Open Source

Java-DSP is a freely accessible web-based software, primarily used in signal processing education and research. In this paper, we present Java-DSP modules that have been developed for the study and analysis of the MPEG-1 Layer III algorithm. We have embedded JLayer1.0, an open source MP3 library, to Java-DSP and developed an intuitive interface to expose undergraduate and graduate students to the several modules in the encoding/decoding process. The Java-DSP MP3 decoder block is an interactive function which can be used to examine the characteristics and visualize outputs of different modules in the algorithm. Some of the important functions incorporated in the proposed interface include the analysis of the hybrid filter bank, polyphase filters and the window switching based on perceptual criteria. The MP3 algorithm represents a compelling framework for teaching certain aspects in DSP. We are using this module to introduce filter banks and windowing to undergraduate students.

3-D printing has entered the consumer market because of recent radical price declines. Consumers can save substantial money by offsetting purchases with DIY pre-designed 3-D printed products. However, even more value can be obtained with distributed manufacturing using mass customization. Unfortunately, the average consumer is not technically sophisticated enough to easily design their own products. One solution to this is the use of an overlay on OpenSCAD parametric code, although current solutions force users to relinquish all rights to their own designs. There is thus a substantial need in the open source design community for a libre 3-D model customizer, which can be used in any design repository to democratize design. This study reports on the design, function, and validation of such software: the Free Open Source 3-D Customizer. It is demonstrated with a case study of the customization of 3-D printable external breast prosthetics. The results showed that novice users can adjust the available parameters according to their needs and save these to a new file on a website. This PHP (recursive acronym for PHP: Hypertext Preprocessor) library is free and open source and has potential for increasing the usefulness of online repositories to enable distributed manufacturing using consumer customized 3-D printable products.

The most critical and important aspect of disaster recovery is to protect the data from application fail over, natural disasters and infrastructure failures. Taking frequent backups of the huge volumes of data and storing it is also an integral part of the disaster recovery plan. Various scenarios of database replication strategies and techniques are provided in this survey paper addressing the need for replication of data. A wide range of open source and commercial tools have evolved over a period of time to deal with the issues and challenges involved during the process of database replication. This paper describes the general characteristics of replication & disaster recovery. Later the features of open source and commercial replication tools are compared.

Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). Results: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the Micro-Array Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The * To whom correspondence should be addressed. † The authors wish it to be known that, in their opinion, these two authors should be regarded as joint First Authors. open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. Availability: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/ SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

The paper presents a solution for integrating many aspects of human resource management, with extensible customization possibility (language, interface), to meets specific needs of various organizations, both regarding the organization as a whole, but also in terms of different categories of users that can use the platform. It also provides an overview and perspective on using Open Source Software in human resource management.

With the rapid increase in offshore outsourcing of software development, Global Software Development (GSD) has become the need of the hour. This, in turn, necessitates preparing computer science students to face the challenges associated with GSD. Today’s information technology, in the form of communication networks and tooling opportunities, provides us with a supposedly ready infrastructure to support GSD. However, selecting an appropriate combination of open source tools that cross cultural boundaries and account for unique in-country connectivity situations is not a trivial task. In this paper, we describe our experience of evolving an infrastructure for student GSD projects over a period four years, culminating in an environment to accommodate the needs of five different teams from four globally dispersed universities in countries straddling many technological divides.

The purpose behind this article is to describe the features of Ftklipse, an extendable platform for computer forensics. This document designed to provide a detailed specification for the developers of Ftklipse. Ftklipse is a thick-client solution for forensics investigation. It is designed to collect and preserve evidence, to analyze it and to report on it. It supports chain of custody

A membrane steady state simulator based on an open source concept is discussed. It is believe that this way of developing software will overcome weaknesses posed by available commercial membrane simulators. The application provides a cost effective state of the art tool for membrane modeling and object oriented design and its usage allows for easy incorporation of specific developments either open source or proprietary. This paper presents the components require to produce an open source membrane steady state simulator. This approach of development differs significantly from a close black-box approach. Several membrane models using the simulator will be elaborated and compared with literature results.

Sun has recently announced it will support a form of "best effort" hardware transactional memory in its forthcoming multicore processor, code-named "Rock". In this paper, we report on early results and experience from an exploration of software mechanisms that exploit this feature in a variety of contexts including: explicit transactional programming in the C++ and Java TM programming languages, explicit lock elision in C++ and implicit lock elision in Java, and use in Java concurrency libraries. This work has been conducted using our Adaptive Transactional Memory Test Platform, which we plan to open source soon to allow other researchers to explore the use of Rock's HTM support.

