Open Source Software Components Research Articles

An Open Voice Command Interface Kit

An open-source voice command interface kit has been developed by integrating open-source software and inexpensive hardware components. The software for the kit has been developed as a lightweight modular framework with replaceable components. It also provides a C++ library to support development of applications on top of it. The usefulness of the kit is demonstrated by applying it to voice-steer an electric wheelchair. Three participants voice-steered the wheelchair along a complicated path and found the kit to respond reliably. The average recognition time is $\sim$ 500 ms, indicating utility of the kit for near real-time applications.

Trapper: an open source web‐based application to manage camera trapping projects

Summary Camera trapping is increasingly becoming an important tool in ecological research. However, the organization of large collections of multimedia files and especially efficient searching for subsets of data is a challenging task. While the development of project‐specific software solutions is dominating in the camera trapping community, little attention has been paid to more flexible and open‐source solutions supporting diverse camera trapping research projects. We used state of the art and well‐recognized open source software components and programming language python to design and implement trapper, a flexible data base driven web application to manage, classify, integrate, share and re‐use data in camera trapping projects. The main features of trapper are: (i) it is fully open‐source, (ii) it facilitates analysis of videos as well as images, (iii) it provides spatial filtering and web‐mapping, (iv) it allows flexible implementation of specific data collection protocols, (v) it is a multi‐user and role based system which facilitates collaborative work on camera trapping projects, (vi) it supports data re‐use and (re)discovery. trapper can therefore be widely used by ecologists working with a variety of camera trap studies, alone or in collaboration with each other.

ChemInform Abstract: Continuous Flow Liquid—Liquid Separation Using a Computer‐Vision Control System: The Bromination of Enaminones with N‐Bromosuccinimide.

Incorporating open-source software components (Python, OpenCV), a computer-vision system was used to control the interface level in a gravity-based inline liquid–liquid separation device. This was used in the continuous flow bromination of a series of enaminone substrates. The main byproduct of the reaction, succinimide, was efficiently extracted into the aqueous stream, providing clean products without the need for further purification.

Bridging experiment and theory: a template for unifying NMR data and electronic structure calculations.

BackgroundThe testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory comparisons may be viewed as a workflow comprised of well-defined, rote operations distributed over several distinct computers, as exemplified by the way in which predictions from electronic structure theories are evaluated with results from spectroscopic experiments. For workflows such as this, which may be laborious and time consuming to perform manually, software that could orchestrate the operations and transfer results between computers in a seamless and automated fashion would offer major efficiency gains. Such tools also promise to alter how researchers interact with data outside their field of specialization by, e.g., making raw experimental results more accessible to theorists, and the outputs of theoretical calculations more readily comprehended by experimentalists.ResultsAn implementation of an automated workflow has been developed for the integrated analysis of data from nuclear magnetic resonance (NMR) experiments and electronic structure calculations. Kepler (Altintas et al. 2004) open source software was used to coordinate the processing and transfer of data at each step of the workflow. This workflow incorporated several open source software components, including electronic structure code to compute NMR parameters, a program to simulate NMR signals, NMR data processing programs, and others. The Kepler software was found to be sufficiently flexible to address several minor implementation challenges without recourse to other software solutions. The automated workflow was demonstrated with data from a ^{17}hbox {O} NMR study of uranyl salts described previously (Cho et al. in J Chem Phys 132:084501, 2010).ConclusionsThe functional implementation of an automated process linking NMR data with electronic structure predictions demonstrates that modern software tools such as Kepler can be used to construct programs that comprehensively manage complex, multi-step scientific workflows spanning several different computers. Automation of the workflow can greatly accelerate the pace of discovery, and allows researchers to focus on the fundamental scientific questions rather than mastery of specialized software and data processing techniques. Future developments that would expand the scope and power of this approach include tools to standardize data and associated metadata formats, and the creation of interactive user interfaces to allow real-time exploration of the effects of program inputs on calculated outputs.

