Open Source Components Research Articles

Integrating Data-Mining Support into a Brain-Image Database Using Open-Source Components

Previously, we described our implementation of a brain-image database (braid), based on the proprietary object relational database-management system (ORDBMS) Illustra [1]. In conjunction with our collaborators, we have used this database to manage and analyze image and clinical data from what we call image-based clinical trials (IBCTs). Herein we describe the results of redesigning braid using open-source components, and integrating support for mining image and clinical data from braid's user interface. We re-designed and re-implemented braid using open-source components, including PostgreSQL, gcc, and PHP. We integrated data-mining algorithms into braid, based on PL/R, a PostgreSQL package to support efficient communication between R and PostgreSQL. We present a sample clinical study to demonstrate how clinicians can perform queries for visualization, statistical analysis, and data mining, using a web-based interface. We have developed a database system with data-mining capabilities for managing, querying, analyzing and visualizing brain-MR images. We implemented this system using open-source components, with the express goal of wide dissemination throughout the neuroimaging research community.

EVOKEDB: A KANSEI DATABASE SYSTEM FOR AUTOMATED SURVEYS

Kansei Engineering methods are difficult to implement into the design process due to a lack of specialized tools in the public domain. Surveys are costly to conduct, and the use and analysis of data through simplified models may not explore the deeper meaning of how Kansei relates to complex artifacts. EvokeDB, a Kansei database system for automated surveys, was created to address these issues. It implements a new model of Kansei, where realms and senses are considered important entities, into a flexible and usable web-application based on the Ruby on Rails framework. A database structure is presented, along with a description of how tables are mapped to programming objects in order to create a rich set of relationships that can be used to explore Kansei. The systems' opensource components, and the data flow between them, are explained A simulated project exemplifies the steps needed to set-up and launch an un-supervised, on-line survey to multiple, remote users.

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics.

An empirical study on software development with open source components in the chinese software industry

AbstractChinese software companies are increasingly using open source software (OSS) components in software development. Development with OSS components faces challenges with respect to component selection, component integration, licensing compliance, and system maintenance. Although these issues have been investigated in the industry in other countries, few similar studies have been performed in China. It is therefore difficult for Chinese software companies to be aware of their special issues and to make the necessary improvements. This article describes a questionnaire‐based survey of software development with OSS components in Chinese software companies. Data from 47 completed development projects in 43 companies were collected. The results show that the main motivation behind using OSS components was their modifiability and low license cost. Using a web search engine was the most common method of locating OSS components. Local acquaintance and compliance requirements were the major decisive factors in choosing a suitable component. To avoid legal exposure, the common strategy was to use components without licensing constraints. The major cost of OSS‐based projects was the cost to learn and understand OSS components. Almost 84% of the components needed bug fixing or other changes to the code. However, close participation with the OSS community was rare. Copyright © 2008 John Wiley & Sons, Ltd.

Spatial and multidimensional visualization of Indonesia's village health statistics

BackgroundA community health assessment (CHA) is used to identify and address health issues in a given population. Effective CHA requires timely and comprehensive information from a wide variety of sources, such as: socio-economic data, disease surveillance, healthcare utilization, environmental data, and health resource allocation.Indonesia is a developing country with 235 million inhabitants over 13,000 islands. There are significant barriers to conducting CHA in developing countries like Indonesia, such as the high cost of computing resources and the lack of computing skills necessary to support such an assessment.At the University of Pittsburgh, we have developed the Spatial OLAP (On-Line Analytical Processing) Visualization and Analysis Tool (SOVAT) for performing CHA. SOVAT combines Geographic Information System (GIS) technology along with an advanced multidimensional data warehouse structure to facilitate analysis of large, disparate health, environmental, population, and spatial data.The objective of this paper is to demonstrate the potential of SOVAT for facilitating CHA among developing countries by using health, population, healthcare resources, and spatial data from Indonesia for use in two CHA cases studies.ResultsBureau of Statistics administered data sets from the Indonesian Census, and the Indonesian village statistics, were used in the case studies. The data consisted of: healthcare resources (number of healthcare professionals and facilities), population (census), morbidity and mortality, and spatial (GIS-formatted) information.The data was formatted, combined, and populated into SOVAT for CHA use. Case study 1 involves the distribution of healthcare professionals in Indonesia, while case study 2 involves malaria mortality. Screen shots are shown for both cases. The results for the CHA were retrieved in seconds and presented through the geospatial and numerical SOVAT interface.ConclusionThe case studies show the potential of spatial and multidimensional analysis using SOVAT for community health assessment in developing countries. Since SOVAT is based primarily on open-source components and can be deployed using small personal computers, it is cost-effective for developing countries. Also, combining the strength in analysis and the ease of use makes tools like SOVAT ideal for healthcare professionals without extensive computer skills.

