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Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 1 15:55:15 2010 UTC (9 years, 2 months ago) by dejongh
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CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.69: +1 -1 lines
Diff to previous 1.69
use a colon to split environmental variable fields rather than a semi-colon, because bash doesn't like semi-colons

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Tue Aug 31 14:40:21 2010 UTC (9 years, 2 months ago) by chenry
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Changes since 1.68: +38 -1 lines
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Bug fixes to pipeline.

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Mon Aug 30 02:41:14 2010 UTC (9 years, 2 months ago) by chenry
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Changes since 1.67: +8 -8 lines
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Adding functions to support new model features.

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Wed Aug 25 20:38:40 2010 UTC (9 years, 2 months ago) by chenry
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CVS Tags: rast_rel_2010_0827
Changes since 1.66: +39 -0 lines
Diff to previous 1.66
Bug fixes for tutorial.

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Fri Aug 20 14:34:51 2010 UTC (9 years, 3 months ago) by chenry
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Changes since 1.65: +135 -102 lines
Diff to previous 1.65
Bug fixes and changes relating to a switch to PPO database.

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Thu Aug 5 07:51:26 2010 UTC (9 years, 3 months ago) by chenry
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Changes since 1.64: +14 -0 lines
Diff to previous 1.64
New functions added

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Wed Jul 28 22:09:15 2010 UTC (9 years, 3 months ago) by chenry
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Changes since 1.63: +35 -13 lines
Diff to previous 1.63
Enabling use of multiple overriding FIGMODELConfig files

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Mon Jul 26 04:53:39 2010 UTC (9 years, 3 months ago) by chenry
Branch: MAIN
Changes since 1.62: +17 -9 lines
Diff to previous 1.62
Bug fixes.

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Sun Jul 11 06:04:27 2010 UTC (9 years, 4 months ago) by chenry
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Changes since 1.61: +0 -25 lines
Diff to previous 1.61
Removing obsolete functions.

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Sat Jul 10 22:40:07 2010 UTC (9 years, 4 months ago) by chenry
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Changes since 1.60: +56 -18 lines
Diff to previous 1.60
Adding functionality and removing bugs.

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Thu Jun 24 13:51:48 2010 UTC (9 years, 5 months ago) by dejongh
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Changes since 1.59: +27 -22 lines
Diff to previous 1.59
Move loading of FIGModelConfig to a separate subroutine to enable loading a file with user-specific overrides

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Sat Jun 19 05:25:28 2010 UTC (9 years, 5 months ago) by chenry
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Changes since 1.58: +173 -471 lines
Diff to previous 1.58
Bug fixes.

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Tue Jun 15 04:02:56 2010 UTC (9 years, 5 months ago) by chenry
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Changes since 1.57: +5 -6 lines
Diff to previous 1.57
Bug corrections.

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Wed Jun 2 08:05:00 2010 UTC (9 years, 5 months ago) by chenry
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Changes since 1.56: +21 -0 lines
Diff to previous 1.56
Corrected bugs in FIGMODEL.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 26 23:15:13 2010 UTC (9 years, 5 months ago) by chenry
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Changes since 1.55: +232 -21 lines
Diff to previous 1.55
Dealing with conflicts, removing windows line endings, adding some code for Minimal Organism review paper.

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Tue May 25 20:22:56 2010 UTC (9 years, 6 months ago) by devoid
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Changes since 1.54: +14045 -13996 lines
Diff to previous 1.54
Added functions for processing experimental conditions on microarrays.

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Wed May 19 21:03:09 2010 UTC (9 years, 6 months ago) by chenry
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Changes since 1.53: +13997 -13996 lines
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Bug fixes in reconstruction functions.

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Mon May 17 17:50:38 2010 UTC (9 years, 6 months ago) by parrello
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Changes since 1.52: +13996 -13997 lines
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Fixed line endings.

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Thu May 13 05:03:31 2010 UTC (9 years, 6 months ago) by chenry
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Changes since 1.51: +356 -118 lines
Diff to previous 1.51
Switching models over to PPO database.

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Fri Apr 23 22:37:27 2010 UTC (9 years, 7 months ago) by chenry
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.50: +1 -1 lines
Diff to previous 1.50
More bug fixes for the model viewer.

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Thu Apr 22 20:35:37 2010 UTC (9 years, 7 months ago) by chenry
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Changes since 1.49: +27 -1 lines
Diff to previous 1.49
Fixes made to redundant reaction finder.

