Free Software Platform Research Articles

Streamlining Foodborne Disease Surveillance with Open-Source Data Management Software

Objective: The “ledsmanageR”, a data management platform built in R, aims to improve the timeliness and accuracy of national foodborne surveillance data submitted to the Laboratory-based Enteric Disease Surveillance (LEDS) system by automating the data processing, validating, and reporting workflow.Introduction: The National Surveillance Team in the Enteric Diseases Epidemiology Branch of the Centers for Disease Control and Prevention (CDC) collects electronic data from all state and regional public health laboratories on human infections caused by Campylobacter, Salmonella, Shiga toxin-producing E. coli, and Shigella in LEDS. These data inform annual estimates of the burden of illness, assessments of patterns in bacterial subtypes, and can be used to describe trends in incidence. Robust digital infrastructure is required to process, validate, and summarize data on approximately 60,000 infections annually while optimizing use of financial and personnel resources.Methods: We leveraged the robust and extensible programming facilities of the R programming language and the active community of R users to develop a data integration, processing, and reporting pipeline for LEDS via an internal software package we named “ledsmanageR”. We designed all data retrieval, cleaning, and provisioning algorithms using tools from RStudio software packages1–3 and tracked changes to source code and data using CDC’s internal Gitlab server. We automated data validation requests to reporting partners by generating customizable emails directly from the R console4. We streamlined the data reconciliation process using OpenRefine5, a point-and-click tool for cleaning big data. We automated generation of annual reports, a process that was previously manual, using parameterized RMarkdown documents. Staff epidemiologists performed design and implementation internally, requiring no external consulting.Results: Developing our free and open-source software platform for national foodborne surveillance data management has saved the Enteric Diseases Epidemiology Branch thousands of dollars because we no longer depend on proprietary software requiring annual licensing fees. This transition occurred without any disruption in surveillance operations. Partial automation of email-based data validation and annual report generation processes reduced employee time requirement from one full-time position to one part-time position. The modular nature of ledsmanageR permitted LEDS to collect an expanded set of data elements with no changes to the core data processing and reporting workflow.Conclusions: We developed and implemented a flexible tool that helps maintain the integrity of surveillance data and reduces the need for manual data cleaning, which can be laborious and error-prone. The user-friendly design features of ledsmanageR demonstrate that data management can be optimized using programming skills that are increasingly common among epidemiologists. Our work on improving the accuracy and efficiency of enteric disease surveillance has served as a proof of concept for plans to streamline data processing for other surveillance systems.

Scientific reuse of open biodiversity information from national Living Atlases infrastructures: Using ALA4R for reproducible research studies

During the last few years, a large number of countries have deployed national customized versions of The Atlas of Living Australia (ALA) (https://www.ala.org.au/), which is a collaboratively developed, open infrastructure for collecting and presenting biodiversity data nationally and for sharing it globally through GBIF (https://gbif.org). The increasing number of national nodes deploying this free and open source software platform has built a worldwide community involving more than 17 countries, that collaborate openly in a decentralized way (https://living-atlases.gbif.org/), helping each other out by organizing technical workshops and by developing and sharing new software modules using GitHub. One of these modules in the Living Atlases infrastructure is an R package called ALA4R originally created by Ben Raymond (https://github.com/AtlasOfLivingAustralia/ALA4R). It provides the research community with programmatic data access to many of the Living Atlases data services using R. This presentation will show how ALA4R can be used to access data from different national Living Atlases nodes and how this R package can enable research studies that utilize methods and practices for reproducible workflows that are being increasingly established within the research community (https://www.britishecologicalsociety.org/wp-content/uploads/2017/12/guide-to-reproducible-code.pdf).

Automatic aeroponic irrigation system based on Arduino’s platform

The recirculating hydroponic culture techniques, as aeroponics, has several advantages over traditional agriculture, aimed to improve the efficiently and environmental impact of agriculture. These techniques require continuous monitoring and automation for proper operation. In this work was developed an automatic monitored aeroponic-irrigation system based on the Arduino’s free software platform. Analog and digital sensors for measuring the temperature, flow and level of a nutrient solution in a real greenhouse were implemented. In addition, the pH and electric conductivity of nutritive solutions are monitored using the Arduino’s differential configuration. The sensor network, the acquisition and automation system are managed by two Arduinos modules in master-slave configuration, which communicate one each other wireless by Wi-Fi. Further, data are stored in micro SD memories and the information is loaded on a web page in real time. The developed device brings important agronomic information when is tested with an arugula culture (Eruca sativa Mill). The system also could be employ as an early warning system to prevent irrigation malfunctions.

