Open Source Software Tools Research Articles

Musketeer: a software tool for the analysis of titration data.

Musketeer is a powerful open-source software tool for the analysis of titration data, featuring a simple cross-platform graphical interface for importing data directly from UV-vis, fluorescence and NMR spectrometers, or from spreadsheets. The fast data analysis algorithm can be used to obtain equilibrium constants for simple binding isotherms, as well as for more complicated systems with multiple competing equilibria. Applications of Musketeer for the analysis of a range of different supramolecular and biomolecular systems are illustrated, including titrations with multiple spectroscopically active species, competitive binding assays, denaturation experiments, optimisation of concentrations as variables. The software also includes a number of tools that can be used to select the binding isotherm that represents the best model to describe a dataset.

Spatial Mapping of Polling Units using Open-Source Software

The feasibility for adopting emerging Open-Source software and free mobile GIS data collection tools for Polling Unit mapping (PUs) and inventory was tested. The dynamism of KOBO COLLECT and QGIS Open-Source technologies were used in mapping and analyzing the spatial distribution of polling units in Eket Local Government Area. The study maximized the potentials of Open-Source technologies to provide a graphical inventory of polling units and area coverage for information management in the electioneering process. Spatial analysis tool of QGIS was used for solving shortest path problem centered around emergency response routing scenarios based on travel time and distance impedance from an origin to a destination. It also helped to portray the distribution within the study area in a bid to reveal pattern and accessibility to the populace. Results obtained will allow citizens and electorates access information on the locations of various polling units, which ultimately serve as a decision supporting system that would enhance their participation. The maps are also useful for future distribution of polling booths, security personnel, for solving transportation issues and in service delivery during election periods.

IMPROVING REHABILITATION OUTCOMES FOR PEOPLE AGING WITH LONG-TERM HAND IMPAIRMENTS

Abstract Despite the importance of hand and upper extremity function in ADL performance and successful aging-in-place, contextual and engaging in-home rehabilitation interventions that promote use, feedback of progress, and long-term monitoring of changes in functional ability among individuals with chronic upper limb deficits are lacking. This presentation will present the findings from three TechSAge pilot projects focused on the use of technology to support in-home rehabilitation for individuals aging with long-term upper extremity disabilities. DigiHand, is a smartphone-based application combined with sensor-embedded objects used in daily activities (e.g., coffee cup) that enables users to self-manage their own rehabilitation, obtain feedback on progress to refine movements, and allow remote monitoring by therapists. Similarly, KeyStroke is an in-home piano training mobile app that provides engaging music exercises to promote long-term rehabilitation and therapists’ monitoring of progress of stroke survivors. Finally, 3DP for AT is generating design requirements to support the development of an open-source software tool that would allow assistive technology service providers, who are novice users of 3D printers, to create and fabricate highly customized 3D-printed assistive devices that are more durable, aesthetic, and will better meet the unique needs of people aging with long-term hand impairments.

Optimal Power Flow for Unbalanced Three-Phase Microgrids Using an Interior Point Optimizer

Optimal power flow (OPF) analysis enables the in-depth study and examination of islanded microgrid design and operation. The development of the analysis framework, including modeling, formulating, and selecting effective OPF solvers, however, is a nontrivial task. As a result, this paper presents a tutorial on an OPF modeling framework, offering a mathematical model that can be readily implemented using established open-source software tools such as OpenDSS, Pyomo, and IPOPT. The framework is versatile, capable of representing single-phase and unbalanced three-phase islanded microgrids. Various inverter models, such as those of grid forming and following equipped with their operating characteristics, can be incorporated. The efficacy of the proposed framework is demonstrated in studying the OPF of single-phase and three-phase microgrids.

