Charlotte Herzeel

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Coordination languages for ad hoc networks with a fluid topology do not offer adequate support to detect and deal with device disconnection. Such a disconnection is particularly relevant if the device provided context information rather than emitting messages, as such context information then becomes invalid. This paper proposed the Fact Space Model which(More)
Some program concerns cannot be cleanly modularized, and their implementation leads to code that is both hard to understand and maintain. In this paper we consider extending an e-commerce application, written in CLOS, with two of such crosscutting concerns. Though most of the time Common Lisp's macro facilities and CLOS' method combinations can be used to(More)
Aspects based on join points that occurred in the execution history of a program provide a powerful way to make applications aware of their context. We present HALO, a logic metaprogramming approach based on temporal logic, that is designed with context-awareness in mind. A number of illustrative examples demonstrate HALO's expressivity, including(More)
MOTIVATION Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine. RESULTS We present Halvade, a framework that enables sequencing pipelines to be executed in parallel on a(More)
Software transactional memory (STM) is a promising approach for coordinating concurrent threads, for which many implementation strategies are currently being researched. Although some first steps exist to ease experimenting with different strategies, this still remains a relatively complex and cumbersome task. The reason is that software transactions(More)
While most approaches to automatic parallelization focus on compilation approaches for parallelizing loop iterations, we advocate the need for new virtual machines that can parallelize the execution of recursive programs. In this paper, we show that recursive programs can be effectively parallelized when arguments to procedures are evaluated concurrently(More)
Software transactional memory (STM) is a promising approach for coordinating concurrent threads, for which many different implementation strategies are currently being researched. In this paper we show that if a language implementation provides reflective access to explicit memory locations, it becomes straightforward to both (a) build a STM framework for(More)
elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software(More)
Acknowledgements This document would not be what it is today without the outstanding support of various people. First of all we would like to thank professor Theo D'Hondt for promoting this thesis and giving us the opportunity to conduct our apprenticeship at the Programming Technology Lab. Furthermore, special thanks go to our advisors Stijn Mostinckx and(More)