ROS networks: designs, aging, Parkinson's disease and precision therapies
DownloadDOI: 10.15490/fairdomhub.1.investigation.399.3
Zenodo URL: None
Created at: 20th Jul 2020 at 16:13
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)
No description specified
Comprehensive model of ROS management
No description specified
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
Main Figure 1
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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 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.
Supplementary_Information_Data_Model_Archives
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Created: 20th Jul 2020 at 16:13
Last updated: 20th Jul 2020 at 16:14
