Timeline



Dec 1, 2008:

12:54 PM Download edited by Fredrik Levander
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12:54 PM Download edited by Fredrik Levander
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12:52 PM Problems edited by Fredrik Levander
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12:49 PM KnownIssuesProteios edited by Fredrik Levander
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12:46 PM Releases edited by Fredrik Levander
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12:39 PM WikiStart edited by Fredrik Levander
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11:28 AM Releases edited by Fredrik Levander
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11:23 AM Releases edited by Fredrik Levander
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11:20 AM Ticket #499 (Update UML diagrams) created by Fredrik Levander
The UML diagrams should be updated to reflect the current database …
11:16 AM WikiStart edited by Fredrik Levander
Added link to Releases page (diff)
11:13 AM Releases created by Fredrik Levander
9:09 AM ImplementAction edited by Fredrik Levander
(diff)

Nov 26, 2008:

1:36 PM WorkingWithHitReports edited by Fredrik Levander
(diff)
11:56 AM ReleaseProcedure edited by Gregory Vincic
Fixed headings (diff)
11:55 AM ReleaseProcedure edited by Gregory Vincic
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11:55 AM ReleaseProcedure edited by Gregory Vincic
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11:54 AM ReleaseProcedure edited by Gregory Vincic
Added outline (diff)
11:53 AM ReleaseProcedure edited by Gregory Vincic
Adding plugins section (diff)
10:46 AM Milestone Proteios SE 2.5 completed
Extended search engine access from ProSE. Improved search results …
10:46 AM ReleaseProcedure edited by Gregory Vincic
(diff)
9:49 AM ReleaseProcedure edited by Gregory Vincic
(diff)
9:18 AM WikiStart edited by Gregory Vincic
Switching to 2.5.0 release as latest stable (diff)
9:17 AM Download edited by Gregory Vincic
Switching to 2.5.0 release as latest stable (diff)
9:01 AM Changeset [2970] by Gregory Vincic
Tagging 2.5.0 release
8:52 AM Changeset [2969] by Gregory Vincic
Updating version for 2.5.0 release, also added a separate target for …

Nov 24, 2008:

4:27 PM Ticket #491 (Add precursor information to spectrum interface) closed by olle
fixed: Ticket closed as the requested functionality has been added.
3:54 PM Ticket #497 (Installation script spelling error) closed by olle
fixed: Ticket closed as the described typo was fixed.
3:53 PM Changeset [2968] by olle
Refs #497. Installation script typo fixed: 1. Installation script …
3:22 PM Ticket #423 (No permissions are checked when updating the remaining quantity of a ...) closed by Fredrik Levander
fixed: The questions raised have been transfered to ticket #498
3:21 PM Ticket #498 (Usage permission checking of biomaterials) created by Fredrik Levander
Refs #423. The core doesn't check usage permissions for a biomaterial …
3:11 PM Ticket #470 (Import of OMSSA search results) closed by Fredrik Levander
fixed: The import is functional, but will have to be expanded to get …
3:05 PM Changeset [2967] by Fredrik Levander
Refs #423. Checking write permission before updating remaining …
2:05 PM ReleaseProcedure edited by Gregory Vincic
(diff)
2:01 PM ReleaseProcedure edited by Gregory Vincic
(diff)
1:59 PM ReleaseProcedure edited by Gregory Vincic
(diff)
1:36 PM Ticket #497 (Installation script spelling error) created by Gregory Vincic
When running ./install-linux.sh in step (9) Mail "from"-address …
1:27 PM Developers edited by Gregory Vincic
Linking ReleaseProcedure page (diff)
1:26 PM ReleaseProcedure edited by Gregory Vincic
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1:13 PM ReleaseProcedure edited by Gregory Vincic
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1:11 PM ReleaseProcedure edited by Gregory Vincic
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1:00 PM ReleaseProcedure edited by Gregory Vincic
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12:59 PM ReleaseProcedure edited by Gregory Vincic
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12:07 PM Ticket #483 (PIKE annotation of protein lists) closed by olle
fixed: Ticket closed as the basic functionality of retrieving protein …
11:43 AM Ticket #481 (Support for "Save As..." functionality when editing an X!Tandem ...) closed by olle
fixed: Ticket closed again as it has not been possible to reproduce the error …
11:24 AM ReleaseProcedure edited by Gregory Vincic
(diff)
11:23 AM Ticket #471 (Searching OMSSA from Proteios SE) closed by olle
fixed: Ticket closed as the requested functionality has been added.
11:22 AM ReleaseProcedure edited by Gregory Vincic
(diff)
11:21 AM Ticket #496 (Database schema version number should be updated before release) closed by olle
fixed: Ticket closed as the requested functionality has been added.
11:18 AM Changeset [2966] by olle
Refs #496. Database update routine updated to new schema version: 1. …
11:11 AM KnownIssuesProteios edited by Fredrik Levander
(diff)
11:08 AM Problems edited by Fredrik Levander
(diff)
11:02 AM Ticket #496 (Database schema version number should be updated before release) created by olle
The database schema has been updated in a number of tickets, e.g. …
10:06 AM ReleaseProcedure edited by Gregory Vincic
(diff)
9:27 AM ReleaseProcedure created by Gregory Vincic
Initial revision

