Chris Myers
b11268ec9c
Updated to suppot later Java versions
2024-11-26 20:27:58 -07:00
Chris Myers
515c7634a2
Remove objects with same displayId before creating new
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Fix run deadlock on errors
2020-05-10 13:37:36 -06:00
Pedro Fontanarrosa
4baa96f442
Changed visibility of SBOL2SBML methods to 'package' so that
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CelloModeling can use them
2019-08-07 14:41:32 -03:00
Chris Myers
415b419719
Reverted initial zone and fixed uniform mean calc
2018-07-12 13:50:00 -06:00
Chris Myers
261944f4a7
Fixed issue with initializing continuous variables with non-zero initial
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rate
2018-07-10 21:55:44 -06:00
Chris Myers
69d2ab477f
De-warp continuous variables in expressions.
2018-07-09 17:14:33 -06:00
Chris Myers
e97d028dba
Fix bug in LPN expression parser
2018-06-11 17:43:27 -06:00
Chris Myers
432a6dd983
Fix ^ precedence in ExprTree parsing
2018-06-11 09:46:57 -06:00
Curtis Madsen
87ccb76c15
Fixed LPN generation
2018-05-27 23:44:49 -04:00
Chris Myers
446db8a3c4
Fixed a couple bugs in the LPN data model
2018-05-10 15:11:37 -06:00
thakurneupane
399187bd0e
Fix threshold selection based on the transition rate
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Ample selection based on transition rate is now only for Markovian model
2018-04-25 16:18:44 -06:00
thakurneupane
def26b6ab2
Threshold selection based on the transition rate
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Assumptions:
-> Dependency determination based on the ratio of transition rate.
(Dependent if MAX(trans_rate_1,trans_rate_2)/MIN(trans_rate_1,trans_rate_2)
<= epsilon )
-> Minimum ratio of transition rates to make two transition
independent: epsilon = 2.0
-> Selected Ample set based on the average rate of transitions on
Dependent
Set.
2018-04-23 13:06:03 -06:00
Zhen Zhang
0f97c5ad0b
Merge remote-tracking branch 'origin/master' into ctmcPOR
2018-03-28 22:10:09 -06:00
Chris Myers
f695ec8eeb
Fixed case of TRUE and FALSE.
2018-03-08 12:36:07 -07:00
thakurneupane
75fe340233
Initial Commit for Birth-Death Process
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Assumptions:
-> Dependencies are only caused by the rates. (Manually cleared other
dependencies to make things simpler)
-> Minimum ratio of transition rates to make two transition
independent: 2.0
-> Selected Ample set based on the rate of seed transition on Dependent
Set.
2018-02-12 11:09:07 -07:00
Zhen Zhang
1fe8006829
Corrected errors in StaticDependencySets.
2018-01-25 20:53:21 -07:00
thakurneupane
cce19919c0
#490 Fix missing "-" operator in expression evaluation
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Assignment-expression on transition of LPN is evaluated to 0.0 if it has
"-" operator.
2018-01-24 12:52:47 -07:00
Chris Myers
ef5e4006db
Add main method for verification.
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Add jlibsedml snapshot dependency
2018-01-20 21:29:46 -07:00
leandrohw
c739774cf7
variableInUse notifies observers and observables now.
2018-01-10 22:09:29 -07:00
Chris Myers
949a517c87
Updates for L3V2
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Fix for #434
2017-11-22 14:51:38 -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
leandrohw
442f0868f2
Created custom observe pattern implementation.
2017-08-24 13:17:46 -06:00
Chris Myers
5810d56b4a
Fix windows file separator bug
2017-07-09 19:41:17 -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
Tramy Nguyen
30ab7c9119
removed verification module from iBioSim
2017-06-09 17:22:52 -06:00
Tramy Nguyen
871d0e2e36
merge
2017-06-09 10:49:30 -06:00
Chris Myers
870a58c960
Refactor out LEMA code
2017-06-09 10:39:00 -06:00
leandrohw
0c7ace6f1d
Fixed package name from biosim to ibiosim.
2017-04-17 11:07:55 -06:00
leandrohw
18236018a9
Added biosim prefix to package names
2017-04-17 11:04:48 -06:00
Chris Myers
d3220ceb84
Refactor code from data models to verification
2017-04-17 17:05:33 +01:00
Chris Myers
0e3ae9e841
Refactor
2017-04-17 16:23:01 +01:00
Chris Myers
2e698dd72d
Update .gitignores
2017-04-13 23:33:26 +01:00
Tramy Nguyen
5b661bce28
Renamed frontend to gui and updated package names to convention
2017-04-13 16:09:28 -06:00
Tramy Nguyen
dcf091421f
Restructured backend
2017-04-13 15:53:09 -06:00