A Telemedicine Application Using WebRTC

ICT in healthcare businesses has been growing in Portugal in the past few decades. The implementation of large scale information systems in hospitals, the deployment of electronic prescription and electronic patient records applications are just a few examples. Telemedicine is another emergent and widely used ICT solution to smooth the communication between patients and healthcare professionals, by allowing video and voice transfer over the Internet. Although there are several implementations of telemedicine solutions, they usually have some drawbacks, namely: i) too specific for a purpose; ii) based on proprietary applications; iii) require additional software installation; iv) and usually have associated costs.In this paper we propose a telemedicine solution based on WebRTC Application Programming Interface (API) to transmit video and voice in real time over the Internet, through a web browser. Besides microphone and webcam control, we have also included two additional functionalities that may be useful to both patients and healthcare professionals during the communication, namelyi) bidirectional sending files capability and ii) shared whiteboard which allows free drawing. The proposed solution uses exclusively open source software components and requires solely a WebRTC compatible web browser, like Google Chrome or Firefox. We have made two types of tests in healthcare environment: i) a bidirectional patient-doctor communication; ii) and connecting at one end an external USB medical device with an integrated webcam. The results were promising, since they revealed the potential of using WebRTC API to control microphone and webcam in a telemedicine application, as well as the appropriateness and acceptance of the features included.

Continuous Flow Liquid–Liquid Separation Using a Computer-Vision Control System: The Bromination of Enaminones with N-Bromosuccinimide

Incorporating open-source software components (Python, OpenCV), a computer-vision system was used to control the interface level in a gravity-based inline liquid–liquid separation device. This was used in the continuous flow bromination of a series of enaminone substrates. The main byproduct of the reaction, succinimide, was efficiently extracted into the aqueous stream, providing clean products without the need for further purification.

SINCERITY: the making of a search engine for images indexed with a bilingual taxonomy

Purpose– This paper aims to present the third stage of a research project that aims to develop a bilingual interface for the retrieval of digital images. The requirements and implementation of the search engine are described. Image search engines attempt to give access to a range of online images available on the web.Design/methodology/approach– The strategy of using open-source software components as much as possible was chosen for the advantages of this approach: low initial cost and accessibility to evaluate and develop enhancements independently and driven by research objectives rather than financial viability.Findings– Open-source software components can be used to develop the interface. The implementation of the image search engine and its indexes uses: Apache Solr, AJAX-Solr, jsTree and jQuery. Microsoft Translator web service was integrated into the interface to provide the optional user query translation.Originality/value– The search interface is intended to be an innovative tool for image searchers who are looking for digital images. The search interface gives the image searchers the opportunity to easily access a variety of visual resources and facilitates searching for images in two different languages (English and French).

Adoption of OSS components: A goal-oriented approach

Open Source Software (OSS) has become a strategic asset for a number of reasons, such as short time-to-market software delivery, reduced development and maintenance costs, and its customization capabilities. Therefore, organizations are increasingly becoming OSS adopters, either as a result of a strategic decision or because it is almost unavoidable nowadays, given the fact that most commercial software also relies at some extent in OSS infrastructure. The way in which organizations adopt OSS affects and shapes their businesses. Therefore, knowing the impact of different OSS adoption strategies in the context of an organization may help improving the processes undertaken inside this organization and ultimately pave the road to strategic moves. In this paper, we propose to model OSS adoption strategies using a goal-oriented notation, in which different actors state their objectives and dependencies on each other. These models describe the consequences of adopting one such strategy or another: which are the strategic and operational goals that are supported, which are the resources that emerge, etc. The models rely on an OSS ontology, built upon a systematic literature review, which comprises the activities and resources that characterize these strategies. Different OSS adoption strategy models arrange these ontology elements in diverse ways. In order to assess which is the OSS adoption strategy that better fits the organization needs, the notion of model coverage is introduced, which allows to measure the degree of concordance among every strategy with the model of the organization by comparing the respective models. The approach is illustrated with an example of application in a big telecommunications company.

Guaranteeing Isochronous Control of Networked Motion Control Systems Using Phase Offset Adjustment.

