NWN_CElegans_VPC_model

This repository contains a computational model of The Vulval Precursor Cells (VPC) specification between the L3 and L4 stages of larval development in C. Elegans.

The model is based on the use of the Nets-Within-Nets Petri Nets formalism. Its goal is to show the potential of this formalism in the description and simulation of ontogenetic processes.

For details refer to: https://www.biorxiv.org/content/10.1101/2021.02.15.430983v2.

Repo structure and organization

├── README.md
├── results                                                         //Simulation results
├── scripts                                                         //Scripts running the simulations
└── src
    ├── model
    │   ├── collect_and_assemble.class
    │   ├── collect_and_assemble$Cell
    │   ├── collect_and_assemble.java                               //Java class used within the fate manager to perform the classification 
    │   ├── compileclass.sh			                               // script to compile the collect_and_assemble class for renew		
    │   ├── lin12_ko_model                                          //Same organization as wt_model
    │   │   ├── LIN3.rnw
    │   │   ├── VPC_CElegans_ac.rnw
    │   │   ├── VPC_CElegans_cell_building_blocks.rnw
    │   │   ├── VPC_CElegans_hyp7.rnw
    │   │   ├── VPC_CElegans_spatial_grid.rnw
    │   │   ├── VPC_CElegans_spatial_grid.sns
    │   │   └── VPC_CElegans_states_landscape.rnw
    │   ├── lst_lf_dpy23_lf                                         //Same organization as wt_model
    │   │   ├── LIN3.rnw
    │   │   ├── VPC_CElegans_ac.rnw
    │   │   ├── VPC_CElegans_cell_building_blocks.rnw
    │   │   ├── VPC_CElegans_hyp7.rnw
    │   │   ├── VPC_CElegans_spatial_grid.rnw
    │   │   ├── VPC_CElegans_spatial_grid.sns
    │   │   └── VPC_CElegans_states_landscape.rnw
    │   ├── lst_lf_model                                            //Same organization as wt_model
    │   │   ├── LIN3.rnw
    │   │   ├── VPC_CElegans_ac.rnw
    │   │   ├── VPC_CElegans_cell_building_blocks.rnw
    │   │   ├── VPC_CElegans_hyp7.rnw
    │   │   ├── VPC_CElegans_spatial_grid.rnw
    │   │   ├── VPC_CElegans_spatial_grid.sns
    │   │   └── VPC_CElegans_states_landscape.rnw
    │   ├── vul_ko_model                                            //Same organization as wt_model
    │   │   ├── LIN3.rnw
    │   │   ├── VPC_CElegans_ac.rnw
    │   │   ├── VPC_CElegans_cell_building_blocks.rnw
    │   │   ├── VPC_CElegans_hyp7.rnw
    │   │   ├── VPC_CElegans_spatial_grid.rnw
    │   │   ├── VPC_CElegans_spatial_grid.sns
    │   │   └── VPC_CElegans_states_landscape.rnw
    │   ├── wt_model                                                //The wild-type model
    │   │   ├── LIN3.rnw					                        //The LIN3 net-token
    │   │   ├── VPC_CElegans_ac.rnw                                 //The AC net-token 
    │   │   ├── VPC_CElegans_cell_building_blocks.rnw               //The Pnp net-token
    │   │   ├── VPC_CElegans_hyp7.rnw                               //The Hyp7 cell net-token
    │   │   ├── VPC_CElegans_spatial_grid.rnw                       //The system-net
    │   │   ├── VPC_CElegans_spatial_grid.sns                       //The compiled model (.sns, Shadow Net System)
    │   │   └── VPC_CElegans_states_landscape.rnw                   //The Fates Manager (FM) net-token
    │   └── Figures                                                 //The Figures of the wild-type model
    │       ├── VPC_CElegans_ac.pdf                                 //The AC net-token figure in pdf 
    │       ├── VPC_CElegans_cell_building_blocks.pdf               //The Pnp net token figure in pdf 
    │       ├── VPC_CElegans_hyp7.pdf                               //The Hyp7 cell net-token  figure in pdf 
    │       ├── VPC_CElegans_spatial_grid.pdf                       //The system-net figure in pdf 
    ├── renew2.5.1                                                  // Renew v2.5.1 jar required to run simulations
    ├── weka.jar                                                    // Weka jar required to implement the FM
    └── weka-src.jar                                                // Weka-src jar required to implement the FM
    

Requirements

The model has been tested on Java 11 under Linux.

How to run a simulation

• Open the terminal.
• Change dir to the folder containing the scripts of the desired model (e.g. scripts/wt_model for the wild-type condition).
• Run the simulation by entering the command: source launch_script.sh <number_of_simulations> where <number_of_simulations> is an integer number indicating how many simulations to perform.
• The simulation creates a folder named outputs. The folder contains:
  • One file named Simulation_<number>.log for each simulation containing full log of the simulation generated by Renew. This log can be used to reconstruct signal traces.
  • One file named cells_unlabeled_<number>.arff for each simulation. This is the file format used to exchange data beetween Renew and Weka.
  • One file named fates.csv containing the fate predictions (every line is a simulation).

N.B. Every time you run the simulation the output file is erased and recreated. Move your results outside if you want to keep them.