Publications (2)0 Total impact
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ABSTRACT: Nowadays, clinician can take advantage of insilico technologies to get faster estimations on clinical treatments without performing time-consuming and expansive invivo experimentations. Among these techniques, tumor growth simulators can estimate tumor volume and the quantity of cells (stem, proliferating...) in function of the time and from a set of parameters. Within the framework of the ACGT European project, we are working on the development of the ACGT Oncosimulator which is based on the mathematical model from ICCS. In this paper, we relate the current computation techniques for increasing the ACGT Oncosimulator efficiency.
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ABSTRACT: Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple seeds, subset seeds) provide better sensitivity/specificity ratios. We present an implementation of such a seed-based technique onto parallel specialized hardware embedding reconfigurable architecture (FPGA), where the FPGA is tightly connected to large capacity Flash memories. This parallel system allows large databases to be fully indexed and rapidly accessed. Compared to traditional approaches like the Blastp software, we obtain both significant speed-up and better results. As our knowledge, this is the first attempt to exploit modern seed features for parallelizing similarity search.
