MARlea

A project aiming at revamping Aleae, a tool for "Stochastic Simulation of Molecular Reactions", written by Marc Riedel of the University of Minnesota Twin-Cities. The original project is available here: https://cctbio.ece.umn.edu/aleae/

This is very much expirimental and just written for fun. Don't expect this to be completely accurate. We aren't biologists or chemists.

I will not provide support for this project... if it's broken for you my answer is simply that you should download the source code and fix it yourself. It's open for a reason. Good luck and happy simulating!!!

about

A command line program for simulating DNA based chemical reaction networks.

This program takes some CSV as input and performs stochastic simulation on the provided system, then prints results either to a specified output file or the command line.

Usage: Marlea <QUERY> <INPUT_FILE> [Options]

Arguments:

• <QUERY> - Specify the operation/query to perform. Possible values: "simulate", "help".
• <INPUT_FILE> - Input file path to use.

Options:

• -i, --init-file <FILE_NAME> Specifies a file to read starting conditions from. By default if no file is specified the default is to assign species a count of 0, this is also the default for species not listed within the specified file.
• -o, --output-file <FILE_NAME> Specifies a file where the program should write its results. If omitted program will only print to the command line. By default this will simply use console output.
• --timeline <FILE_NAME> Advanced Sets the program to write a full history of the solution at each step for all trials... This can easily be gigabytes of data.
• -t, --num-trials <NUM_TRIALS> Specifies the number of times the simulation should simulate the chemical reaction network. By default this is 100 trials
• -r, --max-runtime <MAX_RUNTIME> Specifies the maximum time the simulation is allowed to run for in seconds. By default runtime is unbounded
• -s, Advanced sets how tollerant each simulation will be of semi stable states. By defualt each trial will terminate after being semi stable for 100 steps.

input syntax

reactants/products

<coefficient> <species name>

• Note: If coefficient is ommited it defaults to 1

reaction

<reactant + <reactant> => <product> + <product>, <reaction_rate>

• Note: there may be any number of reactants or products including 0
• Note: recursive inputs such as my_var => my_var + my_other_var, some_rate will cause the program to hang if no reaction consumes my_var elsewhere in the network for a reaction which may occure at all times please simply use null reactants such as => my_other_var, some_rate this will not hang.

init syntax

<species_name>, <initial_count>\n

• Note: only non zero values must be specified in init