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

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DOI: 10.15490/fairdomhub.1.investigation.399.1

Created at: 13th Jul 2020 at 02:09

Contents

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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Comprehensive model of ROS management

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Calibrated comprehensive model of ROS management

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.
...

  • Calibrated_Comprehensive_model_D'.cps
  • Comprehensive ROS model picture.png

Calibrated comprehensive model of ROS management Improved

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.
...

  • Menadione_fit_20200509.cps
  • Menadione_fit_20200509.xml
  • detailed diagram improved May9 2019-19.40.png

Detailed model of ROS management

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  • Detailed model fitted -Steady State.cps

Main Figure 1

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Main Figure 1

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  • MainFigure_ 1_2020.png

Main Figure 2

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Main Figure 2 Excel files

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  • Main Figure 2 Excel files.zip

Main Figure 2 COPASI

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  • Main Figure 2 COPASI.zip

Main Figure 3

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Main Figure 3

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  • Fig_3_Detailed_model_High_Resolution_2019.05.21.pdf

Main Figure 4

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Main Figure 4 Excel data

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  • Menadione_fit_20200509.xlsx

Main Figure 4 Models_Copasi

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  • Main Figure 4 Models_Copasi.zip

Main Figure 4 Image

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  • Main_Figure_4_2020_pdf.pdf

Supplementary_Information_Data_Model_Archives

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Section A

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  • Data_Model_Archives_SM.A.zip

Section B1

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  • Data_Model_Archives_SM.B1.zip

Section B2A

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  • Data_Model_Archives_SM.B2A.zip

Section B2B

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  • Data_Model_Archives_SM.B2B.zip

Section B3

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  • Data_Model_Archives_SM.B3.zip

Section B4

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  • Data_Model_Archives_SM.B4.zip

Section B5

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  • Data_Model_Archives_SM.B5.zip

Section C

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  • Data_Model_Archives_SM.C.zip

Section D

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  • Data_Model_Archives_SM.D.zip

Section E

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  • Data_Model_Archives_SM.E.zip

Section F

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  • Data_Model_Archives_SM.F.zip

Section G

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  • Data_Model_Archives_SM.G.zip

Section H

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  • Data_Model_Archives_SM.H.zip

Section I

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  • Data_Model_Archives_SM.I.zip
Fingerprints

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MD5: 0ba91ddb8f3d648ca0f518226a205fb6

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Citation
Kolodkin, A., Westerhoff, H., & Sharma, R. P. (2020). ROS networks: designs, aging, Parkinson's disease and precision therapies. FAIRDOMHub. http://doi.org/10.15490/FAIRDOMHUB.1.INVESTIGATION.399.1
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Created: 13th Jul 2020 at 02:09

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