This is the README for model published in the following paper:


Hemalatha Sasidharakurup, and Shyam Diwakar. "Computational modelling of TNFα related pathways regulated by neuroinflammation, oxidative stress and insulin resistance in neurodegeneration." Applied Network Science 5 (2020): 1-21. Acccessible at https://appliednetsci.springeropen.com/articles/10.1007/s41109-020-00307-w

Major pathways focuses on TNFα related pathways regulated by neuroinflammation, oxidative stress and insulin
resistance in Alzheimer's (AD)and Parkinson's disease (PD) conditions have been modelled using biochemical systems theory. Some of the common cellular components found in both AD and PD, that trigger TNFα signalling such as Aβ, αS, tau phosphorylation, calcium, glutamate etc. have included in the model. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. 

Last updated 03-April-2020
Developed by : Hemalatha Sasidharakurup & Shyam Diwakar    
Mind Brain Center, Amrita Vishwa Vidyapeetham, India.
Email: [email protected], [email protected]
www.amrita.edu/compneuro 


How to run the code
===================

1. Download the given code and save the file in a folder.

2. Load the file in CellDesigner (http://www.celldesigner.org/).

3. To reconstruct our graphs, copy and paste each pathway reactions into a new window in CellDesigner.

4. Set the initial values for each reactant as given in the paper.

5. Go to Simulations, select ControlPanel and click "execute" button to run the simulation.   
   A graph will be produced for each pathway.

6. One may have to rearrange the species in CellDesigner by dragging it manually, to have the look and feel of the pathway as published at https://appliednetsci.springeropen.com/articles/10.1007/s41109-020-00307-w.