How to calculate pair-wise similarity?
Owing to the fact that drug nodes are linked to each other by their pair-wise similarity, there are quite a large number of methods to calculate a similarity score between two drugs pairs. To name a few: similarity between two drug-induced gene expressions, two chemical structures, set of side effects, set of targets, etc. For each similarity measure, various methods exist to calculate a numerical score to represent the similarity distance between two drugs.
The unavailability of specific similarity metrics in a homogeneous drug network, which may limit the use of such graph based models.
Felt obliged to add few references:
- F. Iorio, et al. Discovery of drug mode of action and drug repositioning from transcriptional responses. Proceedings of the National Academy of Sciences, 107(33):14621-14626, 2010.
- M. Campillos, et al. Drug target identification using side-effect similarity. Science, 321(5886):263-266, 2008. doi: 10.1126/science.1158140.
- L. Perlman, et al. Combining drug and gene similarity measures for drug-target elucidation. Journal of computational biology, 18(2):133-145, 2011. doi: 10.1089/cmb.2010.0213.
As the third year group project, me and my colleagues (Shazan, Maheshya, Ruwan and Naduni) implemented a sensor based mobile viewer which is able to interact with any remotely deployed virtual environment in real time. The papers we published addressing the design challenges, can be found under the "publications" tab. Our product now serves as a virtual nautical telescope for Vidusayura maritime learning environment. More information can be found here. This project is affiliated with the Modelling and Simulation group at University of Colombo School of Computing.
Radar Simulation for Virtual Maritime Environments
Affiliated with Sri Lanka Navy and University of Colombo School of Computing, Me and my colleagues (Shazan, Maheshya, Ruwan and Naduni) collaboratively contributed to the project of researching and developing a light-weight radar simulation for virtual maritime environments. The virtual radar, as we call it, is capable of detecting obstacles that fall within a particular radius of the ship which is navigated inside the virtual environment. Although we've taken a very light-weight approach, the algorithm used in the virtual radar does simulate the electromagnetic wave propagation of an actual radar system. Its mother project, Vidusayura, is funded by the National Research Council Sri Lanka.