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278 commits

Author SHA1 Message Date
Chris Myers
9de95ab6eb Fix issues with model generation libraries 2025-12-23 09:59:23 -07:00
Chris Myers
d4d40a9084 Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim 2024-11-26 20:28:24 -07:00
Chris Myers
b11268ec9c Updated to suppot later Java versions 2024-11-26 20:27:58 -07:00
cjmyers
484ae5d58e
Merge branch 'master' into sbml-to-prism 2023-03-28 08:57:59 -06:00
LukasBuecherl
7e8f2e6f9f Print props file 2023-03-28 15:11:14 +01:00
LukasBuecherl
2674494894 Working 2023-03-06 12:20:29 +00:00
LukasBuecherl
4bf6c6e1e6 Refactor code for SBML2PRISM 2022-07-25 14:27:39 -06:00
LukasBuecherl
a93e650de2 refactor 2022-07-25 13:39:02 -06:00
LukasBuecherl
8cffc3062b Flatten works 2022-07-25 13:28:58 -06:00
LukasBuecherl
1c24b1edc5 Initial work on hierarchy support 2022-07-21 14:08:19 -06:00
LukasBuecherl
927062edeb Bound/Unbound option is now available and works 2022-07-20 09:26:09 -06:00
LukasBuecherl
b8cad2fe48 Added comments to SBML2PRISM 2022-07-14 13:15:28 -06:00
LukasBuecherl
5453e5031d Updated Conversion 2022-07-14 12:53:08 -06:00
LukasBuecherl
75911f5931 FirstDraft 2022-06-24 06:42:38 +02:00
LukasBuecherl
b435eb5c87 Updated Files for the Translator 2022-06-02 15:17:02 -06:00
Pedro Fontanarrosa
2adf6d6425 Update Converter.java 
Fixed trying to read a document without specifying outputdir
Fixed code trying to read only .xml and not also .sbol files
 2022-04-18 12:15:35 -04:00
Pedro Fontanarrosa
c2f67b7035 Update Converter.java 2022-03-18 12:18:26 -06:00
Chris Myers
f94c30f85b Add topModelId field 2022-03-17 17:50:20 -06:00
Chris Myers
a1259bb46a Removed test file 2021-10-18 14:40:05 -06:00
Chris Myers
fe229873e7 Updated pom files 2021-06-24 19:34:08 -06:00
Chris Myers
6a39d140bc Missing javadoc comment 2020-10-23 17:20:26 -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
Pedro Fontanarrosa
96d3e8e738 Removed TODO tags 
Removed TODO tags
 2020-01-22 20:01:09 -03:00
Pedro Fontanarrosa
7c2074fbfb Ordered promoters 
Added code to check order of tandem promoters, so that the roadblocking effect is in the correct promoter
 2020-01-18 19:13:00 -03:00
Pedro Fontanarrosa
e0b7c2a22f Sensor Promoter Roadblock effect 
Added alpha and beta roadblocking effect for when sensor promoter is the downstream promoter
 2020-01-17 15:46:50 -03:00
Pedro Fontanarrosa
62a2411a49 Updated code to have promoters listed in order 2020-01-16 11:06:59 -03:00
Pedro Fontanarrosa
4f86b52eee Updated promoterInteractions method 
This update retrieves alpha and beta parameters from sensor gate
interactions
 2020-01-11 09:59:48 -03:00
Pedro Fontanarrosa
1d53561bc8 Fixed bug for default parameters 2020-01-08 18:26:43 -03:00
Tramy Nguyen
2d61736103 resolved merge conflict for verilogCompiler to master branch 2019-11-24 17:56:26 -05:00
Pedro Fontanarrosa
ffc71b1bb4 Update README.md 
Fixed indentation
 2019-11-14 17:23:51 -03:00
Pedro Fontanarrosa
f94355e970 Update README.md 
Added Cello conversion option in readme
 2019-11-14 17:16:01 -03:00
cjmyers
687471d2b2
Merge branch 'master' into ModelingGenerator 2019-11-11 16:25:06 -07:00
Chris Myers
6dee2c1592 Fix a few issues causing problems with mvn build 2019-11-06 17:13:25 -07:00
cjmyers
180cc0179e
Merge branch 'master' into ModelingGenerator 2019-11-06 11:36:30 -07:00
Pedro Fontanarrosa
79305aa46d Cleaning up code 2019-11-04 14:58:38 -03:00
Pedro Fontanarrosa
e301b76604 Gui option for Cello Modeling 
Added neccesary changes to make cello modeling an option for the user through the Gui interface
 2019-11-01 20:17:16 -03:00
Pedro Fontanarrosa
299bf44d17 added TODOS 2019-10-25 17:34:45 -03:00
Pedro Fontanarrosa
9033eb6869 Merge branch 'ModelingGenerator' of 
https://github.com/MyersResearchGroup/iBioSim.git into ModelingGenerator

Conflicts:
	conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/CelloModeling.java
	conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2SBOL.java
	conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBOL2SBML.java
 2019-09-16 12:03:47 -03:00
Pedro Fontanarrosa
703b6e9e1a This changes are me trying to re-install previous commit before messing 
up
 2019-09-16 11:38:05 -03:00
Pedro Fontanarrosa
c68526ca98 Change visibility of methods in SBOL2SBML to package 
this is so that CelloModeling.java can use them
 2019-09-13 17:39:36 -03:00
Tramy Nguyen
dbe40b6d3a technology mapping tested for covering 2019-08-07 23:20:07 -06:00
Pedro Fontanarrosa
1ecc671b03 Converter commit 2019-08-07 14:42:28 -03:00
Pedro Fontanarrosa
579794a8c7 Creating measure class toy example for Model Generator 2019-08-07 14:42:28 -03:00
Pedro Fontanarrosa
71a9ae4a38 Updated Converter 
This allows for creation of Top Module with circuit name
 2019-08-07 14:41:51 -03:00
Pedro Fontanarrosa
878d0ff031 Code Cleaning 2019-08-07 14:41:51 -03:00
Pedro Fontanarrosa
507aa6f3f7 Added Java AutoDocs 
CelloModeling removed unnecessary code
 2019-08-07 14:41:50 -03:00
Pedro Fontanarrosa
412c01c44a Option to import Simulation Environment 2019-08-07 14:41:50 -03:00
Pedro Fontanarrosa
a1a86ffdb5 Updated CelloModeling to skip sensorMolecules 
Now the model generator doesn't generate species for sensorMolecules and
removes the relevant MapsTo's that reference them.
 2019-08-07 14:41:50 -03:00
Pedro Fontanarrosa
1703505fcc Removed unnecessary code 2019-08-07 14:41:49 -03:00
Pedro Fontanarrosa
418e45e39e Updated VPR version from 2.0.14-SNAPSHOT to 2.0.16-SNAPSHOT 
Updated conversion.java to be able to generate VPR model
 2019-08-07 14:41:49 -03:00