ProtoSim

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- Calculates and visualizes the variation of internal protocell material over time - Implements specific differential equations to simulate protocell behavior - Allows users to customize input parameters and conditions - Allows the graphic visualization via Pajek of the graphs of physical and chemical variations

🏁 Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

💻 Download Repo

If you don't have Git installed on your system, follow these steps to install it:

Windows

1. Download Git from the official website: https://git-scm.com/.

2. Run the downloaded file (.exe) and follow the installer instructions.

3. During installation, make sure to select "Use Git from the Windows Command Prompt" to add Git to your PATH.

4. Verify the installation by running the following command in the command prompt or PowerShell:

   git --version

MacOS

1. Open the terminal.

2. Install Git using Homebrew (if you don't have Homebrew, follow the instructions at https://brew.sh/):

   brew install git

3. Verify the installation by running the following command in the terminal:

   git --version

Linux (Debian/Ubuntu):

1. Open the terminal.

2. Run the following commands:

   sudo apt-get update
   sudo apt-get install git

3. Verify the installation by running the following command in the terminal:

   git --version

Now you are ready! Run the following command to clone repo:

git clone https://github.com/Piltxi/ProtoSim

🔮 Start simulation

cd ProtoSim/src
python3 main.py

Note

📤 To enable printing of some additional information or debug printing:

cd src
python3 main.py -v

📥 To delete the directory with output information:

cd src
python3 main.py -r

📥 To specify input file with parameters and reactions:

default: parameters in input/parameters.txt and reactions in input/chimica.txt
❌ respect the semantic order of parameters and values ❗

cd src
python3 main.py -f

📥 To ONLY check the correct import of the parameters:

cd src
python3 main.py -i

📥 To save RAM memory during simulations: this disables saving the data of each individual generation

cd src
python3 main.py -e

🕸️ To generate the .pajek configuration of the reaction network
option also allows the printing of any flows

cd src
python3 pajeko.py

🕸️ To activate some control prints when importing data from the simulation file

cd src
python3 pajeko.py -v

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ProtoSim reads the input parameters and reactions from two text files. The files are located in input/ . You can edit them to change a parameter or insert new reactions. ProtoSim saves all the data on the simulation, the summary of all generations and any expanded generations, in the path out/data/sim. All directories are automatically named with the simulation date and time information.

Pajeko, the additional tool for generating the .pajek, configuration file works with the sim.xlsx generated by ProtoSim.
In particular, it expects to find the file with the data within the path /input/pajeko. At the end of export, pajeko saves data to the path /out/pajeko.

✍️ Authors

• @piltxi student engaged in scientific research on the behavior of protocells