Guaranteeing isochronous transfer of control commands is an essential function for networked motion control systems. The adoption of real-time Ethernet (RTE) technologies may be profitable in guaranteeing deterministic transfer of control messages. However, unpredictable behavior of software in the motion controller often results in unexpectedly large deviation in control message transmission intervals, and thus leads to imprecise motion. This paper presents a simple and efficient heuristic to guarantee the end-to-end isochronous control with very small jitter. The key idea of our approach is to adjust the phase offset of control message transmission time in the motion controller by investigating the behavior of motion control task. In realizing the idea, we performed a pre-runtime analysis to determine a safe and reliable phase offset and applied the phase offset to the runtime code of motion controller by customizing an open-source based integrated development environment (IDE). We also constructed an EtherCAT-based motion control system testbed and performed extensive experiments on the testbed to verify the effectiveness of our approach. The experimental results show that our heuristic is highly effective even for low-end embedded controller implemented in open-source software components under various configurations of control period and the number of motor drives.

고정밀 동기 모션 제어 응용을 위한 Xenomai 기반 임베디드 제어기

Motion control systems are widely deployed in various industrial automation processes. The motion controller, which is a key element of motion control systems, has stringent real-time constraints. The controller must provide a short and deterministic control message transmission cycle, and minimize the actuation deviation among motor drives. To meet these requirements, hardware-based proprietary controllers have been prevalent. However, since it is becoming difficult for such an approach to meet increasing needs of system interoperability and scalability, nowadays, software-based universal motion controllers are regarded as their substitutes. Recently, embedded motion controller solutions are gaining attention due to low cost and relatively high performance. In this paper, we designed and implemented an embedded motion controller on an ARM-based evaluation board by using Xenomai real-time kernel and other open source software components. We also measured and analyzed the performance of our embedded controller under a realistic test-bed environment. The experimental results show that our embedded motion controller can provide relatively deterministic performance with synchronized control of three motor axis at 2 ms control cycle.

A FRAMEWORK FOR COLLABORATIVE REVIEW OF CANDIDATE EVENTS IN HIGH DATA RATE STREAMS: THE V-FASTR EXPERIMENT AS A CASE STUDY

ABSTRACT “Fast radio transients” are defined here as bright millisecond pulses of radio-frequency energy. These short-duration pulses can be produced by known objects such as pulsars or potentially by more exotic objects such as evaporating black holes. The identification and verification of such an event would be of great scientific value. This is one major goal of the Very Long Baseline Array (VLBA) Fast Transient Experiment (V-FASTR), a software-based detection system installed at the VLBA. V-FASTR uses a “commensal” (piggy-back) approach, analyzing all array data continually during routine VLBA observations and identifying candidate fast transient events. Raw data can be stored from a buffer memory, which enables a comprehensive off-line analysis. This is invaluable for validating the astrophysical origin of any detection. Candidates discovered by the automatic system must be reviewed each day by analysts to identify any promising signals that warrant a more in-depth investigation. To support the timely analysis of fast transient detection candidates by V-FASTR scientists, we have developed a metadata-driven, collaborative candidate review framework. The framework consists of a software pipeline for metadata processing composed of both open source software components and project-specific code written expressly to extract and catalog metadata from the incoming V-FASTR data products, and a web-based data portal that facilitates browsing and inspection of the available metadata for candidate events extracted from the VLBA radio data.

BSense: A Flexible and Open-Source Broadband Mapping Framework

We present, BSense, a flexible broadband mapping system for broadband coverage and quality assessment of broadband connections in a given geographic region. For coverage related analysis, it relies on data that is either obtained from ISPs or generated based on technology models and information about infrastructure sites. Broadband quality assessment in BSense is via host-based measurements using our multi-platform and technology-adaptive software client which periodically runs as a background process on users' computers. The host-based software measurement approach employed in BSense is not only cost-effective but is also flexible and reduces measurement bias. BSense also incorporates a flexible broadband quality index for summarizing the collective effect of various underlying attributes such as download/upload speeds and latency. BSense system has been implemented based on open-source software components. We conduct extensive evaluations of the measurement component of BSense aimed at quantifying system effects and to compare against other measurement techniques and approaches, the latter showing that BSense is fairly close to sophisticated and expensive alternatives. The usefulness of the BSense system is demonstrated using two real world case studies, one on identifying notspots in Scotland and the other on broadband quality assessment in a rural part of Scotland through pilot deployment.

