Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages.

ABSTRACT:

Motivation

Cells are complex systems composed of hundreds of genes whose products interact to produce elaborated behaviors. To control such behaviors, cells rely on transcription factors to regulate gene expression, and gene regulatory networks (GRNs) are employed to describe and understand such behavior. However, GRNs are static models, and dynamic models are difficult to obtain due to their size, complexity, stochastic dynamics and interactions with other cell processes.

Results

We developed Atlas, a Python software that converts genome graphs and gene regulatory, interaction and metabolic networks into dynamic models. The software employs these biological networks to write rule-based models for the PySB framework. The underlying method is a divide-and-conquer strategy to

SUBMITTER: Santibanez R 

PROVIDER: S-EPMC8016457 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature