Application of software engineering to biomedicine

• Main Author: Ng, Clement Zheng Yang
• Other Authors: Zheng Jie
• Format: Final Year Project
• Language: English
• Published: 2014
• Subjects: DRNTU::Engineering::Computer science and engineering
• Online Access: http://hdl.handle.net/10356/61932
• Institution: Nanyang Technological University

The application of software engineering technique to biomedicine complements the biomedical process. Biological systems are extremely complex reactive systems that require a lot of analysis and comprehension. The use of formal methods can be beneficial for gaining new biological insights and experimental avenues. The model created could be analysed by model checking. This research was done to find out more about the use of PRISM, a probabilistic model checker to model signaling pathways and to study the drug effect by simulating perturbation on the network system. Results obtained from the model checker were evaluated to learn more about the system. A significant part of the project focused on speeding up the time needed for the computations by testing for the best combinations possible. By switching to better hardware workstations significant increased the model checking rate. The usage of the sparse engine instead of the default hybrid engine helped to reduce the model checking time required by 45% on average. The power linear equation method had a slight speed up in comparison to other methods while the memory usages between methods are about the same. It can be observed that the knock out of Sos does not have an influence on the model and therefore could be considered when a speed up in computation is required. The results and observations in this report hope to contribute a better understand on how to use the PRISM model checker and learn more about Fibroblast Growth Factor pathway to be useful to future research.