Supplementary_Information_Data_Model_Archives

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SEEK ID: https://fairdomhub.org/assays/1317

Class: Modelling analysis

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)

Investigation: ROS networks: designs, aging, Parkinson's disease and precision therapies

Study: 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)

Assay position:

Biological problem addressed: Model Analysis Type

Organisms: No organisms

Data:

Section A
Section B1
Section B2A
Section B2B
Section B3
Section B4
Section B5
Section C
Section D
Section E
Section F
Section G
Section H
Section I

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Creators and Submitter

Creators

Alexey Kolodkin
Hans V. Westerhoff
Raju Prasad Sharma

Submitter

Alexey Kolodkin

Activity

Views: 1298

Created: 12th Jul 2020 at 23:37

Last updated: 13th Jul 2020 at 00:08

Related items

People (3)
Programmes (2)
Projects (4)
Investigations (1)
Studies (1)
Data files (14)

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Alexey Kolodkin

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, Systems Biomedicine Center, 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.

Raju Prasad Sharma

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

Expertise: PBPK modeling, Pharmacology, Pharmacokinetics, Mechanistic Modelling

Tools: R, Berkeley Madonna, Copasi, Cell designer

Hans V. Westerhoff

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, Thermotables for biochemistry, Thermotables

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

Expertise: Systems Biology, Thermodynamics, Biochemistry, Dynamic modelling, Mathematical modelling, Metabolic Engineering, Microbiology, Molecular Biology, standards

Tools: Computational Systems Biology, Dynamic modelling, Biochemistry

Systems Biologist at University of Amsterdam, Free University Amsterdam, University of Manchester, Infrastructure Systems Biology.NL (ISBE.NL), Systems Biology Amsterdam.

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Innate immunity

A study of the systems biology of innate immunity

Projects: Make Me My Model

Web page: http://sysba.nl

Model repository for M4 (Make Me My Model) clients of ISBE

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.

Web page: http://www.isbe.nl

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Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW)

No description specified

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

Organisms: Homo sapiens

ROS detailed model for MSB manucript

No description specified

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

Organisms: Homo sapiens

Make Me My Model

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/

Organisms: Not specified

Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW)

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

Organisms: Homo sapiens

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ROS networks: designs, aging, Parkinson's disease and precision therapies

Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), ROS detailed model for MSB manucript

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All creators

Alexey Kolodkin

Hans V. Westerhoff

Raju Prasad Sharma

No description specified