Force-chain finder: A software tool for the recursive detection of force-chains in granular materials via minor principal stress

Force transmission in granular media occurs through an inhomogeneous network of inter-particle contacts referred to as force-chains. A thorough understanding of the structure of these chains is indispensable for a better comprehension of the macroscopic signatures they generate. This paper introduces Force-Chain Finder (FCF), an open-source software tool designed for detecting force-chains in granular materials. Leveraging the stress tensor computed for each particle based on its interactions with neighbouring particles, the tool effectively identifies the magnitude and direction of the most compressive principal stress. Through a recursive traversal of particles and their neighbours, force-chains are robustly detected based on the alignment of the principal stress directions, which is decided by a parameter α (an angle in radians). The software provides a comprehensive suite of post-processing features, including the exportation of results in different formats, enabling detailed analysis of specific regions and dynamic phenomena. Additionally, the software facilitates the computation of statistical measures pertaining to chain size and population. By streamlining the identification and characterization of force-chains within discrete element method (DEM) simulations, this tool significantly enhances the efficiency and accuracy of force-chain analysis. Thus, the software promotes deeper insights into the behaviour of granular materials by enabling researchers to effortlessly detect and analyse force-chains. PROGRAM SUMMARYProgram Title: Force Chain Finder (FCF)CPC Library link to program files:https://doi.org/10.17632/33pkc4f63t.1Developer's repository link:https://github.com/Particles-Research/Force_Chain_Finder_Public/tree/mainLicensing provisions: GNU General Public License 3Programming Language: C++, PythonSupplementary material: Illustrative examplesNature of the Problem: FCF has been developed with the primary objective of efficiently and comprehensively detecting force networks that arise in Discrete Element Modelling (DEM) simulations of granular flow.Solution Method: The method is based on the work of “J. Peters, M. Muthuswamy, J. Wibowo, and A. Tordesillas, Characterization of force chains in granular material, Physical Review E 72, 041307 (2005)”. It utilizes the concept of minor principal stress to identify quasilinear chains, each consisting of at least three particles. However, significant algorithmic modifications have been implemented to enhance the accuracy of the procedure, enabling the detection of chain branching and merging.

Realizing in-house algorithm-driven free fibula flap set up within 24 hours: a pilot study evaluating accuracy with open-source tools.

This study aims to critically evaluate the effectiveness and accuracy of a time safing and cost-efficient open-source algorithm for in-house planning of mandibular reconstructions using the free osteocutaneous fibula graft. The evaluation focuses on quantifying anatomical accuracy and assessing the impact on ischemia time. A pilot study was conducted, including patients who underwent in-house planned computer-aided design and manufacturing (CAD/CAM) of free fibula flaps between 2021 and 2023. Out of all patient cases, we included all with postoperative 3D imaging in the study. The study utilized open-source software tools for the planning step, and three-dimensional (3D) printing techniques. The Hausdorff distance and Dice coefficient metrics were used to evaluate the accuracy of the planning procedure. The study assessed eight patients (five males and three females, mean age 61.75 ± 3.69 years) with different diagnoses such as osteoradionecrosis and oral squamous cell carcinoma. The average ischemia time was 68.38 ± 27.95 min. For the evaluation of preoperative planning vs. the postoperative outcome, the mean Hausdorff Distance was 1.22 ± 0.40. The Dice Coefficients yielded a mean of 0.77 ± 0.07, suggesting a satisfactory concordance between the planned and postoperative states. Dice Coefficient and Hausdorff Distance revealed significant correlations with ischemia time (Spearman's rho = -0.810, p = 0.015 and Spearman's rho = 0.762, p = 0.028, respectively). Linear regression models adjusting for disease type further substantiated these findings. The in-house planning algorithm not only achieved high anatomical accuracy, as reflected by the Dice Coefficients and Hausdorff Distance metrics, but this accuracy also exhibited a significant correlation with reduced ischemia time. This underlines the critical role of meticulous planning in surgical outcomes. Additionally, the algorithm's open-source nature renders it cost-efficient, easy to learn, and broadly applicable, offering promising avenues for enhancing both healthcare affordability and accessibility.

