Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network
Authors: Emilia M. Wysocka, Matthew Page, James Snowden, T. Ian Simpson
Repository storing molecular rule-based models in Kappa language and Python-based figures published in PeerJ
- Variable "cAMP_delay" value = 200
./ode_model/originalModel/sbmlFormat/pcbi.0020176.sd002_cAMPdelay200.xml
- Variable "cAMP_delay" value = 400
./ode_model/originalModel/sbmlFormat/pcbi.0020176.sd002.xml
./ode_model/originalModel_mutants/constSer_pcbi.0020176.sd002_cAMPdelay200.xml
./ode_model/originalModel_mutants/ser2ala_pcbi.0020176.sd002_cAMPdelay200.xml
Go to https://copasi.org/Download/ and download COPASI version >= 4.20, compatible with your OS. COPASI does not have to be installed.
To run COPASI from the command line using CopasiSE, export the .cps file from the COPASI GUI. Parameters to set in the COPASI GUI:
- StepNumber = 1400
- StepSize = 0.5
- Duration = 700
- Method name = "Stochastic (Direct method)" OR "LSODA"
First, set a temporary variable to the COPASI executable files in termial, replacing the directory where COPASI was placed:
export COPASIDIR=<copasi-path>
To run COPASI GUI from command line:
$COPASIDIR/CopasiUI
To run COPASI from command line:
$COPASIDIR/CopasiSE
To use the KaSim release compatible with the syntax used in the model, download and unpack archives from the releases on the Kappa repository.
For macOS and Linux, open Terminal and type:
cd <path_to_KaSim_folder>
wget https://github.com/Kappa-Dev/KappaTools/archive/refs/tags/v3.5-250915.zip
unzip v3.5-250915.zip
cd KappaTools-3.5-250915/bin
Run KaSim with a suffix corresponding to your OS ( linux / mac_OSX) to get the usage instruction:
./KaSim_3.5_linux_x86
KaSim 3.5-121114:
Usage is KaSim -i input_file [-e events | -t time] [-p points] [-o output_file]
Set a temporary variable to the KaSim executable files in termial, replacing the directory where KaSim was placed:
export KASIMDIR=<kasim-path>
To run KaSim, type:
$KASIMDIR/KaSim
-
Figure 3
(A): ODE W-T deterministic trajectories
- generated with GUI
- OUTPUT: ./ode_model/withCopasiGUI_SE/ODEresults/tc_LSODA_700_1400.txt
(B): ODE W-T stochastic trajectories - Ensemble of 40-model runs
./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_run.sh
- OUTPUT: ./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_40runs_tc_directmethod700_1400
(C): RB W-T stochastic trajectories - Ensemble of 40-model runs
./rb_model/wildType/models/oneBindingSite_DARPP/run_basic.sh
./rb_model/wildType/models/oneBindingSite_DARPP/run4tracking.sh
- OUTPUT: ./rb_model/wildType/models/oneBindingSite_DARPP/out_ensemble/data_*.out
-
Figure 4
./rb_model/wildType/models/oneBindingSite_DARPP/run_basic.sh
- OUTPUT: ./rb_model/wildType/models/oneBindingSite_DARPP/out_ensemble/data_*.out
./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_run.sh
- OUTPUT: ./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_40runs_tc_directmethod700_1400
- OUTPUT: ./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_out
-
Figures 6, 7, S1, S2
./rb_model/wildType/models/threeBindingSites_DARPP/run_basic_ca_18.sh
- OUTPUT: ./rb_model/wildType/models/threeBindingSites_DARPP/out_ensemble_ca_all/data_*
./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_run.sh
- OUTPUT: ./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_40runs_tc_directmethod700_1400
- OUTPUT: ./ode_model/withCopasiGUI_SE/DirMethresults/ensemble_out
-
Figure 8
(A) ODE Constitutive Serine
./ode_model/withCopasiGUI_SE/DirMethresults_mutants/ensemble_run.sh
- OUTPUT: ./ode_model/withCopasiGUI_SE/DirMethresults_mutants/constSer_directMethod_700_1400.txt
(B) RB Constitutie Serine
./rb_model/constitutiveSer137p/threeBindingSites_DARPP/run_basic.sh
- OUTPUT: ./rb_model/constitutiveSer137p/threeBindingSites_DARPP/out_ensemble
-
Figure S3
-
Figure S4
./rb_model/wildType/models/oneBindingSite_DARPP/run_KaDE.sh
./rb_model/wildType/models/oneBindingSite_DARPP/run_KaSa.sh
./rb_model/wildType/models/threeBindingSites_DARPP/run_basic.sh
./rb_model/wildType/models/threeBindingSites_DARPP/tracking/run4tracking.sh
./rb_model/wildType/models/threeBindingSites_DARPP/tracking/run4tracking_for_KaSim4.0.sh