Numerous (mostly commercial) web-based systems for the assessment of programming assignments have emerged in the past few years to support the teaching and learning of programming fundamentals. WeBWorK, an initiative led by the University of Rochester to support Mathematics education, is unusual in that it is an open-source and extensible system. Since

Secure access to patient data and analysis tools to run on that data will revolutionize the treatment of a wide range of diseases, by using advanced simulation techniques to underpin the clinical decision making process. To achieve these goals, suitable e-Science infrastructures are required to allow clinicians and researchers to trivially access data and launch simulations. In this paper we describe the open source Individualized MEdiciNe Simulation Environment (IMENSE), which provides a platform to securely manage clinical data, and to perform wide ranging analysis on that data, ultimately with the intention of enhancing clinical decision making with direct impact on patient health care. We motivate the design decisions taken in the development of the IMENSE system by considering the needs of researchers in the ContraCancrum project, which provides a paradigmatic case in which clinicians and researchers require coordinated access to data and simulation tools. We show how the modular nature of the IMENSE system makes it applicable to a wide range of biomedical computing scenarios, from within a single hospital to major international research projects.

The demands for cost-effective information and communications technology solutions within the prevailing economic flux and instability calls for both new and radical approaches to cope with contemporary business challenges. The rapid pace of technology innovation notwithstanding is making technology choices even more difficult. The time to recoup return on investments seems unforgiving and justification for every extra dollar for information systems and technology investments prove more ambitious and difficult for chief information officers. Often overlooked by industry specialists are the immense benefits that open source software presents to enterprises. Open source is relatively cost-effective, adaptable, scalable, and secure. Open source software use a bazaar development methodology that incorporates durability and functionality in more advanced and secure ways than traditional proprietary software. Yet, information and communications technology professionals seem too reluctant to engage their benefits because of a lackluster attitude toward learning "innovative" endeavors. However, with prevailing cost-cutting measures, ignoring alternative cost-effective solutions are becoming less of an option to respective stakeholders. Free and open source software will therefore gain the recognition it genuinely deserve as the software of choice for scalable and costsensitive implementation and use. Free and open source software is the appropriate driver for organizational strategic endeavors in the face of a grueling world of globalizations and the phenomenological socio-technical principles and practices that governs business sustainability and longevity in the post-modern era.

This paper presents work in progress concerning the definition of quality criteria for open source computer based assessment, namely platforms for the assessment of skills. The research approach undertaken so far is based on literature reviews and expert interviews which contributed to identify a number of software applications, platforms and tools being currently reviewed according to a pre-defined matrix of descriptive and normative criteria. The results of the evaluation activities will feed the setting-up of a protocol for quality assurance of e-assessment platforms in skills assessment contexts. Background In 2006 the European Parliament and the Council of Europe have passed recommendations on key competences for lifelong learning and the use of a common reference tool to observe and promote progress in terms of the achievement of goals formulated in "Lisbon strategy" in March 2000 (revised in 2006, see http://ec.europa.eu/growthandjobs/) and its follow-up declarations in selected areas (Communication in the mother tongue, communication in foreign languages, mathematical competence and basic competences in science and technology, digital competence, learning to learn, social and civic competences, sense of initiative and entrepreneurship, and cultural awareness and expression) (European Parliament and Council of Europe, 2006). Indicators for the identification of such skills are now needed, as well as instruments for carrying out large-scale assessments in Europe. In this context it is hoped that electronic testing could improve the effectiveness of the needed assessments, i.e. improve identification of skills, and their efficiency, by reducing costs of the whole operation (financial efforts, human resources etc.).

Simulation of quantum computers using classical computers is a hard problem with high memory and computational requirements. Parallelization can alleviate this problem, allowing the simulation of more qubits at the same time or the same number of qubits to be simulated in less time. A promising approach is to exploit the high performance computing capabilities provided by the latest graphical processing units. In this paper we present a parallel implementation of the QC-lib quantum computer simulator on the GPU using the CUDA programming model. The proposed scheme for partitioning the terms that describe the state of a quantum register takes advantage of the specific characteristics of the CUDA memory spaces and allows for an efficient parallelization of the general singe qubit operator. Experimental results indicate that very good speed-ups can be obtained in contrast with the sequential implementation.

