MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

A design environment for deadlock-free concurrent software

Using current software engineering technology, the robustness required for safety critical software is not assurable. However, different approaches are possible which can help to assure software robustness to some extent. For achieving high reliability software, methods should be adopted which avoid introducing faults (fault avoidance); then testing should be carried out to identify any faults which persist (error removal). Finally, techniques should be used which allow any undetected faults to be tolerated (fault tolerance). The verification of correctness in system design specification and performance analysis of the model, are the basic issues in concurrent systems. In this context, modeling distributed concurrent software is one of the most important activities in the software life cycle, and communication analysis is a primary consideration to achieve reliability and safety. By and large fault avoidance requires human analysis which is error prone; by reducing human involvement in the tedious aspect of modelling and analysis of the software it is hoped that fewer faults will persist into its implementation in the real-time environment. The Occam language supports concurrent programming and is a language where interprocess interaction takes place by communications. This may lead to deadlock due to communication failure. Proper systematic methods must be adopted in the design of concurrent software for distributed computing systems if the communication structure is to be free of pathologies, such as deadlock. The objective of this thesis is to provide a design environment which ensures that processes are free from deadlock. A software tool was designed and used to facilitate the production of fault-tolerant software for distributed concurrent systems. Where Occam is used as a design language then state space methods, such as Petri-nets, can be used in analysis and simulation to determine the dynamic behaviour of the software, and to identify structures which may be prone to deadlock so that they may be eliminated from the design before the program is ever run. This design software tool consists of two parts. One takes an input program and translates it into a mathematical model (Petri-net), which is used for modeling and analysis of the concurrent software. The second part is the Petri-net simulator that takes the translated program as its input and starts simulation to generate the reachability tree. The tree identifies `deadlock potential' which the user can explore further. Finally, the software tool has been applied to a number of Occam programs. Two examples were taken to show how the tool works in the early design phase for fault prevention before the program is ever run.

A stylized software model to explore the free market equality/efficiency tradeoff

This paper provides an agent-based software exploration of the wellknown free market efficiency/equality trade-off. Our study simulates the interaction of agents producing, trading and consuming goods in the presence of different market structures, and looks at how efficient the producers/consumers mapping turn out to be as well as the resulting distribution of welfare among agents at the end of an arbitrarily large number of iterations. Two market mechanisms are compared: the competitive market (a double auction market in which agents outbid each other in order to buy and sell products) and the random one (in which products are allocated randomly). Our results confirm that the superior efficiency of the competitive market (an effective and never stopping producers/consumers mapping and a superior aggregative welfare) comes at a very high price in terms of inequality (above all when severe budget constraints are in play).

Value creation and value capture fro open source software publisher : a new business model based on mutualisation

Key topics: Since the birth of the Open Source movement in the mid-80's, open source software has become more and more widespread. Amongst others, the Linux operating system, the Apache web server and the Firefox internet explorer have taken substantial market shares to their proprietary competitors. Open source software is governed by particular types of licenses. As proprietary licenses only allow the software's use in exchange for a fee, open source licenses grant users more rights like the free use, free copy, free modification and free distribution of the software, as well as free access to the source code. This new phenomenon has raised many managerial questions: organizational issues related to the system of governance that underlie such open source communities (Raymond, 1999a; Lerner and Tirole, 2002; Lee and Cole 2003; Mockus et al. 2000; Tuomi, 2000; Demil and Lecocq, 2006; O'Mahony and Ferraro, 2007;Fleming and Waguespack, 2007), collaborative innovation issues (Von Hippel, 2003; Von Krogh et al., 2003; Von Hippel and Von Krogh, 2003; Dahlander, 2005; Osterloh, 2007; David, 2008), issues related to the nature as well as the motivations of developers (Lerner and Tirole, 2002; Hertel, 2003; Dahlander and McKelvey, 2005; Jeppesen and Frederiksen, 2006), public policy and innovation issues (Jullien and Zimmermann, 2005; Lee, 2006), technological competitions issues related to standard battles between proprietary and open source software (Bonaccorsi and Rossi, 2003; Bonaccorsi et al. 2004, Economides and Katsamakas, 2005; Chen, 2007), intellectual property rights and licensing issues (Laat 2005; Lerner and Tirole, 2005; Gambardella, 2006; Determann et al., 2007). A major unresolved issue concerns open source business models and revenue capture, given that open source licenses imply no fee for users. On this topic, articles show that a commercial activity based on open source software is possible, as they describe different possible ways of doing business around open source (Raymond, 1999; Dahlander, 2004; Daffara, 2007; Bonaccorsi and Merito, 2007). These studies usually look at open source-based companies. Open source-based companies encompass a wide range of firms with different categories of activities: providers of packaged open source solutions, IT Services&Software Engineering firms and open source software publishers. However, business models implications are different for each of these categories: providers of packaged solutions and IT Services&Software Engineering firms' activities are based on software developed outside their boundaries, whereas commercial software publishers sponsor the development of the open source software. This paper focuses on open source software publishers' business models as this issue is even more crucial for this category of firms which take the risk of investing in the development of the software. Literature at last identifies and depicts only two generic types of business models for open source software publishers: the business models of ''bundling'' (Pal and Madanmohan, 2002; Dahlander 2004) and the dual licensing business models (Välimäki, 2003; Comino and Manenti, 2007). Nevertheless, these business models are not applicable in all circumstances. Methodology: The objectives of this paper are: (1) to explore in which contexts the two generic business models described in literature can be implemented successfully and (2) to depict an additional business model for open source software publishers which can be used in a different context. To do so, this paper draws upon an explorative case study of IdealX, a French open source security software publisher. This case study consists in a series of 3 interviews conducted between February 2005 and April 2006 with the co-founder and the business manager. It aims at depicting the process of IdealX's search for the appropriate business model between its creation in 2000 and 2006. This software publisher has tried both generic types of open source software publishers' business models before designing its own. Consequently, through IdealX's trials and errors, I investigate the conditions under which such generic business models can be effective. Moreover, this study describes the business model finally designed and adopted by IdealX: an additional open source software publisher's business model based on the principle of ''mutualisation'', which is applicable in a different context. Results and implications: Finally, this article contributes to ongoing empirical work within entrepreneurship and strategic management on open source software publishers' business models: it provides the characteristics of three generic business models (the business model of bundling, the dual licensing business model and the business model of mutualisation) as well as conditions under which they can be successfully implemented (regarding the type of product developed and the competencies of the firm). This paper also goes further into the traditional concept of business model used by scholars in the open source related literature. In this article, a business model is not only considered as a way of generating incomes (''revenue model'' (Amit and Zott, 2001)), but rather as the necessary conjunction of value creation and value capture, according to the recent literature about business models (Amit and Zott, 2001; Chresbrough and Rosenblum, 2002; Teece, 2007). Consequently, this paper analyses the business models from these two components' point of view.