Nov 21, 2008:

4:50 PM Ticket #494 (Peak list file readers to support two types of ids) closed by olle
fixed: Ticket closed, as the discussed functionality has been added.
4:42 PM Changeset [2965] by olle
Refs #494. Refs #407. Class/file io/MgfFileReader.java in api/core/ …
4:26 PM Changeset [2964] by olle
Refs #407. Refs #494. Class/file io/MgfFileReader.java in api/core/ …
4:19 PM Changeset [2963] by Fredrik Levander
Refs #470. Setting names of modifications and digestion enzyme.

Nov 20, 2008:

3:32 PM Changeset [2962] by Fredrik Levander
Refs #470. Corrected sequence retrieval
3:08 PM Changeset [2961] by Fredrik Levander
Refs #470. First revision of import of OMSSA XML results. …
9:03 AM MoreAboutProteios edited by Fredrik Levander
(diff)

Nov 19, 2008:

12:57 PM Ticket #486 (Spectrum string id) closed by Fredrik Levander
fixed: Working fine. MGF files will get index of spectrum as spectrumId, and …
12:56 PM Ticket #456 (Retrieval of Mascot XML results from Mascot server) closed by Fredrik Levander
fixed: Seems to be working perfectly
12:52 PM Ticket #495 (Isobaric label support) created by Fredrik Levander
Support for calculating ratios of reporter ions from isobaric labels …
12:42 PM WorkingWithHitReports edited by Fredrik Levander
(diff)
11:50 AM Changeset [2960] by olle
Refs #407. Class/file io/MgfFileReader.java in api/core/ updated to …
10:51 AM Changeset [2959] by olle
Refs #491. Refs #407. Class/file io/MgfFileReader.java in api/core/ …
10:48 AM HitsReportTableFeatures edited by Fredrik Levander
Updated hits report info to corrspond to current (diff)

Nov 18, 2008:

4:39 PM Changeset [2958] by Fredrik Levander
Refs #493, refs #490. Support for MGF retention time and total intensity
1:15 PM Changeset [2957] by Fredrik Levander
Refs #456. Added showsubsets option to the retrieval, to be compatible …
11:39 AM Changeset [2956] by Fredrik Levander
Corrected bug in hits imports to allow for MGF.
11:23 AM Ticket #481 (Support for "Save As..." functionality when editing an X!Tandem ...) reopened by Fredrik Levander
The following resulted in an error: Open a X!Tandem parameter set for …

Nov 17, 2008:

2:38 PM Manual edited by olle
Added section "General" at top, with link to wiki page on key concepts … (diff)
2:09 PM Ticket #482 (Only first page of hits report is exported) closed by olle
fixed: Ticket closed as the desired functionality has been added.
2:08 PM Ticket #481 (Support for "Save As..." functionality when editing an X!Tandem ...) closed by olle
fixed: Ticket closed as the desired functionality has been added.
2:07 PM Ticket #480 (MGF (Mascot Generic Format) file reader should give limited support ...) closed by olle
fixed: Ticket closed as the desired functionality has been added.
2:05 PM Ticket #478 (Creating new Gels do not get shared automatically if in active project) closed by olle
worksforme: Ticket closed since the problem described in the ticket description …
1:57 PM Ticket #427 (Howering description of extensions) closed by olle
fixed: Ticket closed as the desired functionality has been added.
1:55 PM Ticket #346 (Batch move file and individually delete file) closed by olle
fixed: Ticket closed as the desired functionality has been added.
12:34 PM SomeConceptsInProteios edited by olle
Section "Extension" updated with note that several jobs may be created … (diff)
12:25 PM SomeConceptsInProteios edited by olle
Section "Extension" updated in initial description. (diff)
8:56 AM Problems edited by olle
Added wiki escape character to "NullPointerException?". (diff)

