Community standards to facilitate development and address challenges in metabolic modeling

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

(2020) Gregory L. Medlock et al.   Cell Systems

SBML Level 3: an extensible format for the exchange and reuse of biological models

(2020) Sarah M Keating et al.   Molecular Systems Biology

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

FAIRsharing as a community approach to standards, repositories and policies

(2019) Susanna-Assunta Sansone et al.   NATURE BIOTECHNOLOGY

Ten quick tips for biocuration

(2019) Y. Amy Tang et al.   PLoS Computational Biology

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries

(2018) Shu Pan et al.   CURRENT OPINION IN BIOTECHNOLOGY

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Critical assessment of genome-scale metabolic networks: the need for a unified standard

(2015) A. Ravikrishnan et al.   BRIEFINGS IN BIOINFORMATICS

The evolution of standards and data management practices in systems biology

(2015) N. J. Stanford et al.   Molecular Systems Biology

Do genome-scale models need exact solvers or clearer standards?

(2015) A. Ebrahim et al.   Molecular Systems Biology

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

(2015) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

(2014) Frank T Bergmann et al.   BMC BIOINFORMATICS

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Minimum Information About a Simulation Experiment (MIASE)

(2011) Dagmar Waltemath et al.   PLoS Computational Biology

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols