This computational systems biology programme “Mechanistic modelling of health and epidemiology” is a DST/NRF (Department of Science and Technology/National Research Foundation) funded SARChI (South African Research Chair Initiative) project. The research chair holder Jacky Snoep, and co-Pi Dawie van Niekerk, are hosted at the Biochemistry department at Stellenbosch University and at SACEMA (South African Centre for Epidemiological Modelling and Analysis).
The SARChI project uses the FAIRDOMHub for data and model management: SARCHI: Mechanistic modelling of health and epidemiology. It currently has 5 projects: Whole body modelling of glucose metabolism in malaria patients, Glucose metabolism in cancer cell lines, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications.
Example project
Whole body modelling of glucose metabolism in malaria patients
The aim of this project is to quantify metabolic contributions to the dysregulation of glucose homeostasis in malaria patients. For these patients, hypoglycaemia and lactic acidosis are key diagnostics for poor chances of survival. The approach is to start with detailed bottom up models for the malaria parasite, Plasmodium falciparum, and then merge these with more coarse grained models at the whole body level.
Features
Data and scripts used for model construction, validation and analyses are provided in the project ISA structure on FAIRDOMHub, together with model SBML files that can be directly simulated in JWS Online from within FAIRDOMHub. Where applicable, SEDML links are also provided to reproduce published simulations in real-time on JWS Online. These simulations also retrieve data directly from FAIRDOMHub to show simulation results with data on the reproduced figures.
More information
Current project assets include 22 Data Files, 34 Models, 17 SOPs and 3 Publications. For more information, please see the SARCHI: Mechanistic modelling of health and epidemiology page on FAIRDOMHub.