Timeline



Mar 27, 2009:

10:59 PM Changeset [1007] by Jari Häkkinen
metadata is split into reporter and assay metadata. Added flags to …
10:57 PM Changeset [1006] by Jari Häkkinen
metadata is split into reporter and assay metadata.
9:51 PM Changeset [1005] by Jari Häkkinen
storeValues typo! Plural importantsvn diff
7:36 PM Changeset [1004] by Jari Häkkinen
Removed warning suppressions, clean up of code, added missing …
5:07 PM Changeset [1003] by Jari Häkkinen
Added support to select assays ... but the select is not used yet.
5:06 PM Changeset [1002] by Jari Häkkinen
Added support to optionally select assays.
3:48 PM Changeset [1001] by Jari Häkkinen
Minor changes to debug_option.
3:37 PM Changeset [1000] by Jari Häkkinen
storeResult interface change, some code moved to super class.
3:35 PM Changeset [999] by Jari Häkkinen
Restructured result storage.
11:05 AM Changeset [998] by Jari Häkkinen
Addresses #118 and #183. Moved export of data to an export method.

Mar 26, 2009:

4:27 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) closed by Jari Häkkinen
fixed: Fixed as of changeset:997
4:22 PM VirtualArray-1.1.tgz.MD5 attached to se.lu.onk.VirtualArray by Jari Häkkinen
4:22 PM VirtualArray-1.1.tgz attached to se.lu.onk.VirtualArray by Jari Häkkinen
4:22 PM se.lu.onk.VirtualArray created by Jari Häkkinen
First version of VirtualArray? page
4:19 PM PluginDownload edited by Jari Häkkinen
Typos. (diff)
4:18 PM PluginDownload edited by Jari Häkkinen
Adding Virtual Array to donwload list. (diff)
4:14 PM Changeset [997] by Jari Häkkinen
Tagging version 1.1 of VirtualArray?.
4:13 PM Changeset [996] by Jari Häkkinen
Preparing release 1.1 of VirtualArray?.
11:14 AM Ticket #189 (Add toolbar extension examples) created by Nicklas Nordborg
BASE 2.12 will add extension points in a lot of toobars. We should …

Mar 25, 2009:

8:48 AM Changeset [995] by Nicklas Nordborg
References #162: Upgrade to MeV 4.3 Got rid of hardcoded 'http' in …
8:46 AM Changeset [994] by Nicklas Nordborg
References #162: Upgrade to MeV 4.3 Fixes a problem that prevented …

Mar 24, 2009:

3:15 PM Ticket #188 (Add IGV as an extension similarly to MEV) created by base
The IGV tool found at http://www.broad.mit.edu/igv/index.html is a …

Mar 16, 2009:

9:26 AM se.lu.onk.BAFsegmentation edited by markus
(diff)

Mar 14, 2009:

3:06 PM Ticket #187 (qQuantileNormalizer should allow user to select the normaliztion ...) created by Jari Häkkinen
There are several ways to normalize the data. The user should select a …
3:03 PM Ticket #186 (qQuantileNormalizer method storeResult must be reimplemented) created by Jari Häkkinen
Many things done in this method should move into the abstract base class.
3:02 PM Ticket #185 (External binary plugins should be interruptable from BASE.) created by Jari Häkkinen
3:00 PM Ticket #184 (qQuantileNormalizer should update progress bar) created by Jari Häkkinen
2:58 PM Changeset [993] by Jari Häkkinen
Addresses #118. First version of working qQuantileNormalizer.
2:52 PM net.sf.basedb.pluginutilties edited by Jari Häkkinen
(diff)
2:46 PM net.sf.basedb.pluginutilties edited by Jari Häkkinen
(diff)
2:43 PM Changeset [992] by Jari Häkkinen
Require BASE 2.5. Restructure build script.
1:50 PM Changeset [991] by Jari Häkkinen
Minor things.
1:50 PM Changeset [990] by Jari Häkkinen
Typo.
1:15 PM Ticket #183 (Change result storage of qQuantilNormalizer when BASE bioassay set ...) created by Jari Häkkinen
Relates to http://base.thep.lu.se/ticket/742 and …
11:55 AM Changeset [989] by Jari Häkkinen
Missing values from BASE are empty fields, need to define field …

