Construction of differential equation model to decribe COVID-19 epidemics
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Governments and policymakers take different measures vis-à-vis the COVID-19 crisis, ranging from advice to reduce social activities, to a complete lock down of society and economy. To support them with tools that enable them to fulfill their tasks we constructed a differential equation model for the COVID-19 epidemics using systems biology methodologies.
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Created: 24th Mar 2020 at 12:38
Last updated: 3rd Apr 2020 at 13:17
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Projects: SulfoSys, FAIRDOM user meeting, Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
Institutions: University of Amsterdam, VU University Amsterdam, Infrastructure Systems Biology Europe, University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB)
I have modelling expertise in precise kinetic models of metabolism and signal transduction; metabolic control analysis, hierarchical regulation analysis, non-equilibrium dynamics, statistical mechanics, enzyme kinetics, flux balance analysis. Energy and carbohydrate metabolism in Archaea, Bacteria and human; ammonium assimilation in Bacteria; differential network-based drug design; cancer metabolic rewiring; cell cycle; genome wide metabolic map and inborn errors of metabolism; epigenetics.
Projects: SysMO-LAB, MOSES, PSYSMO, SulfoSys, SulfoSys - Biotec, EraCoBiotech 2 nd call proposal preparation, Make Me My Model, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, Xenophiles Systems Biology, Thermodynamics, Non equilibrium thermodynamics, Book on Thermodynamics, and kinetics, Teaching Alien Biology, Outdated material, Fusion-fission-mitophagy, Stochastics and bursting
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, VU University Amsterdam, University of Amsterdam, Systems Biology Amsterdam
https://orcid.org/0000-0002-0443-6114
Systems Biologist at University of Amsterdam, Free University Amsterdam, University of Manchester, Infrastructure Systems Biology.NL (ISBE.NL), Systems Biology Amsterdam.
ISBE-Light provides M4 service (Make Me My Mode) where non modelers can request (assistance with) the making of a computational model of their biological system. These models are deposited here.
Projects: Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population
Web page: http://www.isbe.nl
Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Corona virus epidemic. The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that ...
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Start date: 1st Mar 2020
End date: 24th Mar 2023
We examined whether such a lockdown could be intermitted with periods with normal social contact, without endangering the success of the strategy.
Submitter: Alexey Kolodkin
Investigation: Construction of differential equation model to ...
please add your model here - associated to this assay
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: Construction of differential equation model to ...
Creators: Alexey Kolodkin, Hans V. Westerhoff
Submitter: Alexey Kolodkin
This Excel file contains lists of model (Comprehensive model for COVID-19) reactions and species in table format Comprehensive model for COVID-19 coused by SARS-CoV-2
Creators: Alexey Kolodkin, Hans V. Westerhoff
Submitter: Alexey Kolodkin
This file contains description of all model parameters and corresponding references
Creators: Alexey Kolodkin, Hans V. Westerhoff
Submitter: Alexey Kolodkin
Model building:
The module was built using modular bottom-up approach where every module describes a certain process and then, when modules are connected together like domino tiles, we can reconstruct the emergent behavior of the whole system.
This is a blueprint model and might be used for various country/data. If one wans to use it for a particular country/data, we can recommend following steps:
- Adjust total population by changing initial condition of A-Initial_population_innocent_non-tested ...
Creators: Alexey Kolodkin, Hans V. Westerhoff
Submitter: Alexey Kolodkin
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Abstract (Expand)
Authors: Hans V. Westerhoff, Alexey N. Kolodkin
Date Published: 1st Dec 2020
Publication Type: Journal
Creators: Alexey Kolodkin, Hans V. Westerhoff
Submitter: Alexey Kolodkin
The model is also available on JWS Online (https://jjj.bio.vu.nl/models/westerhoff1/simulate). Here you can find instructions how to write it there.
Creator: Alexey Kolodkin
Submitter: Alexey Kolodkin