A Cyber-Physical System Simulator for risk-free transport studies

The article introduces a novel platform for conducting controlled and risk-free driving and traveling behavior studies, called Cyber-Physical System Simulator (CPSS). The key features of CPSS are: (1) simulation of multiuser immersive driving in a threedimensional (3D) virtual environment; (2) integration of traffic and communication simulators with human driving based on dedicated middleware; and (3) accessibility of multiuser driving simulator on popular software and hardware platforms. This combination of features allows us to easily collect large-scale data on interesting phenomena regarding the interaction between multiple user drivers, which is not possible with current single-user driving simulators. The core original contribution of this article is threefold: (1) we introduce a multiuser driving simulator based on DiVE, our original massively multiuser networked 3D virtual environment; (2) we introduce OpenV2X, a middleware for simulating vehicle-to-vehicle and vehicle to infrastructure communication; and (3) we present two experiments based on our CPSS platform. The first experiment investigates the “rubbernecking” phenomenon, where a platoon of four user drivers experiences an accident in the oncoming direction of traffic. Second, we report on a pilot study about the effectiveness of a Cooperative Intelligent Transport Systems advisory system.

Method for planning and executing obstacle-free paths for rotating excavation machinery

This invention concerns the control of rotating excavation machinery, for instance to avoid collisions with obstacles. In a first aspect the invention is a control system for autonomous path planning in excavation machinery, comprising: A map generation subsystem to receive data from an array of disparate and complementary sensors to generate a 3-Dimensional digital terrain and obstacle map referenced to a coordinate frame related to the machine's geometry, during normal operation of the machine. An obstacle detection subsystem to find and identify obstacles in the digital terrain and obstacle map, and then to refine the map by identifying exclusion zones that are within reach of the machine during operation. A collision detection subsystem that uses knowledge of the machine's position and movements, as well as the digital terrain and obstacle map, to identify and predict possible collisions with itself or other obstacles, and then uses a forward motion planner to predict collisions in a planned path. And, a path planning subsystem that uses information from the other subsystems to vary planned paths to avoid obstacles and collisions. In other aspects the invention is excavation machinery including the control system; a method for control of excavation machinery; and firmware and software versions of the control system.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Dataflow analysis for data-race free programs

Memory models for shared-memory concurrent programming languages typically guarantee sequential consistency (SC) semantics for datarace-free (DRF) programs, while providing very weak or no guarantees for non-DRF programs. In effect programmers are expected to write only DRF programs, which are then executed with SC semantics. With this in mind, we propose a novel scalable solution for dataflow analysis of concurrent programs, which is proved to be sound for DRF programs with SC semantics. We use the synchronization structure of the program to propagate dataflow information among threads without requiring to consider all interleavings explicitly. Given a dataflow analysis that is sound for sequential programs and meets certain criteria, our technique automatically converts it to an analysis for concurrent programs.

