krlhBlupine/iBioSim
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions
11503 commits 1 branch 0 tags 832 MiB
Commit graph

11503 commits

This branch
This branch
All branches
Author SHA1 Message Date
Pedro Fontanarrosa
a5b9dd73bd Added comments and removed unused lines of code 2019-08-07 14:41:48 -03:00
Pedro Fontanarrosa
dc29521889 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.
 2019-08-07 14:41:40 -03:00
Pedro Fontanarrosa
931871f053 Uncommented broken MDFlattener code 2019-08-07 14:41:40 -03:00
Pedro Fontanarrosa
9022aba668 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.
 2019-08-07 14:41:32 -03:00
Pedro Fontanarrosa
4baa96f442 Changed visibility of SBOL2SBML methods to 'package' so that 
CelloModeling can use them
 2019-08-07 14:41:32 -03:00
Pedro Fontanarrosa
bd0660462f Testing 2019-08-07 14:41:23 -03:00
Pedro Fontanarrosa
fa5a02ab99 Updated the generateReplacement method in CelloModeling.java to make the 
input (small molecule) replacements correctly.
 2019-08-07 14:41:23 -03:00
Pedro Fontanarrosa
a8f446ef98 MIGRATED TO NEW JAVA CLASS! 2019-08-07 14:41:22 -03:00
Pedro Fontanarrosa
d6ee6a2aa0 Added comments for the functioning of generateModel 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
0ca89998b3 Added sensorMolecules method 
this method will map sensors to complex molecules that will
inhibit/activate different sensor promoters. It will be used when
calling promoterInteracions method
 2019-08-07 14:41:11 -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
aa5efc7bf3 added new decision point for Cello or normal modeling 
moved searching of cello parameters further up
 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
Pedro Fontanarrosa
987dfbc2f1 Comments 2019-08-07 14:40:34 -03:00
Pedro Fontanarrosa
7ec1af4323 Modified isProductionReaction() 
Modified this method so that it won't change the SBO term of a
transcription reaction to SBO_PRODUCTION
 2019-08-07 14:40:22 -03:00
Pedro Fontanarrosa
d032db7881 Updated MDFlattener to compile with multiple promoters 2019-08-07 14:40:22 -03:00
Pedro Fontanarrosa
afa0222dc9 Added creation of species TU 
This is to make TU a species on which to make it a modifier. This may
have to change when we fix MDflatenner
 2019-08-07 14:39:54 -03:00
Pedro Fontanarrosa
ba16b078a9 Created and updated createCelloProductionKineticLaw 
As of now, the cello model generation is complete with reactions and
kinetic law. We are now waiting for a change in the parameter location
in SBOL documents, so we can efficiently model this model.
 2019-08-07 14:39:54 -03:00
Pedro Fontanarrosa
3a4aacaada Added createCelloKineticLaw 
Modified globalConstants kSD and kTF

Modified promoterInteractions
 2019-08-07 14:39:53 -03:00
Pedro Fontanarrosa
5ae563982a Added promoterInteraction method 
This method searches all activation and repression interactions and maps
it to individual promoters (not TUs). This information will be later
used when creating the mathematical model using Hamid's paper for
dynamic modeling using Cello Parameters.
 2019-08-07 14:39:53 -03:00
Pedro Fontanarrosa
309431105d Modified SD and TF production reaction 2019-08-07 14:39:52 -03:00
Pedro Fontanarrosa
2d697f5aef Added the SBO terms for transcription and translation 2019-08-07 14:39:52 -03:00
Pedro Fontanarrosa
922952de68 comments and edits 2019-08-07 14:39:52 -03:00
Pedro Fontanarrosa
33c510ceac Minor changes and rxnID creation 2019-08-07 14:39:51 -03:00
Pedro Fontanarrosa
614d7556a0 Updated CelloDegradationReaction Method 2019-08-07 14:39:51 -03:00
Pedro Fontanarrosa
9a5ce2af35 Added Check to see if we are in Cello Model Generation for both 
Degradation and Production rates

Changed GlobalConstants for Cello Parameters

Added TODOs
 2019-08-07 14:39:50 -03:00
Pedro Fontanarrosa
b4ddcc1bf8 Added parts to the createCelloTFProductionReaction and 
createCelloSDProductionReaction
 2019-08-07 14:39:50 -03:00
Pedro Fontanarrosa
edb8825aec Added comments and headers 2019-08-07 14:39:49 -03:00
Pedro Fontanarrosa
0ebd109066 Added comments and questions 2019-08-07 14:39:49 -03:00
Pedro Fontanarrosa
0152967e9e added comments 2019-08-07 14:39:48 -03:00
Pedro Fontanarrosa
c3a1a3fc15 Created the generateCelloDegradationRxn in SBOL2SBML 
Created generateCelloDegradationReaction in Biomodel
 2019-08-07 14:39:48 -03:00
Pedro Fontanarrosa
b82f0614ad Added comments to generateProductionRXN 2019-08-07 14:39:47 -03:00
Pedro Fontanarrosa
b5eab9de3d Added Cello Parameters to Global Constants 2019-08-07 14:39:47 -03:00
Pedro Fontanarrosa
cb56c133ba Added comments on hasCelloParameters 2019-08-07 14:39:47 -03:00
Pedro Fontanarrosa
ffb967898d Moved code for detecting Cello Parameters out into it's own method call 2019-08-07 14:39:46 -03:00
Pedro Fontanarrosa
7e67035ff5 Verify if parts have Cello parameters, call different 
createproductionRXN method
 2019-08-07 14:39:46 -03:00
Pedro Fontanarrosa
753acc8f95 Added for loops to determine if a flattening has to occur or if we just 
pass back the unflattened ModuleDefinition
 2019-08-07 14:38:35 -03:00
Pedro Fontanarrosa
b0ee16af81 Converter commit 2019-08-07 14:33:22 -03:00
Pedro Fontanarrosa
3ccd43cb4c Creating measure class toy example for Model Generator 2019-07-31 15:10:32 -03:00
Tramy Nguyen
37f2f422eb Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git into verilogCompiler 2019-07-30 18:52:51 -06:00
Tramy Nguyen
7f978c11cb perform tech. map cover with feedback 2019-06-12 00:55:56 -06:00
Chris Myers
d0d2cbbcfd Update libSBOLj 2019-06-03 08:17:44 -06:00
Pedro Fontanarrosa
dcc1a96883 Updated Converter 
This allows for creation of Top Module with circuit name
 2019-05-16 10:15:36 -06:00
Pedro Fontanarrosa
d930671c04 Code Cleaning 2019-04-29 09:26:28 -07:00
Pedro Fontanarrosa
ad963b94cb Added Java AutoDocs 
CelloModeling removed unnecessary code
 2019-04-26 09:52:47 -06:00