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Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 17 21:09:54 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.34: +12 -10 lines
Diff to previous 1.34
make it not a fatal error to not load hope_supersets; this was causing a crash on PSEED.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 22 17:38:16 2010 UTC (9 years, 10 months ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.33: +1 -1 lines
Diff to previous 1.33
fix reference

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 16 17:56:21 2009 UTC (10 years ago) by dejongh
Branch: MAIN
Changes since 1.32: +202 -116 lines
Diff to previous 1.32
Lots of changes

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 2 01:19:02 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.31: +9 -8 lines
Diff to previous 1.31
Fixed a bunch of compiler warnings.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 23 10:28:43 2009 UTC (10 years, 9 months ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.30: +8 -28 lines
Diff to previous 1.30
Deleted checking for pegs in subsystem cells; only using seq_with_roles so it won't matter if a genome is active in a subsystem, or up to date in the subsystem

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 12 23:43:13 2008 UTC (10 years, 11 months ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2008_12_18, rast_rel_2009_02_05
Changes since 1.29: +1 -3 lines
Diff to previous 1.29
debug msg

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 11 17:01:39 2008 UTC (10 years, 11 months ago) by dejongh
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28
fix

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 11 16:54:24 2008 UTC (10 years, 11 months ago) by dejongh
Branch: MAIN
Changes since 1.27: +54 -0 lines
Diff to previous 1.27
check_hope_info process added

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 14:28:04 2008 UTC (11 years ago) by dejongh
Branch: MAIN
Changes since 1.26: +9 -17 lines
Diff to previous 1.26
use seqs_with_roles instead of seqs_with_roles_in_genomes, for FIGV compatibility

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 20 16:28:42 2008 UTC (11 years ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2008_11_24
Changes since 1.25: +3 -18 lines
Diff to previous 1.25
copy path files instead of linking to them

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 17 18:31:54 2008 UTC (11 years ago) by dejongh
Branch: MAIN
Changes since 1.24: +1 -0 lines
Diff to previous 1.24
added debug stmt

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 21:54:41 2008 UTC (11 years ago) by dejongh
Branch: MAIN
Changes since 1.23: +53 -17 lines
Diff to previous 1.23
Move get_hope_reactions_for_genome to model.pm

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 12 18:19:12 2008 UTC (11 years ago) by dejongh
Branch: MAIN
Changes since 1.22: +28 -29 lines
Diff to previous 1.22
switch to scenario_directory

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 5 15:25:06 2008 UTC (11 years, 1 month ago) by dejongh
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2
Changes since 1.21: +0 -6 lines
Diff to previous 1.21
assume supersets are loaded

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 5 15:24:12 2008 UTC (11 years, 1 month ago) by dejongh
Branch: MAIN
Changes since 1.20: +409 -1 lines
Diff to previous 1.20
Add network analysis

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 3 18:38:44 2008 UTC (11 years, 1 month ago) by dejongh
Branch: MAIN
Changes since 1.19: +47 -35 lines
Diff to previous 1.19
Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 15 21:21:33 2008 UTC (11 years, 1 month ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2008_10_29
Changes since 1.18: +68 -17 lines
Diff to previous 1.18
Support for model curation tools

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 31 19:17:09 2008 UTC (11 years, 8 months ago) by dejongh
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924, rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_release_2008_09_29
Changes since 1.17: +15 -12 lines
Diff to previous 1.17
Fixes for excluding . and .. when reading directories for paths

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 2 19:12:58 2007 UTC (12 years, 1 month ago) by dejongh
Branch: MAIN
Changes since 1.16: +103 -53 lines
Diff to previous 1.16
Hope College updates

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 23 15:07:25 2007 UTC (12 years, 4 months ago) by formsma
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
Updated some error statments for better information - Kevin

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 20 18:15:53 2007 UTC (12 years, 4 months ago) by formsma
Branch: MAIN
Changes since 1.14: +2 -1 lines
Diff to previous 1.14
Commented out a line which was causing the model's analysis directory to be deleted. This line was causing the data
from run_model_generation to be wiped out, and it doesn't need to remove the folder there - Kevin

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 17 15:58:27 2007 UTC (12 years, 4 months ago) by formsma
Branch: MAIN
Changes since 1.13: +77 -0 lines
Diff to previous 1.13
Added predict_pegs_used function which will predict what pegs are going to be used by scenarios for a given genome - Kevin

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 30 16:10:24 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.12: +28 -15 lines
Diff to previous 1.12
update to use $fig->model_directory(); change find opts based on mac vs linux.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 30 14:18:03 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.11: +41 -38 lines
Diff to previous 1.11
Changed model.pm to store scenarios under a subdirectory named Scenarios, and analysis under a subdirectory named Analysis

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 29 19:37:12 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.10: +21 -2 lines
Diff to previous 1.10
add FIGV support.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 29 19:16:26 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.9: +39 -36 lines
Diff to previous 1.9
Changes for using $fig->scenario_directory() instead of constructed paths.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 23 22:21:47 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.8: +1 -1 lines
Diff to previous 1.8
Added analysis of scenario connections

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 23 22:06:46 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.7: +59 -29 lines
Diff to previous 1.7
Added analysis of scenario connections

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 22 18:16:57 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6
get_hope_reactions_for_genome now returns a hash of reactions to pegs

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 21 21:46:47 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.5: +11 -2 lines
Diff to previous 1.5
compare_scenario now creates soft links to paths with the same name as the path in the All directory

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 21 20:23:27 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.4: +6 -0 lines
Diff to previous 1.4
compare_scenario now creates placeholder directories for paths with the same name as the path in the All directory

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 18 16:57:26 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.3: +18 -37 lines
Diff to previous 1.3
Added get_hope_reactions_for_genome

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 16:51:43 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.2: +3 -3 lines
Diff to previous 1.2
fix couple of missed temp replacements

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 16:46:24 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.1: +173 -10 lines
Diff to previous 1.1
Changes to hope model stuff

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 15 21:14:31 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
New file for Hope reaction stuff.

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