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

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DOI: 10.15490/fairdomhub.1.investigation.399.3

Created at: 20th Jul 2020 at 18:13

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

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.

Main Figure 2 Excel files

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  • Main Figure 2 Excel files.zip

Main Figure 2 COPASI

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.

  • Main Figure 2 COPASI.zip

Main Figure 3

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Figure-3_Detailed Model Diagram

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

Main Figure 4

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.

Data-Model_Menadione

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  • Menadione_fit_20200509.xlsx

Data_Models_ATP_mRNA

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  • Data_Models_ATP_and_mRNA_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: 458dde6bbd8a0e96639ec0eccf643c10

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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.399.3
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Snapshot 4 (20th Jul 2020) DOI
Snapshot 3 (20th Jul 2020) DOI
Snapshot 2 (16th Jul 2020) DOI
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Created: 20th Jul 2020 at 18:13

Last updated: 20th Jul 2020 at 18:14

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