Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling.

ABSTRACT:

Motivation

Genome-scale metabolic network reconstructions (GENREs) are valuable for understanding cellular metabolism in silico. Several tools exist for automatic GENRE generation. However, these tools frequently (i) do not readily integrate with some of the widely-used suites of packaged methods available for network analysis, (ii) lack effective network curation tools, (iii) are not sufficiently user-friendly, and (iv) often produce low-quality draft reconstructions.

Results

Here, we present Reconstructor, a user-friendly, COBRApy-compatible tool that produces high-quality draft reconstructions with reaction and metabolite naming conventions that are consistent with the ModelSEED biochemistry database and includes a gap-filling technique based on the principles of parsimon

SUBMITTER: Jenior ML 

PROVIDER: S-EPMC10275916 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature