πBUSS:a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked matching machinery for simulation of character evolution along phylogenies. Results: We present a flexible Monte Carlo simulation tool, called piBUSS, that employs the BEAGLE high performance library for phylogenetic computations within BEAST to rapidly generate large sequence alignments under complex evolutionary models. piBUSS sports a user-friendly graphical user interface (GUI) that allows combining a rich array of models across an arbitrary number of partitions. A command-line interface mirrors the options available through the GUI and facilitates scripting in large-scale simulation studies. Analogous to BEAST model and analysis setup, more advanced simulation options are supported through an extensible markup language (XML) specification, which in addition to generating sequence output, also allows users to combine simulation and analysis in a single BEAST run. Conclusions: piBUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Through different interfaces, piBUSS supports simulation studies ranging from modest endeavors for illustrative purposes to complex and large-scale assessments of evolutionary inference procedures. The software aims at implementing new models and data types that are continuously being developed as part of BEAST/BEAGLE.Comment: 13 pages, 2 figures, 1 tabl

Early aspects: aspect-oriented requirements engineering and architecture design

This paper reports on the third Early Aspects: Aspect-Oriented Requirements Engineering and Architecture Design Workshop, which has been held in Lancaster, UK, on March 21, 2004. The workshop included a presentation session and working sessions in which the particular topics on early aspects were discussed. The primary goal of the workshop was to focus on challenges to defining methodical software development processes for aspects from early on in the software life cycle and explore the potential of proposed methods and techniques to scale up to industrial applications

A Model-Driven Engineering Approach for ROS using Ontological Semantics

This paper presents a novel ontology-driven software engineering approach for the development of industrial robotics control software. It introduces the ReApp architecture that synthesizes model-driven engineering with semantic technologies to facilitate the development and reuse of ROS-based components and applications. In ReApp, we show how different ontological classification systems for hardware, software, and capabilities help developers in discovering suitable software components for their tasks and in applying them correctly. The proposed model-driven tooling enables developers to work at higher abstraction levels and fosters automatic code generation. It is underpinned by ontologies to minimize discontinuities in the development workflow, with an integrated development environment presenting a seamless interface to the user. First results show the viability and synergy of the selected approach when searching for or developing software with reuse in mind.Comment: Presented at DSLRob 2015 (arXiv:1601.00877), Stefan Zander, Georg Heppner, Georg Neugschwandtner, Ramez Awad, Marc Essinger and Nadia Ahmed: A Model-Driven Engineering Approach for ROS using Ontological Semantic

Distribution pattern-driven development of service architectures

Distributed systems are being constructed by composing a number of discrete components. This practice is particularly prevalent within the Web service domain in the form of service process orchestration and choreography. Often, enterprise systems are built from many existing discrete applications such as legacy applications exposed using Web service interfaces. There are a number of architectural configurations or distribution patterns, which express how a composed system is to be deployed in a distributed environment. However, the amount of code required to realise these distribution patterns is considerable. In this paper, we propose a distribution pattern-driven approach to service composition and architecting. We develop, based on a catalog of patterns, a UML-compliant framework, which takes existing Web service interfaces as its input and generates executable Web service compositions based on a distribution pattern chosen by the software architect

Integration and verification of parameterized register interfaces

Abstract. This thesis takes an in-depth look on parameterized register models, their generation and use. The aim is to discover improvements to the current method of generating parameterized register models. The thesis is divided into two halves: a practical section that consists of a study on the generation of parameterized register models, and a theory section that supports the topics gone over in the practical section. The practical section studied the generation flow and tools currently used at Nordic Semiconductor. The flow was analyzed to discover changes that would enable the generation of more flexible parameterized register models. The suggested changes were then used to generate a dynamic register model for a highly configurable intellectual property (IP) core. The register model was validated using a register test sequence and functional tests. Finally, the functionality of the generated register model was compared to a manually implemented model. In the end, the test sequences and functional tests passed without errors. The generated register model could be configured directly from the testbench without editing the model manually. This also meant that the applied configurations would not be lost even if the register model were to be regenerated. The resulting register model was significantly more flexible than the previous generated models.Parametrisoitujen rekisterirajapintojen integrointi ja verifiointi. Tiivistelmä. Tässä opinnäytetyössä tutustutaan parametrisoituihin rekisterimalleihin, niiden generointiin, ja niiden käyttöön. Tavoitteena on löytää parannuksia nykyiseen parametrisoitujen rekisterimallien generointitapaan. Opinnäytetyö on jaettu kahteen puoliskoon: käytännön osuuteen, joka koostuu parametrisoitujen rekisterimallien tutkimuksesta, ja teoreettisesta osuudesta, joka tukee käytännön osuudessa käsiteltyjä aiheita. Käytännön osuus tutki Nordic Semiconductorilla tällä hetkellä rekisterimallin generointiin käytettyjä prosesseja ja työkaluja. Niitä analysoimalla pyrittiin löytämään muutoksia, joiden avulla voisi generoida joustavampia parametrisoituja rekisterimalleja. Kyseisten muutosten avulla generoitiin sitten dynaaminen rekisterimalli IP lohkolle, joka sisältää paljon konfiguroitavia parametrejä. Generoitu malli varmennettiin rekisterien testisekvenssillä ja toiminnallisilla testeillä. Lopuksi rekisterimallin toiminnallisuutta verrattiin käsin kirjoitetun rekisterimallin toiminnallisuuteen. Testisekvenssi ja toiminnalliset testit läpäistiin simuloinnissa lopulta ilman virheitä. Generoitu rekisterimalli oli konfiguroitavissa suoraan testipenkistä, eikä sitä tarvinnut muokata manuaalisesti. Tämä tarkoitti myös sitä, että testipenkissä asetettuja konfiguraatioita ei menetetä, jos rekisterimalli generoidaan uudelleen. Lopullinen rekisterimalli oli merkittävästi joustavampi kuin aikaisemmat generoidut mallit

A Distributed Economics-based Infrastructure for Utility Computing

Existing attempts at utility computing revolve around two approaches. The first consists of proprietary solutions involving renting time on dedicated utility computing machines. The second requires the use of heavy, monolithic applications that are difficult to deploy, maintain, and use. We propose a distributed, community-oriented approach to utility computing. Our approach provides an infrastructure built on Web Services in which modular components are combined to create a seemingly simple, yet powerful system. The community-oriented nature generates an economic environment which results in fair transactions between consumers and providers of computing cycles while simultaneously encouraging improvements in the infrastructure of the computational grid itself.Comment: 8 pages, 1 figur

Reactive Rules for Emergency Management

The goal of the following survey on Event-Condition-Action (ECA) Rules is to come to a common understanding and intuition on this topic within EMILI. Thus it does not give an academic overview on Event-Condition-Action Rules which would be valuable for computer scientists only. Instead the survey tries to introduce Event-Condition-Action Rules and their use for emergency management based on real-life examples from the use-cases identified in Deliverable 3.1. In this way we hope to address both, computer scientists and security experts, by showing how the Event-Condition-Action Rule technology can help to solve security issues in emergency management. The survey incorporates information from other work packages, particularly from Deliverable D3.1 and its Annexes, D4.1, D2.1 and D6.2 wherever possible