khmer: Working with Big Data in Bioinformatics

We introduce design and optimization considerations for the 'khmer' package.Comment: Invited chapter for forthcoming book on Performance of Open Source Application

Efficient deep processing of japanese

We present a broad coverage Japanese grammar written in the HPSG formalism with MRS semantics. The grammar is created for use in real world applications, such that robustness and performance issues play an important role. It is connected to a POS tagging and word segmentation tool. This grammar is being developed in a multilingual context, requiring MRS structures that are easily comparable across languages

A Reference Interpreter for the Graph Programming Language GP 2

GP 2 is an experimental programming language for computing by graph transformation. An initial interpreter for GP 2, written in the functional language Haskell, provides a concise and simply structured reference implementation. Despite its simplicity, the performance of the interpreter is sufficient for the comparative investigation of a range of test programs. It also provides a platform for the development of more sophisticated implementations.Comment: In Proceedings GaM 2015, arXiv:1504.0244

A Language and Toolset for the Synthesis and Efficient Simulation of Clock-Cycle-True Signal-Processing Algorithms

Optimal simulation speed and synthesizability are contradictory requirements for a hardware description language. This paper presents a language and toolset that enables both synthesis and fast simulation of fixed-point signal processing algorithms at the register-transfer level using a single system description. This is achieved by separate code generators for different purposes. Code-generators have been developed for fast simulation (using ANSI-C) and for synthesis (using VHDL). The simulation performance of the proposed approach has been compared with other known methods and turns out to be comparable in speed to the fastest among them