ArticleBioinformatics (Oxford, England)2016
AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed.
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- Combined Isotopic Tracer and Modelling Approach Reveals Differences in Nitrogen Metabolism in S. cerevisiae, S. uvarum and S. kudriavzevii Species.Microbial biotechnology · 2025Article
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- A machine learning-based prognostic model integrating mRNA stemness index, hypoxia, and glycolysis‑related biomarkers for colorectal cancer.Open medicine (Warsaw, Poland) · 2025Article
- Microbiological hazards associated with the use of water in the post-harvest handling and processing operations of fresh and frozen fruits, vegetables and herbs (ffFVH). Part 2 - A dynamic mass balance model for handling and processing operations in ffFVH using water.EFSA journal. European Food Safety Authority · 2025Article
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- Mechanisms ofInternational journal of molecular sciences · 2023Article
- A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated with Cold Tolerance in Saccharomyces kudriavzevii.Microbiology spectrum · 2023Article
- Modelling the physiological status of yeast during wine fermentation enables the prediction of secondary metabolism.Microbial biotechnology · 2023Article
- Modeling the growth dependence of Streptococcus thermophilus and Lactobacillus bulgaricus as a function of temperature and pH.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
- ASAS-NANP symposium: Mathematical Modeling in Animal Nutrition: The power of identifiability analysis for dynamic modeling in animal science:a practitioner approach.Journal of animal science · 2023Article
- Improving dynamic predictions with ensembles of observable models.Bioinformatics (Oxford, England) · 2023Article
- Optimization of parameters in coherent spin dynamics of radical pairs in quantum biology.PloS one · 2023Article
- NLoed: A Python Package for Nonlinear Optimal Experimental Design in Systems Biology.ACS synthetic biology · 2022Article
- MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling.BMC bioinformatics · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMany problems of interest in dynamic modeling and control of biological systems can be posed as non-linear optimization problems subject to algebraic and dynamic constraints. In the context of modeling, this is the case of, e.g. parameter estimation, optimal experimental design and dynamic flux balance analysis. In the context of control, model-based metabolic engineering or drug dose optimization problems can be formulated as (multi-objective) optimal control problems. Finding a solution to those problems is a very challenging task which requires advanced numerical methods.
resultsThis work presents the AMIGO2 toolbox: the first multiplatform software tool that automatizes the solution of all those problems, offering a suite of state-of-the-art (multi-objective) global optimizers and advanced simulation approaches. AVAILABILITY AND IMPLEMENTATION: The toolbox and its documentation are available at: sites.google.com/site/amigo2toolbox CONTACT: ebalsa@iim.csic.esSupplementary information: Supplementary data are available at Bioinformatics online.
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