Free cloud hardware and software platform. Analytical review

Free cloud hardware and software platform. Analytical review

Image processing in biodosimetry: A proposal of a generic free software platform.

The scoring of chromosome aberrations is the most reliable biological method for evaluating individual exposure to ionizing radiation. However, microscopic analyses of chromosome human metaphases, generally employed to identify aberrations mainly dicentrics (chromosome with two centromeres), is a laborious task. This method is time consuming and its application in biological dosimetry would be almost impossible in case of a large scale radiation incidents. In this project, a generic software was enhanced for automatic chromosome image processing from a framework originally developed for the Framework V project Simbio, of the European Union for applications in the area of source localization from electroencephalographic signals. The platforms capability is demonstrated by a study comparing automatic segmentation strategies of chromosomes from microscopic images.

LiDARHub: a free and open source software platform for web-based management, visualization and analysis of LiDAR data

LiDAR is an active remote sensing technique with a unique capability to capture three-dimensional information of the earth’s surface even in heavily vegetated areas, and it is proven to be useful in many research applications. Although it is becoming the remote sensing platform of choice for planning and natural resource agencies that require three-dimensional information, the enormous data that are generated and the lack of available software analysis packages make LiDAR still unavailable to a typical user of spatial data. LiDARHub is a free and open source platform for web-based management, visualization and analysis of LiDAR data that enables development of online tools for LiDAR data processing in a web browser. The framework provides a foundation to develop online tools for LiDAR data processing and tools can be shared. The framework is also flexible so that the developed tools can be easily ported to High Performance Computing (HPC) environments that speed up the computationally extensive LiDAR data processing. Two example LiDARHub tools are presented as case studies to demonstrate potential software development scenarios. The developed tools provide easy to use user interface and hide complex computation so that users can take advantage of the LiDAR technology with only a web browser. The LiDARHub allows not only the sharing of large volume of LiDAR data but also developing online LiDAR processing platform for a large audience.

Going open source: some lessons learned from the development of OpenRecLink.

Record linkage is the process of identifying and merging records across different databases belonging to the same entity. The health sector is one of the pioneering areas of record linkage techniques applications. In 1998 we began the development of a software package, called RecLink that implemented probabilistic record linkage techniques. In this article we report the development of a new, open-source version of that program, now named OpenRecLink. The aim of this article is to present the main characteristics of the new version and some of the lessons learned during its development. The new version is a total rewrite of the program, based on three goals: (1) to migrate to a free and open source software (FOSS) platform; (2) to implement a multiplatform version; (3) to implement the support for internationalization. We describe the tools that we adopted, the process of development and some of the problems encountered.

Evaluating Moodle As An Open Source E-Learning Software Tools For Teaching In Tertiary Institutions

The continuous and rapid growth in information and communication technology (ICT) has led to a significant change in the learning environment. ICT, for example, have led to the creation of new learning models where traditional learning is mixed with information technology tools to provide learners with an environment that enable them to freely choose their learning material from anywhere around the globe. In addition to these advances in the learning models, learners can also share their comments and questions with their colleagues and teachers as well as assess the knowledge they gained. In tertiary education, the term Electronic learning (E-learning) is normally used and/or associated with many of the different learning models used. Due to the rapid growth of Internet technologies, E-learning has become an increasingly popular learning approach in many different tertiary institutions. E-learning, in the context of this paper is, thus, defined as the use of ICT to enable people learn or to enhance and facilitate teaching and learning anytime, anywhere around the globe. For this reason, this paper aims at evaluating Modular Object-Oriented Dynamic Learning Environment (MOODLE) as an open source e-learning software tool for teaching and learning in tertiary institutions. Moodle is a free and open-source e-learning software platform designed to help educators create quality online courses. Sample experimental groups of students were used during the evaluation process. We, therefore, discuss the evaluation process and present our findings in this paper. Keywords: E-learning, open source e-learning software tools, Moodle, teaching and learning, evaluation process, tertiary education