QGIS AND OPEN DATA CUBE APPLICATIONS FOR LOCAL CLIMATE ZONES ANALYSIS LEVERAGING PRISMA HYPERSPECTRAL SATELLITE DATA

Abstract. Climate change poses a significant threat to humans and biodiversity, impacting various aspects of livelihoods, infrastructure, and ecosystems. Understanding climate change and its interaction with the environment is crucial for achieving Sustainable Development Goals. Local Climate Zones (LCZ) play a key role in comprehending climate change by categorizing urban areas also based on their thermal characteristics. This study presents prototype open-source software tools developed to integrate ground and satellite data for LCZ analysis in the Metropolitan City of Milan (Northern Italy). These tools consist of a QGIS plugin to access and preprocess ground-based meteorological sensor data and a client-server platform, based on the Open Data Cube and Docker technologies, for the exploitation of multispectral and hyperspectral satellite data in LCZ mapping and analysis. The tools’ architecture, data retrieval methods, and analysis capabilities are described in detail. The QGIS plugin facilitates the access and preprocessing of ground-based sensor data within the user-friendly QGIS environment. The platform enables seamless ground-sensor and satellite data management and analysis, using Jupyter Notebooks as an interface to support programmatic operations on the data. The proposed tools provide a framework for studying climate change and its local impacts on urban environments, with the potential of empowering users to effectively analyze and mitigate its effects.

Software Tools for Evaluating Renewable Energy Sources

In this paper a review of existing software tools for the evaluating and modeling of renewable energy sources, which allow to determine various aspects, such as: the amount of incoming energy for a particular area, the economic feasibility of involving an alternative source, the impact on the environment, the cost of the projected system, the features of the terrain, etc. Programs for the evaluation of solar and wind energy, as well as solutions allowing the evaluation of several different types of renewable energy sources were considered. As a result, open-source software tools, such as: QGIS, SAGA GIS, which can be integrated into the implementation of a comprehensive assessment of renewable energy sources to perform certain functions, such as a preliminary assessment of the gross renewable energy potential in specific geographical conditions and identifying topographical features of the regions under consideration, were defined.

Metamedian: An R package for meta-analyzing studies reporting medians.

When performing an aggregate data meta-analysis of a continuous outcome, researchers often come across primary studies that report the sample median of the outcome. However, standard meta-analytic methods typically cannot be directly applied in this setting. In recent years, there has been substantial development in statistical methods to incorporate primary studies reporting sample medians in meta-analysis, yet there are currently no comprehensive software tools implementing these methods. In this paper, we present the metamedian R package, a freely available and open-source software tool for meta-analyzing primary studies that report sample medians. We summarize the main features of the software and illustrate its application through real data examples involving risk factors for a severe course of COVID-19.

Computational Analysis Tutorial for Chimeric Small Noncoding RNA: Target RNA Sequencing Libraries.

An understanding of the in vivo gene regulatory interactions of small noncoding RNAs (sncRNAs), such as microRNAs (miRNAs), with their target RNAs has been advanced in recent years by biochemical approaches which use cross-linking followed by ligation to capture sncRNA:target RNA interactions through the formation of chimeric RNAs and subsequent sequencing libraries. While datasets from chimeric RNA sequencing provide genome-wide and substantially less ambiguous input than miRNA prediction software, distilling this data into meaningful and actionable information requires additional analyses and may dissuade investigators lacking a computational background. This report provides a tutorial to support entry-level computational biologists in installing and applying a recent open-source software tool: Small Chimeric RNA Analysis Pipeline (SCRAP). Platform requirements, updates, and an explanation of pipeline steps and manipulation of key user-input variables is provided. Reducing a barrier for biologists to gain insights from chimeric RNA sequencing approaches has the potential to springboard discovery-based investigations of regulatory sncRNA:target RNA interactions in multiple biological contexts.

An Open-Source Cross-Section Tool for Hydrodynamic Model Geometric Input Development

Hydrodynamic models are widely used in simulating water dynamics in riverine and estuarine systems. A reasonably realistic representation of the geometry (e.g., channel length, junctions, cross-sections, etc.) of the study area is imperative for any successful hydrodynamic modeling application. Typically, hydrodynamic models do not digest these data directly but rely on pre-processing tools to convert the data to a readable format. This study presents a parsimonious open-source and user-friendly Java software tool, the Cross-Section Development Program (CSDP), that is developed by the authors to prepare geometric inputs for hydrodynamic models. The CSDP allows the user to select bathymetry data collected in different years by different agencies and create cross-sections and computational points in a channel automatically. This study further illustrates the application of this tool to the Delta Simulation Model II, which is the operational forecasting and planning hydrodynamic and water quality model developed for the Sacramento–San Joaquin Delta in California, United States. Model simulations on water levels and flow rates at key stations are evaluated against corresponding observations. The simulations mimic the patterns of the corresponding observations very well. The square of the correlation coefficient is generally over 0.95 during the calibration period and over 0.80 during the validation period. The absolute bias is generally less than 5% and 10% during the calibration and validation periods, respectively. The Kling–Gupta efficiency index is generally over 0.70 during both calibration and validation periods. The results illustrate that CSDP can be efficiently applied to generate geometric inputs for hydrodynamic models.