The open source model of software development has received substantial attention in the industry and popular media; nevertheless, critics frequently contend that open source softwares are inferior in quality compared to closed source softwares because of lack of incentives and project management, while proponents argue the opposite. This paper examines this quality debate by modeling and analyzing software quality, demand, profitability, and welfare under open and closed source environments in monopoly and competitive markets. The results show no dominant quality advantage of one method over another under all circumstances. Both open source and closed source qualities decrease in a competitive market. Conditions under which each method can generate higher quality software are examined.

In order to provide a portable and accurate typing system for the unambiguous characterization of pathogenic Escherichia coli isolates to the scientific community, we have constructed an online database for MultiLocus Sequence Typing of pathogenic E. coli (EcMLST) using current internet and open source technology. The system consists of an XML specification of the E. coli MLST system, and a set of perl modules defining the database tables and generating dynamic web pages for querying the database. It is implemented on a Sun server running the Apache web server. The underlying tier is the MySQL database system. Currently, the database contains nucleotide sequence data and annotated allelic profile data of 15 housekeeping genes for 600 representative E. coli isolates. Access to the central-held typing and epidemiology data is supported by parametric searching, full-text searching, as well as query interface links to the reference center of Shiga Toxin-producing E. coli (STEC, http://www.shigatox.net/stec). EcMLST has been used by public health laboratories and researchers for epidemiology and evolutionary studies. The system can be accessed at

More and more, developers use reusable components like li- braries to produce high quality software systems. These sys tems need to satisfy not only the initial demands of their stakeho lders, but they need to also offer support for future, changing requ ire- ments. While several studies have looked at the cost of modif ying systems, there exists no work

Source code analysis is important for software management. It enables us recognize strengths and weaknesses in our earlier projects or releases. We developed a source code analysis tool. This tool gathers several metrics from C/C++, C# or Java source codes. In this paper, we will use the tool to analyze some of the open source code projects. We will study the selected projects release evolutions and compare some characteristics between the same project releases, as well as among different projects. Different programming language code and development styles will be studied through those open source projects.

The Sonification Application and Research Toolbox (SonART) is an open-source effort to develop a platform-independent collection of methods to map data to sonification parameters. A set of graphical user interface tools that will provide practical and intuitive utilities for experimentation and auditory display. SonART aims to provide publicly available, well-documented code that will be easily adapted to address a broad range of sonification needs. The effort will build upon the Synthesis ToolKit (STK) [1]. In this paper we describe SonART's parameter engine framework, its interface to STK, and relevant recent developments in STK. We present an example of sonified stock market data to illustrate the principles of SonART.

Arterial spin labeling (ASL) perfusion fMRI data differ in important respects from the more familiar blood oxygen level-dependent (BOLD) fMRI data and require specific processing strategies. In this paper, we examined several factors that may influence ASL data analysis, including data storage bit resolution, motion correction, preprocessing for cerebral blood flow (CBF) calculations and nuisance covariate modeling. Continuous ASL data were collected at 3 T from 10 subjects while they performed a simple sensorimotor task with an epoch length of 48 s. These data were then analyzed using systematic variations of the factors listed above to identify the approach that yielded optimal signal detection for task activation. Improvements in statistical power were found for use of at least 10 bits for data storage at 3 T. No significant difference was found in motor cortex regarding using simple subtraction or sinc subtraction, but the former presented minor but significantly (Pb.024) larger peak t value in visual cortex. While artifactual head motion patterns were observed in synthetic data and background-suppressed ASL data when label/control images were realigned to a common target, independent realignment of label and control images did not yield significant improvements in activation in the sensorimotor data. It was also found that CBF calculations should be performed prior to spatial normalization and that modeling of global fluctuations yielded significantly increased peak t value in motor cortex. The implementation of all ASL data processing approaches is easily accomplished within an open-source toolbox, ASLtbx, and is advocated for most perfusion fMRI data sets.

For the last decade or so, the biggest category of the IT investment has unarguably been Enterprise Resource Planning (ERP). Most of the bigger corporations in the developed countries have implemented ERP systems with an aim to achieving competitive edge in their respective business areas. Now that the top end of the ERP market has been saturated, the main interest has moved to non-commercial sectors such as universities and small and medium-sized enterprises (SMEs). These organisations have not been able to benefit directly from the ERP revolution because an ERP implementation requires huge resources and entails high risks.

