Nicklas Nordborg
References #127: Update to final release of Apache Mina FTP server …

Dec 11, 2008:

10:21 PM Changeset [916] by Nicklas Nordborg
References #127: Update to final release of Apache Mina FTP server …
10:16 PM Changeset [915] by Nicklas Nordborg
References #127: Update to final release of Apache Mina FTP server I …

Dec 10, 2008:

10:01 PM Ticket #162 (Upgrade to MeV 4.3) created by Nicklas Nordborg
Reports on the mailing lists indicate that MeV 4.3 has solved a lot of …
1:09 PM Changeset [914] by Nicklas Nordborg
Adding note about checking that the information on the download page …
1:07 PM PluginDownload edited by Nicklas Nordborg
(diff)
1:06 PM net.sf.basedb.illumina edited by Nicklas Nordborg
(diff)
1:05 PM Changeset [913] by Nicklas Nordborg
Preparing for future release 1.3
1:04 PM Milestone Illumina package v1.2 completed
See Illumina plug-ins package for BASE
1:02 PM net.sf.basedb.illumina edited by Nicklas Nordborg
Releasing Illumina package 1.2 (diff)
1:00 PM illumina-plugins-1.2.tar.gz attached to net.sf.basedb.illumina by Nicklas Nordborg
12:59 PM Changeset [912] by Nicklas Nordborg
Tagging Illumina package 1.2
12:59 PM Changeset [911] by Nicklas Nordborg
Preparing release of Illumina package 1.2

Dec 9, 2008:

1:26 PM Ticket #161 ((net.sf.basedb.normalizers) Automatic download of BASE API) created by Jari Häkkinen
The build process should detect whether the required BASE jars are …
1:05 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Changing to GPL3 (diff)
1:01 PM Changeset [910] by Jari Häkkinen
Changing normalizer package license to GPL3.
11:38 AM Changeset [909] by Jari Häkkinen
Addresses #120.

Dec 8, 2008:

11:18 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Updated TODO section (diff)
11:13 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Added browse svn link (diff)
10:58 PM Ticket #88 (extra values pass through) closed by Jari Häkkinen
wontfix
10:52 PM Ticket #75 (base2.xml genespring connection) closed by Jari Häkkinen
wontfix: Will not fix this. External contributions welcome.
10:48 PM Ticket #41 (Add data to output: sign flag, sign specific rank) closed by Jari Häkkinen
wontfix
10:30 PM Changeset [908] by Jari Häkkinen
Addresses #50. Running nni with phony weights.
10:07 PM Changeset [907] by Peter Johansson
using ACLOCAL_AMFLAGS requires Automake 1.10
10:01 PM Changeset [906] by Jari Häkkinen
Some external binary will output result to stdout ... optionally …
9:31 PM Changeset [905] by Peter Johansson
WeNNI.java should be included in dist
9:19 PM Changeset [904] by Peter Johansson
installing jars with chmod 644
9:11 PM Changeset [903] by Peter Johansson
Style is everything
4:49 PM Changeset [902] by Peter Johansson
timestamp of downloaded jar file will be old. Fixing deps to reflect …
4:25 PM Changeset [901] by Peter Johansson
improve dependency
10:56 AM Changeset [900] by Jari Häkkinen
Refs #159
10:53 AM Changeset [899] by Jari Häkkinen
Address #159. Renaming BASE1 plugin definition and minor changes to …
10:50 AM Changeset [898] by Jari Häkkinen
Adding URL.
10:48 AM Changeset [897] by Jari Häkkinen
Correcting URL
10:42 AM Changeset [896] by Jari Häkkinen
Refs #56. Removing branches and tags directories since they will never …
10:39 AM Changeset [895] by Jari Häkkinen
Addresses #56 and #159. Creating VirtualArray? module.
10:27 AM Changeset [894] by Jari Häkkinen
Adding missing svn property.
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