Modelling of the Optimal Impact of Photovoltaic Technology on a Sustainable Energetic Mix as Function of the Climate Conditions

Abstract: The current global trend towards decarbonized energy systems forces countries to encourage the inclusion of renewable energy. Among the main challenges, intermittent electricity production due to the fluctuation of the solar resource. In addition, the variability of costs associated with the availability of the local resource may limit its contribution toward the demand side. The trend of these possible medium-term limitations of PV energy production associated to the capacity of solar resources has been estimated. Across the OSeMOSYS open-source software tool, two optimizations have been modeled, one merely economic and the other including energy sustainability estimators. As main result, the medium-long term PV contribution appears as residual for cold and moderate climates with medial day-to-day irradiation of less than 3.2 Peak Solar Hours. In addition, a trend towards saturation 40% of the energy coverage for highly irradiated areas is observed. This effect, associated with the non-availability of resources at night, can be mitigated by incorporating accumulation technologies. The inclusion of energy sustainability criteria enhances previous considerations.

Cheminformatics Microservice: unifying access to open cheminformatics toolkits

In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net. The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-microservice.Graphical

ROE (Radiotherapy Outcomes Estimator): An open-source tool for optimizing radiotherapy prescriptions

Background and objectivesRadiotherapy prescriptions currently derive from population-wide guidelines established through large clinical trials. We provide an open-source software tool for patient-specific prescription determination using personalized dose-response curves. MethodsWe developed ROE, a plugin to the Computational Environment for Radiotherapy Research to visualize predicted tumor control and normal tissue complication simultaneously, as a function of prescription dose. ROE can be used natively with MATLAB and is additionally made accessible in GNU Octave and Python, eliminating the need for commercial licenses. It provides a curated library of published and validated predictive models and incorporates clinical restrictions on normal tissue outcomes. ROE additionally provides batch-mode tools to evaluate and select among different fractionation schemes and analyze radiotherapy outcomes across patient cohorts. ConclusionROE is an open-source, GPL-copyrighted tool for interactive exploration of the dose-response relationship to aid in radiotherapy planning. We demonstrate its potential clinical relevance in (1) improving patient awareness by quantifying the risks and benefits of a given treatment protocol (2) assessing the potential for dose escalation across patient cohorts and (3) estimating accrual rates of new protocols.

Tridimensional characterization of open cells and hollow strut cavities from SiC and ZrO2 foams: A study accomplished with open-source software tools

The characterization of ceramic foams via X-ray microtomography imaging method is often restricted to a general overview of samples, either to perform qualitative or quantitative analyses. To assess the foam with a focus on some specific components of its structure, such as hollow struts’ cavities and open cells, the generalized characterizations must be overcome. This work presents image analysis methodologies, based on open-source software, tools, and plugins, to achieve the aforementioned characterizations. SiC and ZrO2 foams samples were analyzed and some of the results were compared with those accomplished with pieces of commercial software. The results show good agreement between open-source and commercial software applications, indicating that the presented methodologies can be freely applied by any researcher to analyze their foams.

Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis

Mass-Suite (MSS) is a Python-based, open-source software package designed to analyze high-resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) data, particularly for water quality assessment and other environmental applications. MSS provides flexible, user-defined workflows for HRMS data processing and analysis, including both basic functions (e.g., feature extraction, data reduction, feature annotation, data visualization, and statistical analyses) and advanced exploratory data mining and predictive modeling capabilities that are not provided by currently available open-source software (e.g., unsupervised clustering analyses, a machine learning-based source tracking and apportionment tool). As a key advance, most core MSS functions are supported by machine learning algorithms (e.g., clustering algorithms and predictive modeling algorithms) to facilitate function accuracy and/or efficiency. MSS reliability was validated with mixed chemical standards of known composition, with 99.5% feature extraction accuracy and ~ 52% overlap of extracted features relative to other open-source software tools. Example user cases of laboratory data evaluation are provided to illustrate MSS functionalities and demonstrate reliability. MSS expands available HRMS data analysis workflows for water quality evaluation and environmental forensics, and is readily integrated with existing capabilities. As an open-source package, we anticipate further development of improved data analysis capabilities in collaboration with interested users.Graphical abstract