Nov 14, 2008:

4:53 PM Changeset [2955] by olle
Refs #483. Class/file plugins/SearchPIKEPlugin.java in plugin/ updated …
11:03 AM Changeset [2954] by olle
Refs #491. Class/file gui/form/FormFactory.java in client/servlet/ …
10:02 AM Changeset [2953] by olle
Refs #491. Class/file gui/form/FormFactory.java in client/servlet/ …
9:51 AM Changeset [2952] by olle
Refs #491. Spectrum display from spectrum file via link in Hits report …
8:50 AM Changeset [2951] by olle
Refs #491. Class/file io/MgfFileReader.java in api/core/ updated to …
8:44 AM Changeset [2950] by olle
Refs #491. Class/file io/PklFileReader.java in api/core/ updated to …

Nov 13, 2008:

11:16 AM Changeset [2949] by Fredrik Levander
Refs #492. Added build dependency.
9:41 AM Ticket #493 (Add retention time to Hits report) closed by Fredrik Levander
fixed: Seems to be working

Nov 12, 2008:

4:58 PM Changeset [2948] by Fredrik Levander
Fixes #492. Added actions and plugin for export of exclusion lists …
4:58 PM Ticket #492 (Exclusion list generation) closed by Fredrik Levander
fixed: (In [2948]) Fixes #492. Added actions and plugin for export of …
2:48 PM Changeset [2947] by olle
Refs #491. Class/file io/MzMLFileReader.java in api/core/ updated to …
2:19 PM Changeset [2946] by Fredrik Levander
Refs #486. Avoiding potential exception when spectrum id is null
2:03 PM Changeset [2945] by Fredrik Levander
Refs #486. Corrected Mascot results file reader. Also added missing …
1:35 PM Changeset [2944] by Fredrik Levander
refs #493. refs #486. Added reading of spectrum string ids to search …
1:07 PM Ticket #494 (Peak list file readers to support two types of ids) created by Fredrik Levander
The peak list file readers should be able to distinguish between index …
1:00 PM Ticket #489 (Install script doesn't work under dash) closed by olle
fixed: Ticket closed as the documentation was updated with a description on …
11:58 AM Installation edited by olle
Added sub-section "Note on Shell Interpreter on Unix/Linux? Systens" … (diff)
11:38 AM Changeset [2943] by Fredrik Levander
Refs #486, Refs #493. Added retentionTime and spectrumStringId to Hits …
11:35 AM ServerAdministration edited by olle
Added initial line [[PageOutline]] to create a page outline box for … (diff)
11:25 AM ServerAdministration edited by olle
Added new section "PIKE configuration". (diff)
11:25 AM Changeset [2942] by Fredrik Levander
Refs #486. Added spectrum string id. Refs #493. Added retention time. …
11:15 AM ServerAdministration edited by olle
Fixed typo and formatting in section "Mascot configuration". (diff)
11:02 AM Manual edited by olle
Added more readable name for link to wiki page … (diff)
10:54 AM Ticket #493 (Add retention time to Hits report) created by Fredrik Levander
The hits table doesn't currently contain retention time for peptide …

Nov 11, 2008:

3:57 PM Changeset [2941] by olle
Refs #483. Refs #287. First revision of PIKE search in Proteios via …
3:34 PM Changeset [2940] by olle
Refs #483. Added new source directory action/pike in client/servlet/ …
3:27 PM Changeset [2939] by olle
Refs #483. Installation scripts updated to create PIKE properties …
3:15 PM Changeset [2938] by olle
Refs #483. Configuration and template files for PIKE search added: 1. …
2:51 PM SettingUpEclipse edited by Fredrik Levander
(diff)
1:08 PM Ticket #492 (Exclusion list generation) created by Fredrik Levander
It should be possible to generate an exclusion list from peptides with …

Nov 6, 2008:

11:07 AM ServerAdministration edited by Fredrik Levander
(diff)
11:06 AM ServerAdministration edited by Fredrik Levander
(diff)

Nov 5, 2008:

