krlhBlupine/iBioSim
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245 commits

Author SHA1 Message Date
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
Chris Myers
f74c41aa59 Added a few null pointer checks 2022-10-02 16:59:34 -06:00
LukasBuecherl
8cffc3062b Flatten works 2022-07-25 13:28:58 -06:00
Chris Myers
88d02ca2d4 Fix default model conversion parameters 2022-06-23 17:12:47 -06:00
LukasBuecherl
b435eb5c87 Updated Files for the Translator 2022-06-02 15:17:02 -06:00
Chris Myers
518bbc1383 Update jsbml 2022-05-19 06:37:25 -06:00
Chris Myers
73196545f6 Updated JSBML 2022-04-21 16:25:26 -06:00
Chris Myers
7672cd24b9 Added stub code 2022-03-31 15:31:04 -06:00
Chris Myers
82c020dddb Fix bug with meta ids 2021-11-30 18:19:36 -07:00
Chris Myers
fe229873e7 Updated pom files 2021-06-24 19:34:08 -06:00
Chris Myers
e8cde0e3ab Update to SBML Level 3 Version 2 2020-07-10 12:07:35 -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
Chris Myers
ca58aa4f9d Fixed an issue with math flattening 2020-04-12 15:17:45 -06:00
Chris Myers
896b33ca3b Fix for null pointer sBase 2020-04-12 11:36:12 -06:00
Pedro Fontanarrosa
9081123a7a Fixed tandem promoter bug 2020-02-12 16:14:59 -03:00
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
97d125c54f Updated createCelloProductionKineticLaw 
This update adds roadblocking effects to when creating the kinetic model of the genetic circuit. This is only added if there are 2 tandem promoters.
 2020-01-11 10:03:20 -03:00
Pedro Fontanarrosa
1d53561bc8 Fixed bug for default parameters 2020-01-08 18:26:43 -03:00
Pedro Fontanarrosa
828ff0dfb5 Added default parameters for sensor parts 2019-12-26 17:44:35 -03:00
Fontanapink
e6b9a2e17e
Merge pull request #592 from MyersResearchGroup/Default_Parameters 
Default parameters
 2019-12-12 10:24:51 -03:00
Pedro Fontanarrosa
f349ecc3c3 Added comments that fix line endings 
Making it easier to compare files
 2019-12-11 15:58:07 -03:00
Pedro Fontanarrosa
ab858c8f3c Comments 2019-12-11 15:55:58 -03:00
Pedro Fontanarrosa
2921359f36 remove spaces 2019-12-07 15:17:54 -03:00
Pedro Fontanarrosa
af24032df5 Introduced default parameters if no other is found for Cello Modeling 2019-12-07 14:46:36 -03:00
Pedro Fontanarrosa
93fcf66a1f Added Global constants for Cello parameters K, n, ymax, ymin, alpha and 
beta
 2019-12-07 13:16:11 -03:00
Tramy Nguyen
2d61736103 resolved merge conflict for verilogCompiler to master branch 2019-11-24 17:56:26 -05:00
cjmyers
180cc0179e
Merge branch 'master' into ModelingGenerator 2019-11-06 11:36:30 -07:00
Tramy Nguyen
ced01407d3 set up run for tech map to synthesis view 2019-10-01 13:34:49 -06:00
Tramy Nguyen
5458c21eb7 successful run for yosys but not sbol tech. map 2019-09-27 12:56:15 -06:00
Tramy Nguyen
e3fb409ec2 load verilog synthesis property 2019-09-25 13:26:16 -06:00
Tramy Nguyen
70e91ff1c5 add verilog file to project tree 2019-09-16 16:22:14 -06:00
Tramy Nguyen
37d4545b6d tech map non recursion for exhaustive and greedy 2019-08-18 12:16:34 -06:00
Tramy Nguyen
dbe40b6d3a technology mapping tested for covering 2019-08-07 23:20:07 -06:00
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
ba1826dd55 Added correct species information for small molecules 
Added correct species information for small molecules
(boundarycondition, substanceunits, etc) in sub-models
 2019-08-07 14:41:49 -03:00
Pedro Fontanarrosa
a8f446ef98 MIGRATED TO NEW JAVA CLASS! 2019-08-07 14:41:22 -03:00
Pedro Fontanarrosa
fe6de14d66 createCelloSDProductionReactions create smallMolecule species 
Added support to create species for input small sensor molecules
 2019-08-07 14:41:21 -03:00
Pedro Fontanarrosa
ebf7418573 createCelloSDProduction removal of unnecessary variables 
generateModel removed sensor molecules and complexes from model
 2019-08-07 14:41:21 -03:00
Pedro Fontanarrosa
6f0bb448d6 Updated createCelloProductionKineticLaw 
now it will create kinetic laws for sensor promoters

Updated sensorMolecules

now it correctly pairs complexes/proteins with ligands
 2019-08-07 14:41:12 -03:00
Pedro Fontanarrosa
bfc65e6536 Added kinetic model formula for sensor promoters 
Moved Prot_2_Param before promoterInteractions method so that I can add
Cello parameters from sensor interactions to Prot_2_Param

Added a new Java Document to eventually move everything to New Cello
Model Generator
 2019-08-07 14:41:11 -03:00
Pedro Fontanarrosa
56cc0cfd61 createCelloProductionKineticLaw modifitaction 
Modified the method to be able to assign parameters for k, n, ymax, ymin
from the Cello parameters and promoter interaction lists

pom.xml

Changed VPR version from .12 to .14

productionInteractions

added method that makes a map of promoters, if they are repressed or
activated, and by which protein

hasCelloParameters2

added new method that searches all sbol document, and creates a list
with all components and their Cello parameters, if they exist
 2019-08-07 14:41:10 -03:00
Pedro Fontanarrosa
420fd8a0d7 Changing hashmaps from raw to hashmaps with types 2019-08-07 14:41:02 -03:00
Pedro Fontanarrosa
e09b8395b6 Commenting and deleting unnecessary code 2019-08-07 14:40:34 -03:00