Managing a project with open source components

Managing a project with open source components

Reflections on the Role of Open Source in Health Information System Interoperability

This paper reflects on the role of open source in health information system interoperability. Open source is a driving force in computer science research and the development of information systems. It facilitates the sharing of information and ideas, enables evolutionary development and open collaborative testing of code, and broadens the adoption of interoperability standards. In health care, information systems have been developed largely ad hoc following proprietary specifications and customized design. However, the wide deployment of integrated services such as Electronic Health Records (EHRs) over regional health information networks (RHINs) relies on interoperability of the underlying information systems and medical devices. This reflection is built on the experiences of the PICNIC project that developed shared software infrastructure components in open source for RHINs and the OpenECG network that offers open source components to lower the implementation cost of interoperability standards such as SCP-ECG, in electrocardiography. Open source components implementing standards and a community providing feedback from real-world use are key enablers of health care information system interoperability. Investing in open source is investing in interoperability and a vital aspect of a long term strategy towards comprehensive health services and clinical research.

An Architecture Validation Toolset for Ensuring Patient Safety in an Open Source Software Toolkit for Image-Guided Surgery Applications

As open source software projects gain acceptance in mission critical domains of a technology-enabled society, they must adapt their lightweight processes and tools to address the quality needs of these domains. One such domain is technology-supported surgical interventions. This paper presents an in-development toolset for validating the architecture of the open source Image-guided Surgical Toolkit (IGSTK). IGSTK components must conform to a specific architecture pattern based on state machines. Applications built on top of the IGSTK framework process and route instructions under specific constraints imposed by the architecture. This toolset focuses on validating that component state machines in IGSTK are designed and implemented in accordance with the architecture’s constraints. These tools employ open source components as well, and apply theoretical concepts from computer science to a practical problem of guaranteeing safety in a mission critical domain.

Towards an open architecture for vector GIS

A range of open source software tools are now available to the Geographical Information Systems (GIS) analyst. However these tools are not necessarily interoperable and rarely significantly interoperable with proprietary systems. The open architectures, which have been developed for web-oriented systems, together with those proposed by the Open Geospatial Consortium (OGC), suggest that an open GIS architecture could be developed as an alternative to proprietary systems. The architecture would use open source components to store, translate, analyse, render and visualise GI data and would escape many of the problems of monolithic systems. Particularly what is proposed permits the loose coupling of any number of components and data stores in a manner that is both open and flexible. This paper proposes such an architecture and focuses on determining the suitability of Scalable Vector Graphics (SVG), an open vector-oriented eXtensible Markup Language (XML) grammar, as a significant component of such architecture. SVG is shown as an effective means of rendering GI data, not least because of its compatibility with the WC3 Document Object Model (DOM), permitting GIS-specific client tools to be written and transmitted to the web browser along with the SVG pages. While realising that the technology is in its infancy, the conclusion reached is that SVG currently provides a powerful solution and has enormous future potential.

