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Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 31 19:17:09 2008 UTC (12 years 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, 5 months 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, 8 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, 8 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, 8 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 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, 10 months ago) by olson
Branch: MAIN
New file for Hope reaction stuff.

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