Quick Start Guide

🚧 This guide is still under construction. 🚧

Installing SimBLE

The easiest way to install SimBLE is with pip:

pip install simble

Alternatively, clone the source code from GitHub and install from local files:

# clone the repo however you like, eg
git clone https://github.com/hoehnlab/simble

# in the repo directory, install simble from local files
pip install .

# run
python3 -m simble -flags
# or
simble -flags

To install for development, please refer to Developing in SimBLE.

Basic usage

Run a default simulation with a specified output folder:

simble -o <path-to-folder>

Note

The default simulation runs with selection, with no migration, sampling every 25 generations for 200 generations.

At any time, you can run SimBLE with the -h or --help flag to see all available arguments (also see Command line arguments):

simble -h

To run a neutral-selection BCR simulation (using naive BCRs, heavy and light chains, and S5F mutation/substitution model):

simble --neutral [other args]

To run a uniformly neutral simulation (no selection, randomly generated starting nucleotide sequence, and uniform mutations/substitutions):

simble --uniform [other args]

To run a uniformly neutral simulation with a specified sequence length of 100:

simble --uniform --sequence-length 100 [other args]

To run with expected migration of one cell every 25 generations:

simble --migration-rate 0.04 [other args]

To run 5 clones in parallel across 2 processes, with expected migration of one cell every 10 generations with selection, and sampling every 10 generations for 100 generations:

simble -o ./current-results -n 5 --processes 2 --migration-rate 0.1 --samples 0 100 10

which is equivalent to

simble -o ./current-results -n 5 -p 2 --migration-rate 0.1 -s 0 100 10

Tip

Flags can be provided any order.

Frequently used arguments:

argument	abbr	default	description
–output	-o	cwd/results	folder for results
–number	-n	1	number of clones to simulate
–processes	-p	1	number of processes (multiprocessing)
–neutral			if provided, runs a neutral simulation
–uniform			if provided, runs a uniform neutral simulation
–migration-rate		0	expected number of cells that leave the germinal center each generation
–samples	-s	[0 200 25]	start, stop, step, to specify sample times other than the default
–quiet	-q		don’t display progress bar

Thank you for using SimBLE!