Numerical modeling of the 26 November 1999 Vanuatu tsunami

On 26 November 1999, at 1321 UT, central Vanuatu was struck by a large offshore earthquake (Mw 7.5) followed by a tsunami that killed five people and caused significant damage to nearshore structures, mainly at Martelli Bay, south Pentecost Island. The tsunami is simulated using the Geowave model. The Tsunami Open and Progressive Initial Conditions System (TOPICS) source component of the model simulates the initial water column deformation, and the propagation and runup are simulated with the FUNWAVE fully nonlinear Boussinesq and dispersive model. A special effort was made on the construction of the computational grid through comprehensive bathymetry data sets obtained especially from two multibeam bathymetric surveys performed after the earthquake and tsunami. Three different tsunami sources have been considered. The first one is the fault rupture itself, the second is a landslide located east of Ambrym Island, and the third source is a submarine structure within the Selwyn Strait that will be considered as a landslide, however, with a large uncertainty because it could be a result of lava deposit as well. It is found that the earthquake‐derived tsunami source fits most of the postsurvey observations, in particular the overall wave amplitudes (up to 6–7 m observed and simulated). The timing of the tsunami is also satisfactory when objective interpretation of the eyewitnesses is processed. Thus it is found that the hypothetical landslide‐derived tsunami contributions are not necessary to predict the tsunami. This is because they do not help in the tsunami timing but also because their wave amplitude contributions are one order of magnitude lower than that of the earthquake source.

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support

We have developed Look-Align, an interactive web-based viewer to display pre-computed multiple sequence alignments. Although initially developed to support the visualization needs of the maize diversity website Panzea (http://www.panzea.org), the viewer is a generic stand-alone tool that can be easily integrated into other websites. Look-Align is written in Perl using open-source components and is available under an open-source license. Live installation and download information can be found at the Panzea website (http://www.panzea.org/software/alignment_viewer.html). ware@cshl.edu The Supplementary information includes sample lists of multiple sequence alignment software and sample screenshots of the viewer.

The use of open source software platforms by Independent Software Vendors

The Cast4All Content Conductor Platform is an integration and provisioning suite to manage data broadcasting networks in general and digital cinema networks in particular. The framework makes extensive use of open source components and contains several extensions and modifications to those components. It is a typical case of an Independent Software Vendor (ISV) building application software on top of open source platform software. In the spirit of the open source movement, the extensions or modifications to the open source components could be contributed back to the community. However, in this paper we discuss several issues that companies face in such a situation. They extend far beyond the obvious decision whether to keep the developed code proprietary, and should not be neglected. It is argued that a closer collaboration between open source projects and independent software vendors would be beneficial to all.

Notice of Violation of IEEE Publication Principles: Open source reuse in commercial firms

Notice of Violation of IEEE Publication Principles<br><br>"Open Source Reuse in Commercial Firms"<br>by T.R. Madanmohan and Rahul De<br>in IEEE Software, Vol. 21, Issue 6, November/December 2004, pp. 62-69<br><br>After careful and considered review of the content and authorship of this paper by a duly constituted expert committee, this paper has been found to be in violation of IEEE's Publication Principles.<br><br>This paper contains portions of original text from the sources cited below. Text from Paper 1) was reused without attribution. Text from Paper 2) was reused with attribution but without being clearly delineated from the above authors' own text.<br><br>1)"Open-Source CMS: Prohibitively Fractured"<br>by Tony Byrne<br>in CMS Watch,http://www.cmswatch.com/Feature/89-Open-Src<br>14 May 2003, pp 94-99<br><br>2)"The Amos Project: An Approach to Reusing Open Source Code"<br>by Manuel Carro, German Puebla and Carlo Daffara<br>in Presente y futuro de la ingenieria del software libre<br>URJC, Madrid, May 21, 2003<br><br> <br/> Open source software provides organizations with new options for component-based development. As with commercial off-the-shelf software, project developers acquire open source components from a vendor (or a community) and use them "as is" or with minor modifications. Although they have access to the component's source code, developers aren't required to do anything with it. If the component's community is large and active, the adopting organization can expect frequent software updates, reasonable quality assurance, responsive hug fixes, and good technical support. Also, having freely available source code addresses two typical concerns with using COTS components: unknown implementation quality and long-term vendor support.

PropeR revisited

The PropeR EHR system (PropeRWeb) is a multidisciplinary electronic health record (EHR) system for multidisciplinary use in extramural patient care for stroke patients. The system is built using existing open source components and is based on open standards. It is implemented as a web application using servlets and Java Server Pages (JSP's) with a CORBA connection to the database servers, which are based on the OMG HDTF specifications. PropeRWeb is a generic system which can be readily customized for use in a variety of clinical domains. The system proved to be stable and flexible, although some aspects (a.o. user friendliness) could be improved. These improvements are currently under development in a second version.

Cleopatre: free open-source components for real-time control of robotic applications

This paper is concerned with a software framework for real-time computing which supports a component based system design targeted to robotic applications. We are providing a set of free open-source software components that enhance LINUX/RTAI by supplying it with a library that contains both system-level modules including dynamic schedulers and Fault-tolerance mechanisms, and user-level modules dedicated to real-time vision and automatic control.

IGSTK: a software toolkit for image-guided surgery applications

The Image-Guided Software Toolkit (IGSTK: pronounced IGstick) is a high-level open-source component based software toolkit. The toolkit is currently under development and is intended to make it easy for researchers to prototype and develop image-guided surgery applications. The toolkit has been used to develop an example application incorporating electromagnetic tracking of a surgical needle. This paper presents the development approach, the requirements defined, the components identified and the example application.

Mission-critical development with open source software: lessons learned

Using open source software components in a mission-critical project not only can keep the project within budget but can also result in a more robust and flexible tool. When considering an open source component, prospective users should evaluate the project for several characteristics: maturity, longevity, and flexibility. For greatest benefit, the users should also build and maintain a strong working relationship with the component's developers. We compiled our experiences developing SAP into a developer's guide for those considering using open source in their mission-critical application. In addition to discussing how to evaluate open source components suitability for inclusion in a mission-critical application, the guide suggests strategies for working with open source development teams.

PACSPulse: a web-based DICOM network traffic monitor and analysis tool.

PACSPulse, an open-source tool, was developed to identify and analyze the performance bottlenecks of picture archiving and communication systems (PACS). PACSPulse provides a graphical Web interface for straightforward analysis of PACS performance on the basis of data acquired by tracking usage by network, server, workstation, type of traffic, and time of day. The PACS archive logs performance and usage data on image traffic being sent to it from the imaging units and study data requested by users. The performance log is sent via file transfer protocol (FTP) to a separate server for analysis. The data are parsed and sent to a database server connected to a Web server. The Web site is used to depict trends in the performance of the entire system to detect signs of degradation. The system was built entirely of open-source components for the operating system, database, charting tool, and Web server. Performance monitoring is an essential tool for analyzing, understanding, and predicting the performance characteristics of a PACS.

AliEn—ALICE environment on the GRID

AliEn (http://alien.cern.ch) (ALICE Environment) is a Grid framework built on top of the latest Internet standards for information exchange and authentication (SOAP, PKI) and common Open Source components. AliEn provides a virtual file catalogue that allows transparent access to distributed datasets and a number of collaborating Web services which implement the authentication, job execution, file transport, performance monitor and event logging. In the paper we will present the architecture and components of the system.

ATIDB: Arabidopsis thaliana insertion database

Insertional mutagenesis techniques, including transposon- and T-DNA-mediated mutagenesis, are key resources for systematic identification of gene function in the model plant species Arabidopsis thaliana. We have developed a database (http://atidb.cshl.org/) for archiving, searching and analyzing insertional mutagenesis lines. Flanking sequences from approximately 10 500 insertion lines (including transposon and T-DNA insertions) from several tagging programs in Arabidopsis were mapped to the genome sequence through our annotation system before being entered into the database. The database front end provides World Wide Web searching and analyzing interfaces for genome researchers and other biologists. Users can search the database to identify insertions in a particular gene or perform genome-wide analysis to study the distribution and preference of insertions. Tools integrated with the database include a graphical genome browser, a protein search function, a graphical representation of the insertion distribution and a Blast search function. The database is based on open source components and is available under an open source license.