An interactive environment for solid modeling based on free software

This paper describes an interactive environment built entirely upon public domain or free software, intended to be used as the preprocessor of a finite element package for the simulation of three-dimensional electromagnetic problems.

Empacotamento de experimentos controlados em engenharia de software: uma abordagem baseada em ontologia

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Finestre di vulnerabilità e pacchetti software

I problemi di sicurezza nel software sono in crescita e gli strumenti di analisi adottati nei sistemi GNU/Linux non permettono di evidenziare le finestre di vulnerabilità a cui un pacchetto è stato soggetto. L'obiettivo di questa tesi è quello di sviluppare uno strumento di computer forensics in grado di ricostruire, incrociando informazioni ottenute dal package manager con security advisory ufficiali, i problemi di sicurezza che potrebbero aver causato una compromissione del sistema in esame.

Immunophenotyping of acute leukemia and lymphoproliferative disorders: a consensus proposal of the European LeukemiaNet Work Package 10

The European LeukemiaNet (ELN), workpackage 10 (WP10) was designed to deal with diagnosis matters using morphology and immunophenotyping. This group aimed at establishing a consensus on the required reagents for proper immunophenotyping of acute leukemia and lymphoproliferative disorders. Animated discussions within WP10, together with the application of the Delphi method of proposals circulation, quickly led to post-consensual immunophenotyping panels for disorders on the ELN website. In this report, we established a comprehensive description of these panels, both mandatory and complementary, for both types of clinical conditions. The reason for using each marker, sustained by relevant literature information, is provided in detail. With the constant development of immunophenotyping techniques in flow cytometry and related software, this work aims at providing useful guidelines to perform the most pertinent exploration at diagnosis and for follow-up, with the best cost benefit in diseases, the treatment of which has a strong impact on health systems.

Package Patterns for Visual Architecture Recovery

Recovering the architecture is the first step towards reengineering a software system. Many reverse engineering tools use top-down exploration as a way of providing a visual and interactive process for architecture recovery. During the exploration process, the user navigates through various views on the system by choosing from several exploration operations. Although some sequences of these operations lead to views which, from the architectural point of view, are mode relevant than others, current tools do not provide a way of predicting which exploration paths are worth taking and which are not. In this article we propose a set of package patterns which are used for augmenting the exploration process with in formation about the worthiness of the various exploration paths. The patterns are defined based on the internal package structure and on the relationships between the package and the other packages in the system. To validate our approach, we verify the relevance of the proposed patterns for real-world systems by analyzing their frequency of occurrence in six open-source software projects.

USING THE R PACKAGE crlmm FOR GENOTYPING AND COPY NUMBER ESTIMATION

Genotyping platforms such as Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations at millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools to assess copy number changes are more variable and often discordant. One explanation for the discordance is that copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. Analysis algorithms that do not adjust for batch effects are prone to spurious measures of association. The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number. This paper illustrates a workflow for the estimation of allele-specific copy number, develops markerand study-level summaries of batch effects, and demonstrates how the marker-level estimates can be integrated with complimentary Bioconductor software for inferring regions of copy number gain or loss. All analyses are performed in the statistical environment R. A compendium for reproducing the analysis is available from the author’s website (http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html).

Incorporating Latent Variables into Discrete Choice Models - A Simultaneous Estimation Approach Using SEM Software

Integrated choice and latent variable (ICLV) models represent a promising new class of models which merge classic choice models with the structural equation approach (SEM) for latent variables. Despite their conceptual appeal, applications of ICLV models in marketing remain rare. We extend previous ICLV applications by first estimating a multinomial choice model and, second, by estimating hierarchical relations between latent variables. An empirical study on travel mode choice clearly demonstrates the value of ICLV models to enhance the understanding of choice processes. In addition to the usually studied directly observable variables such as travel time, we show how abstract motivations such as power and hedonism as well as attitudes such as a desire for flexibility impact on travel mode choice. Furthermore, we show that it is possible to estimate such a complex ICLV model with the widely available structural equation modeling package Mplus. This finding is likely to encourage more widespread application of this appealing model class in the marketing field.

gems: An R Package for Simulating from Disease Progression Models

Mathematical models of disease progression predict disease outcomes and are useful epidemiological tools for planners and evaluators of health interventions. The R package gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome. Disease progression is represented by a series of events (e.g., diagnosis, treatment and death), displayed in a directed acyclic graph. The vertices correspond to disease states and the directed edges represent events. The package gems allows simulations based on a generalized multistate model that can be described by a directed acyclic graph with continuous transition-specific hazard functions. The user can specify an arbitrary hazard function and its parameters. The model includes parameter uncertainty, does not need to be a Markov model, and may take the history of previous events into account. Applications are not limited to the medical field and extend to other areas where multistate simulation is of interest. We provide a technical explanation of the multistate models used by gems, explain the functions of gems and their arguments, and show a sample application.

