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Author SHA1 Message Date
Tramy Nguyen
4f37244523 Merge branch 'master' of 
https://github.com/MyersResearchGroup/iBioSim.git into verilogCompiler

Conflicts:
	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java
 2019-04-23 17:28:24 -06:00
Chris Myers
3778cded25 Update to libSBOLj 2.4.0 2019-04-20 17:53:13 -06:00
cjmyers
7672e5ac05
Merge pull request #578 from MyersResearchGroup/biomodels-upgrade 
Biomodels upgrade
 2019-04-20 17:50:59 -06:00
Chris Myers
22b91c89d6 Move to dataModels 2019-04-20 17:49:26 -06:00
Chris Myers
92830cadcf Merge remote-tracking branch 'mihai/biomodelsREST' into biomodels-upgrade 2019-04-20 17:34:15 -06:00
Chris Myers
36aa23378a Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git 2019-04-20 17:29:46 -06:00
Chris Myers
b7ab474bd2 Update DNA to DNA_REGION, RNA to RNA_REGION, update jsbml 2019-04-20 17:29:35 -06:00
Tramy Nguyen
6f548c13a3 Test decomposed gates 2019-04-18 01:55:28 -06:00
Tramy Nguyen
bf8ae50f9a gate identifier revised 2019-04-08 19:02:47 -06:00
Mihai Glonț
eda9078f4c migrate to the BioModels REST API 2019-04-08 20:36:25 +01:00
Mihai Glonț
ab1b1a55a4 ignore Intellij IDEA artefacts. 2019-04-08 20:35:49 +01:00
Tramy Nguyen
6caf6a427c fixed decomposed specification 2019-04-06 22:06:19 -06:00
Tramy Nguyen
0a0a4c1f2b Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git into verilogCompiler 2019-04-06 14:48:22 -06:00
Pedro Fontanarrosa
0bd7263a21 Option to import Simulation Environment 2019-04-01 09:03:39 -06:00
Pedro Fontanarrosa
7b0eff29a2 Updated CelloModeling to skip sensorMolecules 
Now the model generator doesn't generate species for sensorMolecules and
removes the relevant MapsTo's that reference them.
 2019-03-19 13:43:47 -06:00
Pedro Fontanarrosa
9366604a8e Removed unnecessary code 2019-03-14 11:35:13 -06:00
Pedro Fontanarrosa
f9da3f5955 Added correct species information for small molecules 
Added correct species information for small molecules
(boundarycondition, substanceunits, etc) in sub-models
 2019-03-07 12:40:52 -07:00
Pedro Fontanarrosa
a1740ac55c Updated VPR version from 2.0.14-SNAPSHOT to 2.0.16-SNAPSHOT 
Updated conversion.java to be able to generate VPR model
 2019-03-05 17:27:35 -07:00
Pedro Fontanarrosa
a15c9199ab Added comments and removed unused lines of code 2019-02-20 09:00:34 -07:00
Pedro Fontanarrosa
1ee923d0e9 Added SensorGateModule method 
This method checks if the ModuleDefinition in hand is a MD for the
production of sensor proteins by a sensor gate. If it is, it skips the
making of a subModel for this ModuleDefinition.
 2019-02-13 15:50:06 -07:00
Tramy Nguyen
d907c6f28e fix yosys error 2019-02-09 17:47:40 -07:00
Tramy Nguyen
33677d8612 support sbml delay string and real values 2019-02-05 17:03:22 -07:00
Pedro Fontanarrosa
d390c58f95 Uncommented MDFlattener Code 
This section of the code was to "check" for VPR1 or VPR2, but it broke
if the interactions are not going to be present in the TopLevel MD.
 2019-02-01 17:37:56 -06:00
Pedro Fontanarrosa
78fd6c5a92 Uncommented broken MDFlattener code 2019-02-01 17:34:57 -06:00
Tramy Nguyen
abc452161e support gate generation 2019-01-24 18:37:50 -07:00
Pedro Fontanarrosa
072bf1958c Removal of unnecessary code 
Fixed a bug
A bug where YFP reporter with 2 promoters gave a issue with double
promoters for the model, instead of a unified one as the rest.
 2019-01-21 19:14:13 -07:00
Tramy Nguyen
53cb998e69 Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git into verilogCompiler 2019-01-16 22:06:02 -07:00
Tramy Nguyen
56db09039e test cases for replacement and replacedBy 2019-01-16 22:04:04 -07:00
Tramy Nguyen
2111d56e9c support replacedBy and replacement for verilog2sbml 2019-01-15 16:43:30 -07:00
Tramy Nguyen
5da84b3f73 test cases for sbol tech map 2019-01-13 21:36:10 -07:00
Pedro Fontanarrosa
da3efba4f3 Changed visibility of SBOL2SBML methods to 'package' so that 
CelloModeling can use them
 2019-01-11 16:39:44 -07:00
Pedro Fontanarrosa
6ed59624fd Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git 2019-01-11 15:47:35 -07:00
Pedro Fontanarrosa
d5c90ac12f Created Test Suits for MDFlattener and CelloModeling 2019-01-11 15:46:32 -07:00
Pedro Fontanarrosa
067ad608c9 Testing 2019-01-11 14:25:19 -07:00
Tramy Nguyen
94de018064 support export for SBOL Activity 2019-01-11 14:06:26 -07:00
Tramy Nguyen
86167355a8 more tests for sbol tech. map 2019-01-09 15:06:25 -07:00
Tramy Nguyen
da2b475326 sbol tech. map test case 2019-01-07 18:02:36 -07:00
Tramy Nguyen
42ab39cbc0 remaining changes for supporting urandom_range 2019-01-06 21:14:13 -07:00
Tramy Nguyen
569284876d support urandom_range 2019-01-06 21:13:37 -07:00
Tramy Nguyen
ada705e262 test gate generator 2019-01-04 15:20:04 -07:00
Tramy Nguyen
f2c91bc947 test sbol create copy 2019-01-04 15:13:27 -07:00
Tramy Nguyen
d8c8898c7c add file browsing for synthesis testbench 2018-12-28 17:01:19 -07:00
Tramy Nguyen
b86bf01945 refactored GUI features 2018-12-28 13:19:10 -07:00
Tramy Nguyen
f58cf6dfee removed typo for importing verilog 2018-12-27 19:50:58 -07:00
Tramy Nguyen
7704d7d15a support verilog import to workspace 2018-12-27 19:47:33 -07:00
Tramy Nguyen
6b65c00e0c update failing test cases 2018-12-26 23:40:21 -07:00
Tramy Nguyen
90cd29f671 more SBOL tests for VerilogCompiler 2018-12-26 17:13:59 -07:00
Tramy Nguyen
83f5e7b36e test1 for verilog to sbol hierarchy 2018-12-26 16:09:39 -07:00
Tramy Nguyen
ef54a6b481 rename testing classes 2018-12-26 13:01:26 -07:00
Tramy Nguyen
24f6134116 handle feedback for subcircuits for verilog compiler to sbol 2018-12-25 21:38:05 -07:00