ROS Models and Data for NPJ Systems Biology and Application (A. Kolodkin, R.P. Sharma, A.M. Colangelo, H.V. Westerhoff et al, NPJ SBA 2020)
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SEEK ID: https://fairdomhub.org/studies/768
ROS networks: designs, aging, Parkinson's disease and precision therapies
Projects: Make Me My Model, ROS detailed model for MSB manucript, Service to LCSB (Luxembourg) with respect to ROS management in Parkinso..., Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW)
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Created: 10th Jul 2020 at 18:05
Last updated: 10th Jul 2020 at 18:28
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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: Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), EraCoBiotech 2 nd call proposal preparation, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
Institutions: VU University Amsterdam, Universitat Rovira i Virgili
https://orcid.org/0000-0001-9103-9127
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.
A study of the systems biology of innate immunity
Projects: Make Me My Model
Web page: http://sysba.nl
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
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
This is the FAIRDOM hub for the Make Me My Model part of ISBE.NL. Various models for ISDBE.NL clients are stored here.
Programme: Innate immunity
Public web page: http://isbe.nl/
We are modelling ROS management and mitochondrial dysfunction. Mitochondria produce both energy and reactive oxygen species (ROS), and suffer from ROS. Experimental data from University Milan-Bicocca.
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
To obtain each of the figure 2A - 2E please download "Main Figure Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
To obtain each of the figure 4A - 4D please download "Main Figure 4 Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Note: "FigSM.A.1_Model-A.cps" corresponds to "SM-A-no design FigSM.A.1_Model-A.cps" in Suppl. Inform.
Creator: Alexey Kolodkin
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creator: Alexey Kolodkin
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
To obtain each of the figure 2A - 2E please download "Main Figure Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Not specified
Model format: SBML
Environment: Not specified
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Not specified
Model format: Not specified
Environment: Not specified
This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.
Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. ...
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.
Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. ...
Creators: Hans V. Westerhoff, Raju Prasad Sharma, Alexey Kolodkin
Submitter: Hans V. Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Creator: Alexey Kolodkin
Submitter: Alexey Kolodkin
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: JWS Online
Abstract (Expand)
Authors: A. N Kolodkin, R. P. Sharma, A. M. Colangelo, A. Ignatenko, F. Martorana, D. Jennen, J. J. Briede, N. Brady, M. Barberis, T. D. G. A. Mondeel, M. Papa, V. Kumar, B. Peters, A. Skupin, L. Alberghina, R. Balling, H. V. Westerhoff
Date Published: 26th Oct 2020
Publication Type: Journal
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