Editorial: Rapid, reproducible, and robust environmental modeling for decision support: worked examples and open-source software tools

Editorial: Rapid, reproducible, and robust environmental modeling for decision support: worked examples and open-source software tools

OXREF: Open XR for Education Framework

Extended reality (XR), which encompasses virtual reality (VR), augmented reality (AR), and mixed reality (MR), offers powerful affordances for improving teaching and learning experiences in a post-pandemic world. Increasingly, many governments and institutions around the world are making major investments in XR technologies to prepare education systems for the future. However, many of these investments remain isolated pilot projects which, while they attest to the potential of XR in education, are unlikely to be scaled up due to lack of sustainability and collaboration. Based on literature and empirical evidence, I have identified major barriers to the wider adoption of XR in education, including the lack of (a) open content, tools, and skills; (b) sound pedagogy and instructional design; and (c) scalability and sustainability. As a potential solution, I introduce the Open XR for Education Framework (OXREF), an empirical framework that proposes a holistic solution to XR object creation, implementation, and deployment, while covering pedagogical, technological, and policy perspectives. The contribution of the OXREF is its ability to build fit-for-purpose XR experiences in a scalable, sustainable, and collaborative manner while promoting openness, accessibility, equity, and reuse. The novelty of the proposed framework is its use of open educational resources (OER), open educational practices (OEP), as well as free and open-source software (FOSS) tools and platforms. Its cloud-based infrastructure and open licenses support viable operationalization strategies that can be implemented by educational institutions and governments.

The Curricular Asset Warehouse at the University of Illinois: Case study of a digital archive’s sustainability

The production and stewardship of digital objects depends on devices and software with relatively short life cycles. As a result, when it is time to upgrade digital preservation environments and workflows, the devices that host digital objects — hard drives, monitors, computer peripherals, storage media, etc — flow out of digital repositories and contribute to the fastest growing waste stream of the 21st century: electronic waste. This paper discusses how the Center for Innovation in Teaching and Learning (CITL) at the University of Illinois at Urbana-Champaign is currently conducting a study into the sustainable management of its large volumes of digital video and image content production and preservation, within an analysis of its institutional purchasing and waste management paradigms. This analysis seeks to determine how device obsolescence at CITL can be mitigated to avoid future costs and to minimise the department’s contribution to the global e-waste problem. The first half of this paper describes how CITL employs a system called the Curricular Asset Warehouse (CAW), which is a suite of software that serves as the backbone of its media production and archival needs. CAW uses several open source software tools to be an all-in-one production, cataloguing, preservation and discovery tool. The second half of the paper discusses how CITL, which contains a high-throughput video production unit, is minimising its e-waste footprint by employing the CAW suite of tools to minimise its digital storage needs and, by extension, the amount of electronic waste produced by the department. This section also discusses the findings of an in-progress case study about the environmental impacts of CITL’s production tools and tape-based storage infrastructure.

Implementation of 3D printing in an open-source solution in an academic library

With the RepRap project (open-source 3D printer), the possibility of access to rapid prototyping became available for retail customers. From that moment, the market was created for the development of open-source technologies to support 3D printing at each stage of the process. Consequently, several software and devices for 3D printing have been created. This paper confirms the idea that 3DP can be implemented in academic libraries as an OS solution with the benefit of ensuring low costs while maintaining sufficient accuracy. In addition, it explains how to deploy these printers, either partially or fully, and the specific open-source software and hardware tools that are usually employed in these kinds of libraries.The article is based on the author's empirical experience while conducting classes with students in 3D printing and open-source technology and operating the 3DP laboratory at the Maria Curie-Skłodowska University in Lublin, Poland. Additional data were gleaned from 114 public and private university libraries in the USA offering 3D printing services.