Extending BioMASS to construct mathematical models from external knowledge.

ABSTRACT:

Motivation

Mechanistic modeling based on ordinary differential equations has led to numerous findings in systems biology by integrating prior knowledge and experimental data. However, the manual curation of knowledge necessary when constructing models poses a bottleneck. As the speed of knowledge accumulation continues to grow, there is a demand for a scalable means of constructing executable models.

Results

We previously introduced BioMASS-an open-source, Python-based framework-to construct, simulate, and analyze mechanistic models of signaling networks. With one of its features, Text2Model, BioMASS allows users to define models in a natural language-like format, thereby facilitating the construction of large-scale models. We demonstrate that Text2Model can serve as a tool

SUBMITTER: Arakane K 

PROVIDER: S-EPMC11007111 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature