krlhBlupine/iBioSim
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45 commits

Author SHA1 Message Date
Chris Myers
b11268ec9c Updated to suppot later Java versions 2024-11-26 20:27:58 -07:00
Chris Myers
fe229873e7 Updated pom files 2021-06-24 19:34:08 -06:00
Chris Myers
515c7634a2 Remove objects with same displayId before creating new 
Fix run deadlock on errors
 2020-05-10 13:37:36 -06:00
leandrohw
e493cfc7bb Some cleanup and starting test file. 2018-03-25 21:50:32 -07:00
leandrohw
05a355587d Modified simulation constructor for dfba. 2018-03-04 22:10:58 -08:00
leandrohw
5dcf437757 Merge branch 'master' of 
https://github.com/MyersResearchGroup/iBioSim.git into hSSA

Conflicts:
	analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/methods/HierarchicalODERKSimulator.java
	analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/states/VectorWrapper.java
 2018-02-11 21:15:47 -08:00
leandrohw
db8b41038b Just to take care of exception. will fix later 2018-02-03 22:50:29 -08:00
leandrohw
26ba75ccd7 Fixed javadocs for Learn 2018-01-27 08:15:55 -07:00
leandrohw
54237f5780 Hierarchical Simulator makes use of AnalysisProperties 2018-01-27 08:06:51 -07:00
Chris Myers
ff05ae1823 Fixed a javadoc error 2018-01-16 16:38:36 -07:00
leandrohw
7a7f8271f4 Created two types of error dialog for shorter and longer messages. 2018-01-11 20:45:12 -07:00
leandrohw
c739774cf7 variableInUse notifies observers and observables now. 2018-01-10 22:09:29 -07:00
leandrohw
fcec8f6b69 Ensured that biomodel is observed when needed. 2018-01-10 14:06:53 -07:00
leandrohw
541d5d9de3 Allows to run GeneNet java with user values and added option to save 
sbml file.
 2018-01-09 18:56:40 -07:00
leandrohw
f2b929909f Remove try and catch from writer close 2018-01-08 12:05:39 -07:00
leandrohw
c999456ed2 Finished the standalone for learn. 2018-01-08 09:52:02 -07:00
leandrohw
c415c09993 Some reporting messages to standalone. 2018-01-05 11:48:52 -07:00
Leandro Watanabe
a55e6bd8bc
Added information to the learn readme. 2018-01-04 19:03:00 -07:00
leandrohw
a603f01f89 Added the option to run c++ genenet. 2018-01-03 16:22:38 -07:00
leandrohw
99633f1e9b Added new flags for learn. Need to add implementation. 2018-01-02 13:31:07 -07:00
Chris Myers
477b3fa374 Replaced > with > in javadocs 2018-01-01 11:38:26 -07:00
leandrohw
445024befe Some changes to learn standalone 2017-12-29 10:06:31 -07:00
Leandro Watanabe
a736f4eee8
Update README.md 2017-12-14 20:37:47 -07:00
Leandro Watanabe
d51db27bc7
Update README.md 2017-12-13 16:04:33 -07:00
Leandro Watanabe
4ccdabc7eb
Update README.md 2017-12-12 22:07:41 -07:00
leandrohw
6e7e9358b2 Initial commit for instructions on how to use analysis and learn. 2017-12-12 18:05:57 -07:00
leandrohw
c5c1ba9125 Ignore promoters when running genenet in java. 2017-11-29 13:27:31 -07:00
leandrohw
d765c20d4e Fixed iBioSim headings 2017-09-23 22:03:40 -06:00
Chris Myers
3ef4ab4743 Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git 2017-07-09 19:41:28 -06:00
Chris Myers
5810d56b4a Fix windows file separator bug 2017-07-09 19:41:17 -06:00
leandrohw
fde211c4a9 Simple tests for the main function of learn. 2017-07-09 17:18:02 -06:00
leandrohw
d6a68795c0 Added scripts to build executable jar for learn and javadocs. 2017-07-09 17:17:37 -06:00
leandrohw
9d272ec8ab Finished adding javadocs to learn 2017-07-09 17:16:59 -06:00
leandrohw
57cf9a485d Copies the values from parameter estimator to a document 2017-07-09 12:58:34 -06:00
Chris Myers
b2d240f816 Move verification back into iBioSim. 
Update the scripts
Update version to 3.0.0-SNAPSHOT
 2017-07-05 16:13:44 -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
Leandro Watanabe
e5269d967a Merge pull request #322 from MyersResearchGroup/new_sim 
Made changes to the hierarchical simulator
 2017-04-13 16:50:23 -06:00
leandrohw
ae01a4211d Merge remote-tracking branch 'origin' into new_sim 
# Conflicts:
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/HierarchicalSimulation.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/io/HierarchicalWriter.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/methods/HierarchicalFBASimulator.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/methods/HierarchicalMixedSimulator.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/methods/HierarchicalODERKSimulator.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/methods/HierarchicalSSADirectSimulator.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/model/HierarchicalModel.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/HierarchicalUtilities.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/comp/HierarchicalEventComparator.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/comp/ReplacementHandler.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/CompartmentSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/ConstraintSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/CoreSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/EventSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/InitAssignmentSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/ModelSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/ParameterSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/ReactionSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/ReplacementSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/RuleSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/SpeciesReferenceSetup.java
#	analysis/src/main/java/edu/utah/ece/async/analysis/simulation/hierarchical/util/setup/SpeciesSetup.java
 2017-04-13 16:47:56 -06:00
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