Thuy Duong Vu

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This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all(More)
This paper gives a correctness proof for the on-chip COMA cache coherence protocol that supports the Microgrid of microthreaded architecture, a multi-core architecture capable of integrating hundreds to hundreds of thousands of processors on single silicon chip. We use the Abstract State Machine (ASM) as a theoretical framework for the specification of the(More)
Motivation: Equipped with sophisticated biochemical measurement techniques we generate a massive amount of biomedical data that needs to be analyzed computationally. One long-standing challenge in automatic knowledge extraction is clustering. We seek to partition a set of objects into groups such that the objects within the clusters share common traits.(More)
Bergstra, Ponse and van der Zwaag introduced in 2003 the notion of orthogonal bisimulation equivalence on labeled transition systems. This equivalence is a refinement of branching bisimulation, in which consecutive tau’s (silent steps) can be compressed into one (but not zero) tau’s. The main advantage of orthogonal bisimulation is that it combines well(More)