Model-free simulations for compressible mixing layer

Confined supersonic mixing layer is explored through model-free simulations. Both two- and three-dimensional spatio-temporal simulations were carried out employing higher order finite difference scheme as well as finite volume scheme based on open source software (OpenFOAM) to understand the effect of three-dimensionality on the development of mixing layer. It is observed that although the instantaneous structures exhibit three-dimensional features, the average pressure and velocities are predominantly two-dimensional. The computed wall pressures match well with experimental results fairly well, although three-dimensional simulation underpredicts the wall pressure in the downstream direction. The self-similarity of the velocity profiles is obtained within the duct length for all the simulations. Although the mixing layer thicknesses differ among different simulations, their growth rate is nearly the same. Significant differences are observed for species and temperature distribution between two- and three-dimensional calculations, and two-dimensional calculations do not match the experimental observation of smooth variations in species mass fraction profiles as reported in literature. Reynolds stress distribution for three-dimensional calculations show profiles with less peak values compared to two-dimensional calculations; while normal stress anisotropy is higher for three-dimensional case.

Avaliação de sistemas de informações geográficas na internet através de teste de software.

A utilização de sistemas de informações geográficas via Web (Sigweb) tem crescido nos últimos anos pela facilidade na manipulação e visualização de informações de diferentes lugares através da Internet. O objetivo deste estudo é realizar testes de sistemas de informações geográficas na Internet com ênfase na técnica funcional para avaliar a funcionalidade, usabilidade, a navegabilidade dos programas conhecidos como Sigweb prontos para usar. Para tanto, foi necessária a identificação dos casos de uso dos programas propostos para o estudo. Como resultado se pode conferir o comportamento dos sistemas durante os testes, além de distinguir as características de cada SigWeb e as dificuldades encontradas.

Towards topology-free optimization - An application to turbine internal cooling geometries

The application of automated design optimization to real-world, complex geometry problems is a significant challenge - especially if the topology is not known a priori like in turbine internal cooling. The long term goal of our work is to focus on an end-to-end integration of the whole CFD Process, from solid model through meshing, solving and post-processing to enable this type of design optimization to become viable & practical. In recent papers we have reported the integration of a Level Set based geometry kernel with an octree-based cut- Cartesian mesh generator, RANS flow solver, post-processing & geometry editing all within a single piece of software - and all implemented in parallel with commodity PC clusters as the target. The cut-cells which characterize the approach are eliminated by exporting a body-conformal mesh guided by the underpinning Level Set. This paper extends this work still further with a simple scoping study showing how the basic functionality can be scripted & automated and then used as the basis for automated optimization of a generic gas turbine cooling geometry. Copyright © 2008 by W.N.Dawes.

Enhancing and developing the practical optimisation capabilities and intelligence of automatic design software

In the modern engineering design cycle the use of computational tools becomes a neces- sity. The complexity of the engineering systems under consideration for design increases dramatically as the demands for advanced and innovative design concepts and engineering products is expanding. At the same time the advancements in the available technology in terms of computational resources and power, as well as the intelligence of the design software, accommodate these demands and make them a viable approach towards the chal- lenge of real-world engineering problems. This class of design optimisation problems is by nature multi-disciplinary. In the present work we establish enhanced optimisation capabil- ities within the Nimrod/O tool for massively distributed execution of computational tasks through cluster and computational grid resources, and develop the potential to combine and benefit from all the possible available technological advancements, both software and hardware. We develop the interface between a Free Form Deformation geometry manage- ment in-house code with the 2D airfoil aerodynamic efficiency evaluation tool XFoil, and the well established multi-objective heuristic optimisation algorithm NSGA-II. A simple airfoil design problem has been defined to demonstrate the functionality of the design sys- tem, but also to accommodate a framework for future developments and testing with other state-of-the-art optimisation algorithms such as the Multi-Objective Genetic Algorithm (MOGA) and the Multi-Objective Tabu Search (MOTS) techniques. Ultimately, heav- ily computationally expensive industrial design cases can be realised within the presented framework that could not be investigated before. © 2012 by the authors. Published by the American Institute of Aeronautics and Astronautics, Inc.

Enhancing and developing the practical optimisation capabilities and intelligence of automatic design software

In the modern engineering design cycle the use of computational tools becomes a necessity. The complexity of the engineering systems under consideration for design increases dramatically as the demands for advanced and innovative design concepts and engineering products is expanding. At the same time the advancements in the available technology in terms of computational resources and power, as well as the intelligence of the design software, accommodate these demands and make them a viable approach towards the challenge of real-world engineering problems. This class of design optimisation problems is by nature multi-disciplinary. In the present work we establish enhanced optimisation capabilities within the Nimrod/O tool for massively distributed execution of computational tasks through cluster and computational grid resources, and develop the potential to combine and benefit from all the possible available technological advancements, both software and hardware. We develop the interface between a Free Form Deformation geometry management in-house code with the 2D airfoil aerodynamic efficiency evaluation tool XFoil, and the well established multi-objective heuristic optimisation algorithm NSGA-II. A simple airfoil design problem has been defined to demonstrate the functionality of the design system, but also to accommodate a framework for future developments and testing with other state-of-the-art optimisation algorithms such as the Multi-Objective Genetic Algorithm (MOGA) and the Multi-Objective Tabu Search (MOTS) techniques. Ultimately, heavily computationally expensive industrial design cases can be realised within the presented framework that could not be investigated before. ©2012 AIAA.

Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.