Modeling Regional-Scale Wildland Fire Emissions with the Wildland Fire Emissions Information System*

Abstract As carbon modeling tools become more comprehensive, spatial data are needed to improve quantitative maps of carbon emissions from fire. The Wildland Fire Emissions Information System (WFEIS) provides mapped estimates of carbon emissions from historical forest fires in the United States through a web browser. WFEIS improves access to data and provides a consistent approach to estimating emissions at landscape, regional, and continental scales. The system taps into data and tools developed by the U.S. Forest Service to describe fuels, fuel loadings, and fuel consumption and merges information from the U.S. Geological Survey (USGS) and National Aeronautics and Space Administration on fire location and timing. Currently, WFEIS provides web access to Moderate Resolution Imaging Spectroradiometer (MODIS) burned area for North America and U.S. fire-perimeter maps from the Monitoring Trends in Burn Severity products from the USGS, overlays them on 1-km fuel maps for the United States, and calculates fuel consumption and emissions with an open-source version of the Consume model. Mapped fuel moisture is derived from daily meteorological data from remote automated weather stations. In addition to tabular output results, WFEIS produces multiple vector and raster formats. This paper provides an overview of the WFEIS system, including the web-based system functionality and datasets used for emissions estimates. WFEIS operates on the web and is built using open-source software components that work with open international standards such as keyhole markup language (KML). Examples of emissions outputs from WFEIS are presented showing that the system provides results that vary widely across the many ecosystems of North America and are consistent with previous emissions modeling estimates and products.

Tracked ultrasonography snapshots enhance needle guidance for percutaneous renal access: a pilot study.

Although ultrasonography-guided percutaneous nephrostomy is relatively safe, a number of factors make it challenging for inexperienced operators. A computerized needle navigation technique using tracked ultrasonography snapshots was investigated to determine whether performance of percutaneous nephrostomy by inexperienced users could be improved. Ten operators performed the procedure on a phantom model with alternating needle guidance between conventional ultrasonography and tracked ultrasonography snapshots. The needle was reinserted until fluid backflow confirmed calyceal access. Needle trajectories were recorded using the real time needle navigation system for offline evaluation of operator performance. Recorded needle trajectories were used to measure needle motion path length inside the phantom tissue, number of reinsertions, total procedure time, and needle insertion time as end points of this study. Needle path length measured inside the phantom tissue was significantly lower with ultrasonography snapshots guidance (295.0±23.1 mm, average±standard error of the mean) compared with control procedures (977.9±144.4 mm, P<0.01). This was associated with a significantly lower number of needle insertion attempts with ultrasonography snapshots (average 1.27±0.10 vs 2.83±0.31, P<0.01). The total procedure time and the needle insertion time were also significantly lower with ultrasonography snapshots guidance. Tracked ultrasonography snapshots appear to improve the performance of percutaneous nephrostomy in these preliminary investigations, justifying further validation studies. The presented navigation system is reproducible because of commercially available hardware and open-source software components, facilitating its potential role in clinical practice.

Continuous Integration and Deployment Software to Automate Nuclear Data Verification and Validation

We developed and implemented a highly-automated nuclear data quality assurance system ADVANCE (Automated Data Verification and Assurance for Nuclear Calculations Enhancement) which is based on the continuous integration and deployment concept that originated from the software industry. ADVANCE uses readily available open-source software components to deliver its powerful functionalities. This paper presents in detail the system's data verification functionalities which are being used to ensure the quality of every new evaluation submitted to the NNDC. Also discussed are the current development efforts to incorporate data validation capabilities into the system.