Mar 13, 2009:

6:31 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
6:16 PM se.lu.onk.BAFsegmentation edited by markus
(diff)
6:15 PM se.lu.onk.BAFsegmentation edited by markus
(diff)

Mar 11, 2009:

11:02 AM Changeset [988] by Nicklas Nordborg
Changes for future release 1.1
11:01 AM Milestone FTP Server v1.0 completed
Implement an FTP Server as an extension to the web client. For more …
10:57 AM PluginDownload edited by Nicklas Nordborg
(diff)
10:53 AM net.sf.basedb.ftp edited by Nicklas Nordborg
Releasing FTP Server 1.0 (diff)
10:44 AM base-ftpserver-1.0.tar.gz attached to net.sf.basedb.ftp by Nicklas Nordborg
BASE FTP Server Extension 1.0
10:42 AM Changeset [987] by Nicklas Nordborg
Tagging release 1.0
10:41 AM Changeset [986] by Nicklas Nordborg
Preparing release 1.0
10:01 AM Changeset [985] by Nicklas Nordborg
Fixes #127: Update to final release of Apache Mina FTP server
10:01 AM Ticket #127 (Update to final release of Apache Mina FTP server) closed by Nicklas Nordborg
fixed: (In [985]) Fixes #127: Update to final release of Apache Mina FTP server

Mar 10, 2009:

5:54 PM Ticket #182 (Illumina probes not found message should be documented) created by Jari Häkkinen
Extract information from below conversation and add it to the Illumina …
2:45 PM Ticket #181 (Add MeV+R as a BASE extension?) created by Jari Häkkinen
It may be interesting to use MeV+R for visualizing and running R …
2:15 PM Ticket #180 (Overview plot extensions for Illumina expression) created by Jari Häkkinen
When support for overview plot extension are available in BASE, …

Mar 3, 2009:

1:37 PM net.sf.basedb.illumina edited by Jari Häkkinen
Added links to Illumina docs. (diff)

Feb 27, 2009:

2:07 PM Changeset [984] by Jari Häkkinen
Added support to write to stdin of underlying binary ... added missing …
2:06 PM Changeset [983] by Jari Häkkinen
Added support to write to stdin of underlying binary.
12:33 PM Changeset [982] by Nicklas Nordborg
References #178: The MeV launcher should use attached file instead of …
11:16 AM Changeset [981] by Martin Svensson
Changed requirements to version 2.9 of BASE both in documentation and …
11:12 AM Changeset [980] by Nicklas Nordborg
Added license file from MeV.
10:30 AM Changeset [979] by Jari Häkkinen
2.9 BASE core API required since changeset:975
10:03 AM net.sf.basedb.mev edited by Nicklas Nordborg
(diff)
9:45 AM Changeset [978] by Nicklas Nordborg
Fixes #179: Add user-configurable option for JVM max memory
9:45 AM Ticket #179 (Add user-configurable option for JVM max memory) closed by Nicklas Nordborg
fixed: (In [978]) Fixes #179: Add user-configurable option for JVM max memory

Feb 26, 2009:

7:22 PM Ticket #179 (Add user-configurable option for JVM max memory) created by Nicklas Nordborg
Currently, this is hard-coded into the generated JNLP file to 512 MB. …
2:05 PM Changeset [977] by Martin Svensson
References #119 Corrected the calculation of relative rank between …
1:41 PM Changeset [976] by Nicklas Nordborg
References #162: Upgrade to MeV 4. This seems to work now. I'll keep …
12:13 PM Changeset [975] by Martin Svensson
References #119 Some changes in the calculation-part. The plug-in runs …
10:48 AM Changeset [974] by Nicklas Nordborg
Fixes #178: The MeV launcher should use attached file instead of …
10:48 AM Ticket #178 (The MeV launcher should use attached file instead of running ...) closed by Nicklas Nordborg
fixed: (In [974]) Fixes #178: The MeV launcher should use attached file …
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