LibSBML: an API Library for SBML

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The Reactome pathway Knowledgebase

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The Reactome pathway knowledgebase

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COBRApy: COnstraints-Based Reconstruction and Analysis for Python

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

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Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

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BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

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MEMOTE for standardized genome-scale metabolic model testing

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OptFlux: an open-source software platform for in silico metabolic engineering

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RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

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Genome-scale models of bacterial metabolism: reconstruction and applications

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Predicting perturbation patterns from the topology of biological networks

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gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

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Controlled vocabularies and semantics in systems biology

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Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

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

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Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

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Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

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Snoopy – A Unifying Petri Net Tool

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Proceedings of the 2017 Winter Simulation Conference

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Pathway databases and tools for their exploitation: benefits, current limitations and challenges

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Path2Models: large-scale generation of computational models from biochemical pathway maps

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The Physiome Model Repository 2

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Revealing disease-associated pathways by network integration of untargeted metabolomics

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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

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Tellurium: An extensible python-based modeling environment for systems and synthetic biology

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Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism

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libRoadRunner: a high performance SBML simulation and analysis library

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Towards programming languages for genetic engineering of living cells

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MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

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GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models

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Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

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sybil – Efficient constraint-based modelling in R

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Antimony: a modular model definition language

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iBioSim: a tool for the analysis and design of genetic circuits

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Further developments towards a genome-scale metabolic model of yeast

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Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

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Cooperative development of logical modelling standards and tools with CoLoMoTo

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Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium

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Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

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Fine‐tuning the P. pastoris iMT1026 genome‐scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources

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SynBioSS: the synthetic biology modeling suite

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Software support for SBGN maps: SBGN-ML and LibSBGN

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GPU accelerated biochemical network simulation

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StochPy: A Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes

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Flux balance analysis: A geometric perspective

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An overview of the CellML API and its implementation

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JSBML: a flexible Java library for working with SBML

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AMICI: high-performance sensitivity analysis for large ordinary differential equation models

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Harmonizing semantic annotations for computational models in biology

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Random sampling of elementary flux modes in large-scale metabolic networks

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BioModels: Content, Features, Functionality, and Use

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Integrating systems biology models and biomedical ontologies

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Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris

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Modeling and simulation of atrazine biodegradation in bacteria and its effect in other living systems

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Designing and encoding models for synthetic biology

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Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

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Improving Collaboration by Standardization Efforts in Systems Biology

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AutoBioCAD: Full Biodesign Automation of Genetic Circuits

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Large-Scale Metabolic Models: From Reconstruction to Differential Equations

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A Liver-Centric Multiscale Modeling Framework for Xenobiotics

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FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2

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Memote: A community driven effort towards a standardized genome-scale metabolic model test suitePreprint

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In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology.

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von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models

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Defining the nutritional input for genome-scale metabolic models: A roadmap

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Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

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Metabolic Cancer Biology: Structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment

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Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion

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libRoadRunner 2.0: a high performance SBML simulation and analysis library

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Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis

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PSAMM: A Portable System for the Analysis of Metabolic Models

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COBRA Toolbox 2.0

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MitoCore: a curated constraint-based model for simulating human central metabolism

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A genome‐scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost–benefit of nitrogen fixation

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An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

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MEMOSys: Bioinformatics platform for genome-scale metabolic models

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