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

Development of a web application for water resources based on open source software

This article presents research and development of a prototype web application for water resources using latest advancements in Information and Communication Technologies (ICT), open source software and web GIS. The web application has three web services for: (1) managing, presenting and storing of geospatial data, (2) support of water resources modeling and (3) water resources optimization. The web application is developed using several programming languages (PhP, Ajax, JavaScript, Java), libraries (OpenLayers, JQuery) and open source software components (GeoServer, PostgreSQL, PostGIS). The presented web application has several main advantages: it is available all the time, it is accessible from everywhere, it creates a real time multi-user collaboration platform, the programing languages code and components are interoperable and designed to work in a distributed computer environment, it is flexible for adding additional components and services and, it is scalable depending on the workload. The application was successfully tested on a case study with concurrent multi-users access.

Scalable Decision Support at the Point of Care: A Substitutable Electronic Health Record App for Monitoring Medication Adherence

BackgroundNon-adherence to prescribed medications is a serious health problem in the United States, costing an estimated $100 billion per year. While poor adherence should be addressable with point of care health information technology, integrating new solutions with existing electronic health records (EHR) systems require customization within each organization, which is difficult because of the monolithic software design of most EHR products.ObjectiveThe objective of this study was to create a published algorithm for predicting medication adherence problems easily accessible at the point of care through a Web application that runs on the Substitutable Medical Apps, Reusuable Technologies (SMART) platform. The SMART platform is an emerging framework that enables EHR systems to behave as “iPhone like platforms” by exhibiting an application programming interface for easy addition and deletion of third party apps. The app is presented as a point of care solution to monitoring medication adherence as well as a sufficiently general, modular application that may serve as an example and template for other SMART apps.MethodsThe widely used, open source Django framework was used together with the SMART platform to create the interoperable components of this app. Django uses Python as its core programming language. This allows statistical and mathematical modules to be created from a large array of Python numerical libraries and assembled together with the core app to create flexible and sophisticated EHR functionality. Algorithms that predict individual adherence are derived from a retrospective study of dispensed medication claims from a large private insurance plan. Patients’ prescription fill information is accessed through the SMART framework and the embedded algorithms compute adherence information, including predicted adherence one year after the first prescription fill. Open source graphing software is used to display patient medication information and the results of statistical prediction of future adherence on a clinician-facing Web interface.ResultsThe user interface allows the physician to quickly review all medications in a patient record for potential non-adherence problems. A gap-check and current medication possession ratio (MPR) threshold test are applied to all medications in the record to test for current non-adherence. Predictions of 1-year non-adherence are made for certain drug classes for which external data was available. Information is presented graphically to indicate present non-adherence, or predicted non-adherence at one year, based on early prescription fulfillment patterns. The MPR Monitor app is installed in the SMART reference container as the “MPR Monitor”, where it is publically available for use and testing. MPR is an acronym for Medication Possession Ratio, a commonly used measure of adherence to a prescribed medication regime. This app may be used as an example for creating additional functionality by replacing statistical and display algorithms with new code in a cycle of rapid prototyping and implementation or as a framework for a new SMART app.ConclusionsThe MPR Monitor app is a useful pilot project for monitoring medication adherence. It also provides an example that integrates several open source software components, including the Python-based Django Web framework and python-based graphics, to build a SMART app that allows complex decision support methods to be encapsulated to enhance EHR functionality.

A Parallel Grad-Shafranov Solver for Real-Time Control of Tokamak Plasmas

To achieve real-time control of fusion plasmas, the flux distribution and derived quantities have to be calculated within the time of the machine control cycle, which in the case of the ASDEX-Upgrade experiment can be as small as 1 ms. To this end we have developed a fast numerical solver for the Grad-Shafranov equation, which allows exploitation of the parallel capabilities of modern multicore processors. Our implementation, termed GPEC (Garching parallel equilibrium code), is based entirely on open-source software components. For a numerical grid of size 32 × 64, our new code requires only 0.04 ms (0.11 ms for 64 × 128) for a single call of the Grad-Shafranov solver using a standard Intel Xeon quad-core CPU (3.2 GHz). We also show the first GPEC benchmark results obtained on the Intel Sandy Bridge eight-core server processor and demonstrate the relevance of the new solver for application in plasma equilibrium codes.

Phase change in the desert locust: A novel computerised behavioural assay to study the effects of anaesthesia on gregarisation

Phase change in the desert locust: A novel computerised behavioural assay to study the effects of anaesthesia on gregarisation