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In the context of heterogneous computing, even though GPUs are the components of election due to both their intrinsically parallel nature and their flexibility, FPGAs are being investigated and experimented due to superior power efficiency on selected workloads While GPUs are the heterogeneous components of election due to both their intrinsically parallel nature and their flexibility, FPGAs are being...
In the coming years, human genome research will likely transform medical practices. Genome-wide association studies (GWAS) are an example of the research effort made to allowing scientists to identify genes involved in human disease, reaction to treatments or symptom severity. Indeed, the unique genetic profile of an individual and the knowledge of molecular basis of diseases are leading to the development...
N-Body simulation simulates the evolution of a system that is composed of N particles, where each element receives a force that is due to the interaction with all the other elements within the system. Usually, the influence of external physical forces, such as gravity, is involved too. This methodology is widely used in different fields that range from astrophysics, where it is used to study the interaction...
Smith-Waterman is a dynamic programming algorithm that plays a key role in the modern genomics pipeline as it is guaranteed to find the optimal local alignment between two strings of data. The state of the art presents many hardware acceleration solutions that have been implemented in order to exploit the high degree of parallelism available in this algorithm. The majority of these implementations...
The goal of reaching exascale computing is made especially challenging by the highly heterogeneous nature of modern platforms and the energy they consume. As compute nodes typically utilize multiple multi-core CPU and are increasingly equipped with PCIe based accelerators, both are contributing to an ever more dynamic power consumption. In our study we evaluate our target application on a variety...
Protein folding is the physical process by which a sequence of amino acids in a protein folds into its tertiary structure, which determines the functionality of the protein. The knowledge of this structure is crucial for the development of new pharmaceutical therapies. For this reason, many drug industries are interested in applying these kind of algorithms. There are various methods to perform this...
Custom hardware accelerators are widely used to improve the performance of software applications in terms of execution times and to reduce energy consumption. However the realization of an hardware accelerator and its integration in the final system is a difficult and error prone task. For this reason, both Industry and Academy are continuously developing Computer Aided Design (CAD) tools to assist...
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