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

Key websites

• https://kappalanguage.org

• https://www.ebi.ac.uk/biomodels/BIOMD0000000153

• https://copasi.org

The path to the Fernandez (2006) models in the SBML format in this repository:

Wild-type

• 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

Constitutive Ser137 mutatation:

./ode_model/originalModel_mutants/constSer_pcbi.0020176.sd002_cAMPdelay200.xml

Serine to Alanine mutatation:

./ode_model/originalModel_mutants/ser2ala_pcbi.0020176.sd002_cAMPdelay200.xml

Instructions to use COPASI >= 4.20

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

Instructions to use KaSim == 3.5

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

List of figures reproduced in main.ipynb along with scripts for generating time series:

• 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

Additional scripts for RB:

./rb_model/wildType/models/oneBindingSite_DARPP/run_KaDE.sh

./rb_model/wildType/models/oneBindingSite_DARPP/run_KaSa.sh

Three-binding site model:

./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