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Title: 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 parsimony. Reconstructor can generate SBML GENREs from three input types: annotated protein .fasta sequences (Type 1 input), a BLASTp output (Type 2), or an existing SBML GENRE that can be further gap-filled (Type 3). While Reconstructor can be used to create GENREs of any species, we demonstrate the utility of Reconstructor with bacterial reconstructions. We demonstrate how Reconstructor readily generates high-quality GENRES that capture strain, species, and higher taxonomic differences in functional metabolism of bacteria and are useful for further biological discovery.

Availability and implementation

The Reconstructor Python package is freely available for download. Complete installation and usage instructions and benchmarking data are available at http://github.com/emmamglass/reconstructor.

 
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NSF-PAR ID:
10423113
Author(s) / Creator(s):
; ; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
Bioinformatics
Volume:
39
Issue:
6
ISSN:
1367-4811
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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We used a variety of techniques such as the file locking mechanism, multithreading, circular buffers, real-time event decoding, and signal-decision plotting to realize the system. A video demonstrating the system is available at: https://www.isip.piconepress.com/projects/nsf_pfi_tt/resources/videos/realtime_eeg_analysis/v2.5.1/video_2.5.1.mp4. The final conference submission will include a more detailed analysis of the online performance of each module. ACKNOWLEDGMENTS Research reported in this publication was most recently supported by the National Science Foundation Partnership for Innovation award number IIP-1827565 and the Pennsylvania Commonwealth Universal Research Enhancement Program (PA CURE). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the official views of any of these organizations. REFERENCES [1] A. Craik, Y. He, and J. L. 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