Chris Myers
b11268ec9c
Updated to suppot later Java versions
2024-11-26 20:27:58 -07:00
Tramy Nguyen
6caf6a427c
fixed decomposed specification
2019-04-06 22:06:19 -06:00
leandrohw
1efd25c073
Delete binaries from repo
2018-01-08 10:56:06 -07:00
Chris Myers
9c79ea654b
Update reb2sac for mac
2017-12-22 10:16:13 -07:00
Tramy Nguyen
e59928a41c
resolving merge conflict with converter.java
2017-12-18 11:40:41 -07:00
Chris Myers
6f2a438fef
Change SBML to L3V2
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Add new math functions
Remove support for fast reactions
2017-11-18 09:44:48 -07:00
Chris Myers
c34694a08b
Fixed issues with combine archive extraction order of SBML files.
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Updated reb2sac.mac64
Avoid validation for bad library version with infinite loop
Don't try to update replacements if file fails to load
2017-10-17 17:59:22 +02:00
Chris Myers
6f0acc51cb
Fix prefences bug
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Update libSBOLj to 2.2.2-SNAPSHOT
2017-09-19 18:59:54 -06:00
Leandro
a7d4e495bc
Compiled binaries for reb2sac and genenet
2017-09-14 14:38:31 -06:00
Chris Myers
a17533608e
Remove iBioSim.jar
2017-09-14 12:14:13 -06:00
Chris Myers
9a4ae714ce
Update bin directory
2017-09-14 12:11:39 -06:00
Chris Myers
c0041f893e
Cleaned up bin directory
2017-08-18 12:14:59 -06:00
Chris Myers
806fb5903e
Removed
2017-08-18 11:18:31 -06:00
Chris Myers
b2d240f816
Move verification back into iBioSim.
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Update the scripts
Update version to 3.0.0-SNAPSHOT
2017-07-05 16:13:44 -06:00
Chris Myers
558687b17f
Updated script for startup on mac
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Changed some gui variables to protected
Add COMBINE archive import support
Turned off validation due to libsbml bug
Fixed bug in deletion metaIds
Update libSBMLj.jar
2017-07-03 22:49:13 -06:00
leandrohw
bef5ca67b0
Added license header to source code files
2017-02-28 14:38:28 -07:00
Chris Myers
e6f1f5b084
Major refactor Part I
2017-01-04 16:32:14 -07:00
cjmyers
f532808d89
Fixed library path
2016-10-12 13:25:26 +00:00
cjmyers
64207f391c
Updated iBioSim scripts to deal with DYLD_LIBRARY_PATH being dropped.
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Updated GeneNet.mac64 to produce method.dot as well as method.gcm
2016-08-31 01:56:02 +00:00
cjmyers
a5eb3bf325
Removed from bin directory.
2016-07-06 02:42:05 +00:00
cjmyers
b062df916a
Update
2016-07-04 19:35:07 +00:00
cjmyers
aad313689f
Update iBioSim.mac64 to be executable.
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Update reb2sac.mac64 to support SED-ML features.
2016-07-04 19:31:48 +00:00
cjmyers
b8083c718f
Restore deleted binary files.
2016-07-04 19:26:47 +00:00
tramyn
dba1495566
Replaced Assembly internal sort with SequenceAnnotation with libSBOLj library sortSequenceAnnotation() method.
2016-06-28 22:24:18 +00:00
cjmyers
83cfa0766a
Update libsbml.
2015-10-27 01:43:20 +00:00
leandrohw
d18a519c8a
Updated JSBML to fix problem with factorial
2015-03-16 18:55:25 +00:00
cjmyers
48eec2a2c6
Updated libsbml to 5.11.
2015-02-22 04:49:41 +00:00
cjmyers
0a53017ad8
Add path.
2013-02-18 17:57:13 +00:00
cjmyers
1625d1bac8
Update to 5.7.
2013-02-04 19:55:18 +00:00
cmadsen
755eee30fc
Updated reb2sac.
2012-08-10 02:26:01 +00:00
cmadsen
7125f7d147
Updated libsbml libraries for Windows.
2012-08-08 01:45:26 +00:00
cmadsen
1fc724e4c6
Updated libsbml libraries for Windows.
2012-08-07 21:58:06 +00:00
cmadsen
c93901fa2e
Updated libsbml.
2011-12-22 23:18:49 +00:00
cmadsen
9e2ac82546
Updated libsbml.
2011-12-21 02:04:29 +00:00
cjmyers
c8779e6e8b
Use serial garbage collector.
2011-10-07 15:52:43 +00:00
cmadsen
b29c7ff426
Since they do not work, removed 64-bit executables of reb2sac and GeneNet to avoid confusion.
2011-09-09 15:19:29 +00:00
cmadsen
c87e1ec6f0
Fixed LD_LIBRARY_PATH and environment variables in launch scripts.
2011-05-17 01:47:53 +00:00
cjmyers
40c97ab130
Improved scripts to be independent of jar file addition.
2011-05-14 01:31:21 +00:00
nroehner
fbe9c9e60d
Complex and sequestering abstractions are now handled by the AbstractionEngine class, which is called through the abstractExpression method of the GeneticNetwork class to create string kinetic laws and the abstractComplex and sequesterSpecies methods of the visitors to create sbml kinetic laws.
2011-03-18 19:55:36 +00:00
cjmyers
5ba2936ef3
Updated to main.Gui
2011-02-02 18:22:07 +00:00
cjmyers
0e71fe17bc
No change.
2011-02-02 17:27:11 +00:00
nroehner
22854f1f48
Added activated RNAP binding constant Kao = 1, removed fields for isBiochemical, kBio, nDimer, input, and output from the influence panel, and removed the field for kDimer from the species panel.
2011-01-14 00:41:25 +00:00
cmadsen
026c734365
Added gson library to executable
2011-01-05 22:51:34 +00:00
nroehner
3b85c12c7c
"RNAP" and "bound" are now post-pended rather than pre-pended to species during SBML generation.
2010-11-15 23:34:42 +00:00
zgzn
7a5b987a22
Change to use libsbmlj64.jar
2010-09-30 19:18:40 +00:00
cjmyers
685abe9932
removed
2010-09-30 18:19:57 +00:00
nroehner
a46fd27419
Promoters, Reactions, and Species as they are defined in gcm2sbml.network have been changed to accept gcm parameters as properties that can later be accessed with a public method.
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The Activation and Repression BindingVisitors now load parameter values for a species influencing a promoter by accessing the promoter's reaction map with respect to the species. Before, all parameter values were loaded from the species themselves thanks to a hack that pre-loaded species with reaction and promoter parameters, but this precluded having a species influence separate promoters using unique parameter sets.
The PrintDimerization and PrintBiochemicalVisitors are now called within the BindingVisitors and are passed the relevant parameter values rather than called upon to load them.
Checks are made when loading parameters in the BindingVisitors to determine if a species both activates and represses a specific promoter, in which case separate parameter sets are used.
A check is made when building biochemical species in the Genetic Network class to determine if the species was previously built in a different order (i.e. Biochemical_B_A instead of Biochemical_A_B).
When a promoter is both activated and repressed, its rate of transcription when no species are bound is ko instead of kb, i.e. the promoter is treated as a constitutive promoter that can be further activated rather than as a basal promoter for which repression is not as meaningful.
2010-09-27 18:38:20 +00:00
cmadsen
456a5eda6f
Added reb2sac for 64-bit Windows to the repository
2010-09-25 09:51:44 +00:00
cmadsen
9fcdab4a07
Added GeneNet for 64-bit Windows
2010-09-25 08:41:57 +00:00
cjmyers
5d69c19ad2
update
2010-09-14 18:38:42 +00:00