4:37 PM Ticket #490 (Converter from mzData to MGF) closed by Fredrik Levander
fixed: (In [2937]) Fixes #490. Added converter from mzData to MGF. It will …
4:37 PM Changeset [2937] by Fredrik Levander
Fixes #490. Added converter from mzData to MGF. It will currently only …
4:34 PM Changeset [2936] by Fredrik Levander
Refs #491. Added spectrum precursor class for keeping precursor …
4:32 PM Ticket #491 (Add precursor information to spectrum interface) created by Fredrik Levander
It should be possible to retrieve the precursor information for an …
1:09 PM Changeset [2935] by olle
Refs #471. Proteios support for a locally installed OMSSA search …
11:37 AM Ticket #490 (Converter from mzData to MGF) created by Fredrik Levander
There is need for a converter from mzData to MGF files for OMSSA …
8:09 AM XTandemSearchEngineInterface edited by olle
Section "Creating/Editing? an X!Tandem Parameter Set" updated with new … (diff)

Nov 4, 2008:

4:57 PM ServerAdministration edited by olle
Section OMSSA configuration updated with info on new parameter … (diff)
4:39 PM Changeset [2934] by olle
Refs #471. Support for obtaining standard alternatives for OMSSA …
3:02 PM Changeset [2933] by olle
Refs #471. Class/file io/OMSSAParameterSetOptionsUtil.java in …
2:39 PM Changeset [2932] by olle
Refs #471. Examples and comments referring to locally installed OMSSA …
1:56 PM Changeset [2931] by olle
Refs #471. OMSSA search properties template file …
11:42 AM Changeset [2930] by Fredrik Levander
Fixes #484. Added possibility to add new protein hits. Corrected some bugs.
11:42 AM Ticket #484 (Generate protein report from peptide entries) closed by Fredrik Levander
fixed: (In [2930]) Fixes #484. Added possibility to add new protein hits. …
10:26 AM Ticket #489 (Install script doesn't work under dash) created by Fredrik Levander
The install script install-linux.sh breaks at line 55 if dash is the …
7:50 AM ServerAdministration edited by olle
Expressions changed in search configuration sections. (diff)

Nov 3, 2008:

5:25 PM Changeset [2929] by Fredrik Levander
Refs #484. Now retaining best scoring peptide
4:42 PM ServerAdministration edited by olle
Added info in section OMSSA configuration. (diff)
4:30 PM ServerAdministration edited by olle
Added info in section X!Tandem configuration. (diff)
11:48 AM Ticket #479 (Improvement of identification combination) closed by Fredrik Levander
fixed
11:39 AM ServerAdministration edited by Fredrik Levander
(diff)
11:31 AM PluginConfiguration created by Fredrik Levander
11:24 AM UserGuide edited by Fredrik Levander
(diff)
11:11 AM ServerAdministration edited by Fredrik Levander
(diff)
11:07 AM Manual edited by Fredrik Levander
Reformatted user manual (diff)
11:06 AM Changeset [2928] by olle
Refs #482. Refs #287. Function "Export to File" for exporting table …
11:02 AM Manual edited by Fredrik Levander
(diff)
11:00 AM Manual edited by Fredrik Levander
(diff)
10:53 AM ServerAdministration edited by Fredrik Levander
Added Server administration page (diff)
10:47 AM decoy_IPI.pl attached to ServerAdministration by Fredrik Levander
Script to generate random/reverse database entries with prefix
10:46 AM expand_IPI_dat_random.pl attached to ServerAdministration by Fredrik Levander
Script to add decoy entries to .dat file
10:44 AM ServerAdministration edited by Fredrik Levander
(diff)
10:42 AM ServerAdministration created by Fredrik Levander
10:20 AM Installation edited by Fredrik Levander
link to server administration added (diff)
9:34 AM Ticket #488 (Export to File should use Time Stamp in YYYYMMDD_HHMMSS Format) closed by olle
fixed: Ticket closed as the faulty functionality has been fixed.
9:26 AM Changeset [2927] by olle
Refs #488. Class/file action/file/ExportToFile.java in client/servlet/ …
9:20 AM Ticket #488 (Export to File should use Time Stamp in YYYYMMDD_HHMMSS Format) created by olle
Function "Export to File" should use a time stamp in "YYYYMMDD_HHMMSS" …
8:02 AM Changeset [2926] by olle
Refs #362. Refs #427. Core extension class/file …
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