DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

Motivation Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account. Results We developed DEMETER, a COBRA Toolbox extension, that enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the quality standards in the field, agreement with available experimental data, and refinement of pathways based on manually refined genome annotations. Availability DEMETER and tutorials are freely available at https://github.com/opencobra.

MOFA: Multi-Objective Flux Analysis for the COBRA Toolbox

Multi-objective Optimization (MO) is an important tool for quantitative examination of the trade-offs faced by biological organisms. Using genome-scale constraint-based models of metabolism (GSMs),Multi-Objective Flux Analysis (MOFA) allows MO analyses of trade-offs among key biological tasks. The leading software package for conducting a plethora of different types of constraint-based analyses using GSMs is the COBRA Toolbox for MATLAB. We have developed a new add-on tool for this toolbox using Normalized Normal Constraint (NNC) that performs MOFA for a number of objectives only limited by computation power (n≤10). This development will facilitate MOFA analyses by COBRA's large user base and allow greater multi-faceted examination of metabolic trade-offs in complicated biological systems. Availability and Implementation: The MOFA software is freely available for download from https://bbs.llnl.gov under the GPL v2 license. The program runs on MATLAB with the COBRA software on Windows, Linux, and MacOS. It includes a detailed manual explaining the input and output of a simulation, a listing of the code's functions, and an example MOFA run using a well-curated GSM model of E. coli.

EFMviz: A COBRA Toolbox Extension to Visualize Elementary Flux Modes in Genome-Scale Metabolic Models

Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1260) and large (human, Recon 2.2) genome-scale metabolic models. EFMviz is open-source and integrated into COBRA Toolbox. The analysis workflows used for the two use cases are detailed in the two tutorials provided with EFMviz along with the data used in this study.

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

MotivationThe application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.ResultsTo address this shortage, we created a comprehensive toolbox to model i) microbe-microbe and host-microbe metabolic interactions, and ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the COBRA Toolbox.AvailabilityThe Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.

Correction: BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases

Correction for ‘BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases’ by Oveis Jamialahmadi et al., Mol. BioSyst., 2016, DOI: 10.1039/c6mb00532b.

BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases

BiKEGG is a COBRA toolbox extension for (1) inferring reaction correspondences between the KEGG and BiGG databases, and (2) overlaying flux distributions on customized metabolic maps.