Computational Modelling of TNFa Pathway in Parkinson’s Disease – A Systems Theory Perspective
This is the README for model published in the following paper:
Hemalatha Sasidharakurup, Nair, L., Bhaskar, K., and Dr. Shyam Diwakar, “Computational Modelling of TNFa Pathway in Parkinson’s Disease - A Systems Theory Perspective”, in Proceedings of the 8th international conference on Complex Networks and their Applications, Lisbon, Portugal, 2019.
A computational model of mapping TNFa signalling in Parkinson's disease(PD) has been
developed to understand how it mediates glutamate excitotoxicity and
neuroinflammation leading to disease pathogenesis and progression. 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. The model allows
a qualitative analysis of PD and a key signalling pathways for evaluating PD treatment conditions
relating pathophysiology to molecular concentration changes recordable from biological
Last updated 03-April-2020
Developed by : Hemalatha Sasidharakurup, Lakshmi Nair, Kanishka Bhaskar & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita Vishwa Vidyapeetham, India.
Email: firstname.lastname@example.org, email@example.com
How to run the code
1. Download the given code and save the file in a folder.
2. Load the files 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 shown in the paper.