Historical seismograms contain a rich harvest of information useful for the study of past earthquakes. It is necessary to extract this information by digitising the analog records if modern analysis is required. Teseo has been developed for quick and accurate digitisation of seismogram traces from raster files, introducing a vectorisation step based on piecewise cubic Bézier curves. The vectoriser can handle greyscale images stored in a suitable file format and it offers three concurrent vectorisation methods: manual, automatic by colour selection, and automatic by neural networks. The software that implements the methods described is distributed with open source license.

Open-Source-Projekte rücken zunehmend in den Blick der Forschung. So wurden in den letzten Jahren große Anstrengungen unternommen, die den Open-Source-Communities zugrunde liegenden Phänomene zu identifizieren, wie z.B. im EU-Projekt FLOSS. 1Auch die sozialwissenschaftliche Forschung nähert sich diesem Feld (z.B. Holtgrewe/Brand 2007; Taubert 2006). Mit den Arbeiten von v. Hippel (für einen Überblick siehe Hippel 2005) wird ein besonderer Augenmerk auf den Innovationsaspekt bei Open-Source-Projekten geworfen, die insbesondere mit dem Werk von Piller und Reichwald (Reichwald/Piller 2006) in den Wirtschaftswissenschaften rezipiert wurde. Das dabei thematisierte Konzept des „Open Innovation“ wird zum Teil von Entscheidern innerhalb des forschungs-politischen Feldes als mögliche Innovationsstrategie für Deutschland angesehen2.

For many years the full potential of creating and leveraging integrated health ICT systems such as electronic health records to improve healthcare delivery, reducing its cost and promoting prevention has been elusive. Traditional health ICT business, innovation, development and adoption models have failed to address chronic road blocks to realizing its full potential and have led to many high profile failures. The chronic symptoms include persistent barriers to integration and interoperability, high cost, duplication of effort, and poor, to no support for collaborative, "evidence based" medicine. This paper provides a review of case studies and analysis on how open innovation, or open source processes, can break the grid lock and bring the fundamental paradigm shift needed to exploit the full potential of health ICTs. The paper will discuss how the open innovation model, as applied to health ICT, provides a framework for harnessing the naturally occurring "bottom up" forces and emergent behaviour found in complex adaptive systems such as healthcare. It does this by describing a model and context for collaborative, open, peer reviewed, evidence-based innovation and technology transfer processes. Evidence from case studies are presented on how open ICT innovation in healthcare provides essential feed backloops for supporting, researching, developing and disseminating while driving continuous quality improvement at a global scale.

The formal analysis described here detects two so far undetected real deadlock situations per thousand C source files or million lines of code in the open source Linux operating system kernel, and three undetected accesses to freed memory, at a few seconds per file. That is notable because the code has been continuously under scrutiny from thousands of developers' pairs of eyes. In distinction to model-checking techniques, which also use symbolic logic, the analysis uses a "3-phase" compositional Hoare-style programming logic combined with abstract interpretation. The result is a customisable post-hoc semantic analysis of C code that is capable of several different analyses at once.

While many theoretical arguments against or in favor of open source and closed source software development have been presented, the empirical basis for the assessment of arguments and the development of models is still weak. Addressing this research gap, this paper presents the first comprehensive empirical investigation of published vulnerabilities and patches of 17 widely deployed open source and closed source software packages, including operating systems, database systems, web browsers, email clients, and office systems. The empirical analysis uses comprehensive vulnerability data contained in the NIST National Vulnerability Database and a newly compiled data set of vulnerability patches. The results suggest that it is not the particular software development style that determines the severity of vulnerabilities and vendors' patching behavior, but rather the specific application type and the policy of the particular development community, respectively.

We present the Convergence Processor, an innovative component that integrates a high performance 32- bit RISC core, a custom IP core optimised for header-processing and other blocks for specific communication interfaces required for the delivery of broadband residential applications. The component is a System-on-Chip supporting the real time processing of packets and protocol data units from various networking interfaces. Its

Software developers search the web for various kinds of source code for diverse reasons. In a previous study, we found that searches varied along two dimensions: the size of the search target (e.g., block, subsystem, or system) and the motivation for the search (e.g., reference example or as-is reuse). Would each of these kinds of searches require different technological solutions? To answer this question, we conducted an experiment with 36 participants to evaluate three diverse approaches (general purpose information retrieval, source code search, and component reuse), as represented by five web sites (Google, Koders, Krugle, Google Code Search, and SourceForge). The independent variables were search engine, size of search target, and motivation for search. The dependent variable was the participants judgement of the relevance of the first ten hits. We found that it was easier to find reference examples than components for as-is reuse and that participants obtained the best results using a general-purpose information retrieval site. However, we also found an interaction effect: code-specific search engines worked better in searches for subsystems, but Google worked better on searches for blocks. These results can be used to guide the creation of new tools for retrieving source code from the web.