A software process improvement solution for small and medium-size enterprises

The focus of this paper is to outline the main structure of an alternative software process improvement method for small- and medium-size enterprises. This method is based on the action package concept, which helps to institutionalize the effective practices with affordable implementation costs. This paper also presents the results and lessons learned when this method was applied to three enterprises in the requirements engineering domain.

Using configuration management and product line software paradigms to support the experimentation process in software engineering.

There is no empirical evidence whatsoever to support most of the beliefs on which software construction is based. We do not yet know the adequacy, limits, qualities, costs and risks of the technologies used to develop software. Experimentation helps to check and convert beliefs and opinions into facts. This research is concerned with the replication area. Replication is a key component for gathering empirical evidence on software development that can be used in industry to build better software more efficiently. Replication has not been an easy thing to do in software engineering (SE) because the experimental paradigm applied to software development is still immature. Nowadays, a replication is executed mostly using a traditional replication package. But traditional replication packages do not appear, for some reason, to have been as effective as expected for transferring information among researchers in SE experimentation. The trouble spot appears to be the replication setup, caused by version management problems with materials, instruments, documents, etc. This has proved to be an obstacle to obtaining enough details about the experiment to be able to reproduce it as exactly as possible. We address the problem of information exchange among experimenters by developing a schema to characterize replications. We will adapt configuration management and product line ideas to support the experimentation process. This will enable researchers to make systematic decisions based on explicit knowledge rather than assumptions about replications. This research will output a replication support web environment. This environment will not only archive but also manage experimental materials flexibly enough to allow both similar and differentiated replications with massive experimental data storage. The platform should be accessible to several research groups working together on the same families of experiments.

Desarrollo de software de control y medida para goniofotómetro de tipo B

El proyecto trata del desarrollo de un software para realizar el control de la medida de la distribución de intensidad luminosa en luminarias LED. En el trascurso del proyecto se expondrán fundamentos teóricos sobre fotometría básica, de los cuales se extraen las condiciones básicas para realizar dicha medida. Además se realiza una breve descripción del hardware utilizado en el desarrollo de la máquina, el cual se basa en una placa de desarrollo Arduino Mega 2560, que, gracias al paquete de Labview “LIFA” (Labview Interface For Arduino”), será posible utilizarla como tarjeta de adquisición de datos mediante la cual poder manejar tanto sensores como actuadores, para las tareas de control. El instrumento de medida utilizado en este proyecto es el BTS256 de la casa GigaHerzt-Optik, del cual se dispone de un kit de desarrollo tanto en lenguaje C++ como en Labview, haciendo posible programar aplicaciones basadas en este software para realizar cualquier tipo de adaptación a las necesidades del proyecto. El software está desarrollado en la plataforma Labview 2013, esto es gracias a que se dispone del kit de desarrollo del instrumento de medida, y del paquete LIFA. El objetivo global del proyecto es realizar la caracterización de luminarias LED, de forma que se obtengan medidas suficientes de la distribución de intensidad luminosa. Los datos se recogerán en un archivo fotométrico específico, siguiendo la normativa IESNA 2002 sobre formato de archivos fotométricos, que posteriormente será utilizado en la simulación y estudio de instalaciones reales de la luminaria. El sistema propuesto en este proyecto, es un sistema basado en fotometría tipo B, utilizando coordenadas VH, desarrollando un algoritmo de medida que la luminaria describa un ángulo de 180º en ambos ejes, con una resolución de 5º para el eje Vertical y 22.5º para el eje Horizontal, almacenando los datos en un array que será escrito en el formato exigido por la normativa. Una vez obtenidos los datos con el instrumento desarrollado, el fichero generado por la medida, es simulado con el software DIALux, obteniendo unas medidas de iluminación en la simulación que serán comparadas con las medidas reales, intentando reproducir en la simulación las condiciones reales de medida. ABSTRACT. The project involves the development of software for controlling the measurement of light intensity distribution in LEDs. In the course of the project theoretical foundations on basic photometry, of which the basic conditions for such action are extracted will be presented. Besides a brief description of the hardware used in the development of the machine, which is based on a Mega Arduino plate 2560 is made, that through the package Labview "LIFA" (Interface For Arduino Labview "), it is possible to use as data acquisition card by which to handle both sensors and actuators for control tasks. The instrument used in this project is the BTS256 of GigaHerzt-Optik house, which is available a development kit in both C ++ language as LabView, making it possible to program based on this software applications for any kind of adaptation to project needs. The software is developed in Labview 2013 platform, this is thanks to the availability of the SDK of the measuring instrument and the LIFA package. The overall objective of the project is the characterization of LED lights, so that sufficient measures the light intensity distribution are obtained. Data will be collected on a specific photometric file, following the rules IESNA 2002 on photometric format files, which will then be used in the simulation and study of actual installations of the luminaire. The proposed in this project is a system based on photometry type B system using VH coordinates, developing an algorithm as the fixture describe an angle of 180 ° in both axes, with a resolution of 5 ° to the vertical axis and 22.5º for the Horizontal axis, storing data in an array to be written in the format required by the regulations. After obtaining the data with the instrument developed, the file generated by the measure, is simulated with DIALux software, obtaining measures of lighting in the simulation will be compared with the actual measurements, trying to play in the simulation the actual measurement conditions .