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Wed Apr 21 22:17:33 2010 UTC (9 years, 7 months ago) by chenry
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Changes since 1.48: +764 -615 lines
Diff to previous 1.48
Minor changes to implement removal of redundant reactions mostly.

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Mon Apr 12 17:11:21 2010 UTC (9 years, 7 months ago) by chenry
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Changes since 1.47: +80 -37 lines
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Wed Apr 7 13:14:01 2010 UTC (9 years, 7 months ago) by dejongh
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Changes since 1.46: +1 -1 lines
Diff to previous 1.46
Change cgi param name for organism

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Mon Mar 22 16:01:34 2010 UTC (9 years, 8 months ago) by devoid
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Changes since 1.45: +63 -4 lines
Diff to previous 1.45
Added regulon fetching functions GetRegulonByID, etc.

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Sat Mar 20 19:00:37 2010 UTC (9 years, 8 months ago) by chenry
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Changes since 1.44: +2 -19 lines
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Wed Mar 17 18:56:07 2010 UTC (9 years, 8 months ago) by chenry
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Changes since 1.43: +178 -11 lines
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Mon Mar 8 19:52:47 2010 UTC (9 years, 8 months ago) by chenry
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Changes since 1.42: +379 -474 lines
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Mon Dec 21 20:05:25 2009 UTC (9 years, 11 months ago) by chenry
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CVS Tags: rast_rel_2010_0118
Changes since 1.41: +79 -96 lines
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Fri Dec 18 17:41:00 2009 UTC (9 years, 11 months ago) by chenry
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Changes since 1.40: +315 -32 lines
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Fri Dec 11 21:37:02 2009 UTC (9 years, 11 months ago) by chenry
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Changes since 1.39: +2652 -5879 lines
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Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 25 21:38:16 2009 UTC (10 years ago) by chenry
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Changes since 1.38: +16388 -16503 lines
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Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 12 20:27:30 2009 UTC (10 years, 1 month ago) by chenry
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Changes since 1.37: +1496 -1445 lines
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Fri Oct 9 21:54:02 2009 UTC (10 years, 1 month ago) by chenry
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Changes since 1.36: +953 -161 lines
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Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 23 18:41:40 2009 UTC (10 years, 2 months ago) by devoid
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.35: +100 -11 lines
Diff to previous 1.35
Added functions get_role_id, get_role_name, deprecate_role for converting functional role names to functional role IDs.
Modified printSequencesForRole to work properly and run faster.

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Tue Sep 22 21:38:04 2009 UTC (10 years, 2 months ago) by chenry
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Changes since 1.34: +675 -186 lines
Diff to previous 1.34
Added functions to support finding candidate genes to attach to gapfill reactions.

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Thu Sep 10 22:31:14 2009 UTC (10 years, 2 months ago) by chenry
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Changes since 1.33: +83 -0 lines
Diff to previous 1.33
Added stat_of_model and schedule_model_reconstruction functions.

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Sat Sep 5 03:52:02 2009 UTC (10 years, 2 months ago) by chenry
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Changes since 1.32: +2 -2 lines
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Fri Sep 4 23:16:02 2009 UTC (10 years, 2 months ago) by chenry
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Changes since 1.31: +573 -154 lines
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Wed Aug 12 17:01:39 2009 UTC (10 years, 3 months ago) by chenry
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Changes since 1.30: +740 -93 lines
Diff to previous 1.30
Added new pattern matching subroutines written by Ben Linsay.

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Tue Aug 4 19:55:41 2009 UTC (10 years, 3 months ago) by chenry
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Changes since 1.29: +8 -2 lines
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Sorting version IDs in the versions_of_model

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Tue Aug 4 19:13:53 2009 UTC (10 years, 3 months ago) by chenry
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Changes since 1.28: +13 -8 lines
Diff to previous 1.28
Various corrections to versions_of_model function.

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Tue Aug 4 00:23:42 2009 UTC (10 years, 3 months ago) by chenry
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Changes since 1.27: +11 -2 lines
Diff to previous 1.27
Fixed the GetDBModel function to properly load current model versions.

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Mon Aug 3 05:03:36 2009 UTC (10 years, 3 months ago) by chenry
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Changes since 1.26: +268 -58 lines
Diff to previous 1.26
Improved functions for obtaining model stats and corrected bugs in subsystems_of_reaction function.

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Wed Jul 29 06:43:58 2009 UTC (10 years, 3 months ago) by chenry
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Changes since 1.25: +264 -30 lines
Diff to previous 1.25
Added functions to get model version lists.