Toward a wiki guide for obstetrics and gynecology trainees in Ireland

BackgroundThe present paper describes the implementation of a novel, web-based, comprehensive national information hub for trainees in obstetrics and gynecology in Ireland. This was a unique development in the context of an entire medical specialty and was aligned with the communication strategy of the governing professional body. To date, trainee doctors working in Ireland undergo an incoherent and inconsistent new-staff induction and handover. In the healthcare setting, staff integration can have a major impact on the quality of patient care. MethodsA free wiki software platform (PBworks) was used for the website, and freely available software (Google Analytics) was used to determine user interaction and level of engagement. ResultsIn the first year, 442 user visits were recorded. The average duration of site visits was 4minutes 39seconds, which compared favorably with the 4-minute duration for visits to Wikipedia. ConclusionThe project was successful as a proof concept and in practice. Other medical faculties have expressed an interest in adopting the concept and developing it for their trainees. The concept is widely applicable to other countries, with the negligible cost relevant to resource-poor areas.

RNETLOGO: an R package for running and exploring individual‐based models implemented in NETLOGO

Summary1. NetLogo is a free software platform for implementing individual‐based and agent‐based models. However, NetLogo’s support of systematic design, performance and analysis of simulation experiments is limited. The statistics software R includes such support.2. RNetLogo is an R package that links R and NetLogo: any NetLogo program can be controlled and run from R and model results can be transferred back to R for statistical analyses. RNetLogo includes 16 functions, which are explained and demonstrated in the user manual and tutorial. The design of RNetLogo was inspired by a similar link between Mathematica and NetLogo.3. RNetLogo is a powerful tool for making individual‐based modelling more efficient and less ad hoc. It links two fast growing user communities and constitutes a new interface for integrating descriptive statistical analyses and individual‐based modelling.

Dynamic Energy Budget theory meets individual‐based modelling: a generic and accessible implementation

Summary1. Dynamic Energy Budget (DEB) theory was designed to understand the dynamics of biological systems from cells to populations and ecosystems via a mass balance approach of individuals. However, most work so far has focused on the level of the individual. To encourage further use of DEB theory in a population context, we developed DEB‐IBM, a generic individual‐based model (IBM) that is based on DEB theory.2. The generic IBM is implemented as a computer program using NetLogo, a free software platform that is accessible to biologists with little programming background. The IBM uses DEB to represent assimilation, maintenance, growth and reproduction of individuals. The model description follows the overview, design and details (ODD) protocol, a generic format for describing IBMs, and thereby provides a novel and accessible introduction to DEB theory and how it works in a population context.3. Dynamic Energy Budget‐individual‐based model can be used to explore properties of both individual life‐history traits and population dynamics, which emerge from the set of DEB parameters of a species, and their interaction with environmental variables such as food density. Furthermore, DEB‐IBM can be adapted to address specific research questions, for example by including spatial effects. A user manual explains how this can be done.4. Dynamic Energy Budget‐individual‐based model is designed to both facilitate use and testing DEB theory in a population context and to advance individual‐based modelling by basing the representation of individuals on well‐tested physiological principles.

Design storm prediction and hydrologic modeling using a web-GIS approach on a free-software platform

The aim of this work has been to implement a set of procedures useful to automatise the evaluation, the design storm prediction and the flood discharge associated with a selected risk level. For this purpose a Geographic Information System has been implemented using Grass 5.0. One of the main topics of such a system is a georeferenced database of the highest intensity rainfalls and their assigned duration recorded in Sicily. This database contains the main characteristics for more than 250 raingauges, as well as the values of intense rainfall events recorded by these raingauges. These data are managed through the combined use of the PostgreSQL and GRASS-GIS 5.0 databases. Some of the best-known probability distributions have been implemented within the Geographical Information System in order to determine the point and/or areal rain values once duration and return period have been defined. The system also includes a hydrological module necessary to compute the probable flow, for a selected risk level, at points chosen by the user. A peculiarity of the system is the possibility to querying the model using a web-interface. The assumption is that the rising needs of geographic information, and dealing with the rising importance of peoples participation in the decision process, requires new forms for the diffusion of territorial data. Furthermore, technicians as well as public administrators needs to get customized and specialist data to support planning, particularly in emergencies. In this perspective a Web-interface has been developed for the hydrologic system. The aim is to allow remote users to access a centralized database and processing-power to serve the needs of knowledge without complex hardware/software infrastructures.