morsaik 0.1.0

Sequence Motif Reactor Simulation, Analysis and Inference Kit.

Welcome to the Motif Reactor Simulation, Analysis and Inference Kit (morsaik) repository.

Introduction

In order to investigate RNA reactors as candidates for the origins of life, efficient simulations are needed because the space of possible RNA sequences increases exponentially with the length of the strands, as well as the number of reactions between two strands. In addition, simulations have to be compared to experimental data for validation and parameter calibration. Here, we present the MoRSAIK python package for sqeuence motif (or k-mer) reactor simulation, analysis and inference. It enables users to simulate RNA sequence motif dynamics in the mean field approximation as well as to infer the reaction parameters from data with Bayesian methods and to analyze results by computing observables and plotting. MoRSAIK simulates an RNA reactor by following the reactions and the concentrations of all strands inside up to a certain length (of four nucleotides by default). Longer strands are followed indirectly, by tracking the concentrations of their containing sequence motifs of that maximum length.

For a more detailed introduction, please go to the demos in the ./demos directory. For an overview of the package and its aim, please refer to the paper.

Installation

For installation of morsaik, poetry is reommended. Clone this repository and install it with

git clone https://github.com/joharkit/morsaik.git
cd morsaik
poetry init
poetry install

Alternatively, clone this repository, go into the directory and install it via pip:

git clone https://github.com/joharkit/morsaik.git
cd morsaik
pip install .

Contribution

You are very welcome to contribute to this package. Please open an issue and send a PR with your changes. Please remember to upgrade the docs and the manual if needed and adjust the test pipeline, adding new tests eventually. In case of any questions, please contact me.

Tests

All important functions are tested with tests in the test directory. The .gitlab-ci.yml performs all tests automatically.

If you want to run the tests locally, please make sure, everything is installed and just run

pytest

or, if you use poetry run

poetry run pytest

This will start all tests. Since those are quite a lot, please ensure, you have enough computational resources. Else, just specify the test you want to run as an argument directly after the pytest command.