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Parallellizing PsN for a non-dedicated and highly heterogeneous grid. Exprimo

Drug effects can vary considerably between patients and occasions. Pharmacometrics is the field where mathematical models based on biology, pharmacology, disease and physiology are used to describe and quantitate the interaction between drug and patient. Simulation based on these models is used to understand disease processes, to support drug development decisions, compare dosing strategies, to improve therapy with existing drugs, and to design studies of new drugs.

PsN 'Perl speaks NONMEM' - is an open source pharmacometrics software, developed at Uppsala university. It is used by all major pharmaceutical companies, in combination with the commercial software NONMEM. PsN implements computer intensive statistical methods, for example the bootstrap and stepwise model building procedures. For such methods to be practical it is necessary to use parallelization and distributed computing. Presently PsN supports this on dedicated grid and cluster systems. It is desirable, though, to extend this functionality to less tightly integrated and more heterogeneous computing setups ('cloud computing') that can be used without a heavy system administration overhead. The proposed project is to parallelize PsN for such an environment, using the setup of the consulting company Exprimo as an example. The parallelization solution needs to be platform independent (Windows, Linux, MacOS) and may involve technologies such as Dropbox for file transfer. One specific issue that has to be solved is the network latency time-delay in file transfer between the master and client nodes.

Uppdaterad  2010-02-26 15:36:27 av Maya Neytcheva.