We describe the development of a two-way shallow-transfer machine translation system between Norwegian Nynorsk and Norwegian Bokmål built on the Apertium platform, using the Free and Open Source resources Norsk Ordbank and the Oslo–Bergen Constraint Grammar tagger. We detail the integration of these and other resources in the system along with the construction of the lexical and structural transfer, and evaluate the translation quality in comparison with another system. Finally, some future work is suggested.

Inifiniband is becoming an important interconnect technology in high performance computing. Recent efforts in large scale Infiniband deployments are raising scalability questions in the HPC community. Open MPI, a new production grade implementation of the MPI standard, provides several mechanisms to enhance Infiniband scalability. Initial comparisons with MVAPICH, the most widely used Infiniband MPI implementation, show similar performance but with much better scalability characterics. Specifically, small message latency is improved by up to 10% in medium/large jobs and memory usage per host is reduced by as much as 300%. In addition, Open MPI provides predicatable latency that is close to optimal without sacrificing bandwidth performance.

With the rapid advancement and deployment of robotics technology, experts as well as the
public are growing increasingly concerned with its ethical, legal, and societal (ELS) implications.
We posit that open and transparent stakeholder discussions about the technology
can not only inform development and revision of standards and regulations, but also help
develop a framework for advancing robot ethics. The Open Roboethics initiative (ORi),
described in this work, aims to be a dynamic online platform that connects various stakeholders
of robotics technology to advance roboethics discussion and foster informed robot
ethics design.
Using a robotic platform, PR2 (Willow Garage, CA), operating on the widely popular
and open-source Robot Operating System (ROS), we present a proof of concept of the ORi
idea by demonstrating one method in which stakeholder discussion of acceptable robot
behaviours can be implemented in a robotic platform.

Multi-dimensional director calculations have typically taken an inordinate amount of time on all but the fastest computers. In this paper we will report new methods for increasing both the speed and stability of multi-dimensional calculations. We will also present an "open-source" algorithm in which these methods are implemented. Details of the algorithm's design, accuracy and operation are discussed.

This paper compares the accuracy of Decision Tree and Bayesian Network algorithms for predicting the academic performance of undergraduate and postgraduate students at two very different academic institutes: Can Tho University (CTU), a large national university in Viet Nam; and the Asian Institute of Technology (AIT), a small international postgraduate institute in Thailand that draws students from 86 different countries. Although the diversity of these two student populations is very different, the data-mining tools were able to achieve similar levels of accuracy for predicting student performance: 73/71% for {fail, fair, good, very good} and 94/93% for {fail, pass} at the CTU/AIT respectively. These predictions are most useful for identifying and assisting failing students at CTU (64% accurate), and for selecting Very Good students for scholarships at the AIT (82% accurate). In this analysis, the Decision Tree was consistently 3-12% more accurate than the Bayesian Network. The results of these case studies give insight into techniques for accurately predicting student performance, compare the accuracy of data mining algorithms, and demonstrate the maturity of open source tools.

Monitoring software quality in a development project is an important task required of project management, especially for large-scale projects. Our primary interest is evaluating quality of a system's structure and implications of the structure for project management, maintenance, and testing. Without the help of source code analysis tools it is difficult to understand a large project, evaluate its quality, and track progress effectively. In this paper we discuss application of tools developed for this purpose to the open- source Mozilla project.

Smoothed Particle Hydrodynamics (SPH) is used to simulate the movement of a caisson breakwater in the surf zone. The open-source code SPHysics is used with a Riemann solver-based formulation. The friction force between the moving caisson and the bed is modelled with a transition from static to dynamic friction force. Results are presented for two-dimensional simulations and compared with experiments for the movement of a caisson breakwater under the forcing of periodic waves. Promising agreement with experimental data is obtained for the displacement and the horizontal forces on the caisson. It is demonstrated that the peak impact forces are better captured using finer resolution and that a Riemann solver-based formulation produces a better agreement with experiment for the predicted caisson displacement than conventional SPH.