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Thu Jul 23 18:43:14 2009 UTC (10 years, 4 months ago) by chenry
Branch: MAIN
Changes since 1.24: +30 -26 lines
Diff to previous 1.24
Fix ViewModelPermissions function.

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Tue Jul 21 22:22:53 2009 UTC (10 years, 4 months ago) by chenry
Branch: MAIN
Changes since 1.23: +36 -0 lines
Diff to previous 1.23
Added a function for checking if a user has permission to see a model.

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Tue Jul 21 21:31:55 2009 UTC (10 years, 4 months ago) by chenry
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Changes since 1.22: +339 -41 lines
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Added support for converting and typing IDs.

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Thu Jul 16 15:47:46 2009 UTC (10 years, 4 months ago) by blinsay
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Changes since 1.21: +29 -13 lines
Diff to previous 1.21
Added kegg_summary_table function.

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Tue Jun 30 22:10:40 2009 UTC (10 years, 4 months ago) by chenry
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CVS Tags: rast_rel_2009_07_09
Changes since 1.20: +63 -41 lines
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Tue Jun 30 17:02:54 2009 UTC (10 years, 4 months ago) by chenry
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Changes since 1.19: +562 -185 lines
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Fri Jun 26 19:03:50 2009 UTC (10 years, 4 months ago) by chenry
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Changes since 1.18: +2 -1 lines
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Fri Jun 26 18:50:01 2009 UTC (10 years, 4 months ago) by chenry
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Changes since 1.17: +138 -76 lines
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Thu Jun 25 05:39:42 2009 UTC (10 years, 5 months ago) by chenry
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Changes since 1.16: +1452 -235 lines
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Mon Jun 1 20:37:16 2009 UTC (10 years, 5 months ago) by chenry
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Changes since 1.15: +1024 -389 lines
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Wed Apr 29 19:52:17 2009 UTC (10 years, 6 months ago) by chenry
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CVS Tags: rast_rel_2009_05_18
Changes since 1.14: +2702 -2580 lines
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Tue Apr 7 14:09:44 2009 UTC (10 years, 7 months ago) by parrello
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Changes since 1.13: +10678 -10677 lines
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Fixed some compiler warning problems.

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Thu Mar 26 02:11:43 2009 UTC (10 years, 8 months ago) by chenry
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CVS Tags: rast_rel_2009_03_26
Changes since 1.12: +111 -42 lines
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Fri Mar 20 19:10:40 2009 UTC (10 years, 8 months ago) by chenry
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Changes since 1.11: +768 -59 lines
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Fri Mar 6 23:34:01 2009 UTC (10 years, 8 months ago) by chenry
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Changes since 1.10: +9899 -9842 lines
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Wed Mar 4 00:07:47 2009 UTC (10 years, 8 months ago) by parrello
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Changes since 1.9: +9842 -9842 lines
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Minor changes in new-lines and tabs.

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Tue Mar 3 21:46:10 2009 UTC (10 years, 8 months ago) by chenry
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Changes since 1.8: +4390 -2757 lines
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Mon Jan 12 05:37:59 2009 UTC (10 years, 10 months ago) by chenry
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CVS Tags: rast_rel_2009_02_05
Changes since 1.7: +4952 -4560 lines
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Tue Jan 6 19:49:14 2009 UTC (10 years, 10 months ago) by chenry
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Changes since 1.6: +1 -1 lines
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Mon Jan 5 17:44:29 2009 UTC (10 years, 10 months ago) by chenry
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Changes since 1.5: +1875 -669 lines
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Sun Nov 30 17:39:27 2008 UTC (10 years, 11 months ago) by chenry
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CVS Tags: rast_rel_2008_12_18
Changes since 1.4: +1 -1 lines
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Sun Nov 30 17:30:00 2008 UTC (10 years, 11 months ago) by chenry
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Changes since 1.3: +673 -76 lines
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Tue Nov 25 16:53:53 2008 UTC (10 years, 11 months ago) by chenry
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Changes since 1.2: +2284 -578 lines
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Wed Oct 15 19:48:07 2008 UTC (11 years, 1 month ago) by chenry
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CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_10_29, rast_rel_2008_11_24
Changes since 1.1: +5 -3 lines
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Fixing bug in CpdLink function.

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Wed Oct 15 17:46:01 2008 UTC (11 years, 1 month ago) by chenry
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These modules are for interacting with the modeling database Chris Henry and Matt DeJongh are adding to the SEED.

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