Using the R package Shiny to create web applications that facilitate quantitative gene expression analysis

Thesis (Master's)--University of Washington, 2016-06

XSophe, a computer simulation software suite for the analysis of electron paramagnetic resonance spectra

The XSophe computer simulation software suite consisting of a daemon, the XSophe interface and the computational program Sophe is a state of the art package for the simulation of electron paramagnetic resonance spectra. The Sophe program performs the computer simulation and includes a number of new technologies including; the SOPHE partition and interpolation schemes, a field segmentation algorithm, homotopy, parallelisation and spectral optimisation. The SOPHE partition and interpolation scheme along with a field segmentation algorithm greatly increases the speed of simulations for most systems. Multidimensional homotopy provides an efficient method for accurately tracing energy levels and hence tracing transitions in the presence of energy level anticrossings and looping transitions and allowing computer simulations in frequency space. Recent enhancements to Sophe include the generalised treatment of distributions of orientational parameters, termed the mosaic misorientation linewidth model and a faster more efficient algorithm for the calculation of resonant field positions and transition probabilities. For complex systems the parallelisation enables the simulation of these systems on a parallel computer and the optimisation algorithms in the suite provide the experimentalist with the possibility of finding the spin Hamiltonian parameters in a systematic manner rather than a trial-and-error process. The XSophe software suite has been used to simulate multifrequency EPR spectra (200 MHz to 6 00 GHz) from isolated spin systems (S > ~½) and coupled centres (Si, Sj _> I/2). Griffin, M.; Muys, A.; Noble, C.; Wang, D.; Eldershaw, C.; Gates, K.E.; Burrage, K.; Hanson, G.R."XSophe, a Computer Simulation Software Suite for the Analysis of Electron Paramagnetic Resonance Spectra", 1999, Mol. Phys. Rep., 26, 60-84.

Linking the witness simulation software to an expert system to represent a decision-making process

Expert systems, and artificial intelligence more generally, can provide a useful means for representing decision-making processes. By linking expert systems software to simulation software an effective means of including these decision-making processes in a simulation model can be achieved. This paper demonstrates how a commercial-off-the-shelf simulation package (Witness) can be linked to an expert systems package (XpertRule) through a Visual Basic interface. The methodology adopted could be used for models, and possibly software, other than those presented here.

A biography:fabrications in the life of an ERP package

This paper provides an account of the way Enterprise Resource Planning (ERP) systems change over time. These changes are conceptualized as a biographical accumulation that gives the specific ERP technology its present character, attributes and historicity. The paper presents empirics from the implementation of an ERP package within an Australasian organization. Changes to the ERP take place as a result of imperatives which arise during the implementation. Our research and evidence then extends to a different time and place where the new release of the ERP software was being 'sold' to client firms in the UK. We theorize our research through a lens based on ideas from actor network theory (ANT) and the concept of biography. The paper seeks to contribute an additional theorization for ANT studies that places the focus on the technological object and frees it from the ties of the implementation setting. The research illustrates the opportunistic and contested fabrication of a technological object and emphasizes the stability as well as the fluidity of its technologic. Copyright © 2007 SAGE.