Article
Forestry
Jeff W. Atkins, Atticus E. L. Stovall, Carlos Alberto Silva
Summary: This study reveals a lag in the adoption of open-source software in forestry and forest ecology, potentially hindering collaboration, data sharing, and reproducibility. By surveying available packages in the R programming language for forest-related research, the study provides examples to demonstrate their potential and utility.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Article
Chemistry, Multidisciplinary
Fabio Federici Canova, Giorgio Oliva, Matteo Beretta, Domenico Dalessandri
Summary: The introduction of new digital technologies, especially the use of 3D models of dental arches, has had a major impact on modern orthodontics. While dedicated software tends to be more user-friendly but expensive, younger clinicians are increasingly interested in open-source software. The study aimed to introduce and discuss some of the best-known open-source software for analysis of 3D models and the creation of orthodontic devices.
APPLIED SCIENCES-BASEL
(2021)
Article
Computer Science, Interdisciplinary Applications
Nirbhaya Shaji, Florbela Nunes, M. Ines Rocha, Elsa Ferreira Gomes, Helena Castro
Summary: This report introduces a graphical user interface called MigraR, which translates the coordinate positions of moving cells into measurable parameters of cell migration, and plots cell trajectories and migration metrics. By simplifying the data analysis process, this interface helps cell biologists without data analysis experience to quantify and visualize cell migration datasets.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Mamdouh Alenezi
Summary: The evolution of software systems and understanding their internal quality is crucial in software engineering. This study analyzed the evolution of object-oriented open-source software systems in terms of size, internal quality metrics, showing significant differences among systems in LOC, significant correlations between internal quality metrics, and positive effects of complexity and inheritance on LOC. Coupling and Cohesion did not show significant effects on LOC.
APPLIED SCIENCES-BASEL
(2021)
Article
Computer Science, Software Engineering
Damian A. Tamburri, Fabio Palomba, Rick Kazman
Summary: Software engineering success relies on balancing distance, culture, global engineering practices and more. This paper introduces an automated approach, CodeFace4Smells, to identify four community smell types. A large-scale empirical study on 60 open-source communities reveals that community smells are highly diffused in open-source and perceived by developers as significant issues for software community evolution.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Computer Science, Software Engineering
Georgia M. Kapitsaki, Georgia Charalambous
Summary: This paper introduces findOSSLicense, a license recommender that helps users choose the appropriate open source license for their software under creation. The recommendation process is based on a hybrid recommender that considers user needs and system flexibility, and involves analysis of existing open source licenses.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Computer Science, Information Systems
Marc Oriol, Carlos Mueller, Jordi Marco, Pablo Fernandez, Xavier Franch, Antonio Ruiz-Cortes
Summary: Recent surveys show that the use of Open Source Software (OSS) is increasingly important for organizations. However, choosing the right OSS or contributing to its development is a complex task. There is a lack of useful OSSECO analysis tools for potential adopters or contributors.
INTERNET OF THINGS
(2023)
Article
Statistics & Probability
Nascif Abousalh-Neto, Meijian Guan, Ruth Hummel
Summary: JMP is a commercial software designed for interactive data analysis, featuring a high-level, visual interface suitable for teaching and model building. It is also extensible, allowing the embedding and deployment to open-source environments. This paper explores use cases illustrating how JMP users can benefit from open-source software while still leveraging JMP's streamlined interface and robust capabilities.
Article
Computer Science, Artificial Intelligence
Linda Erlenhov, Francisco Gomes de Oliveira Neto, Philipp Leitner
Summary: This paper presents an empirical study on bot activity, using both quantitative and qualitative analysis. The study highlights the differences in definitions of bot activity in open-source software and identifies tools that comply with the characteristics of Devbots. The analysis also reveals that most projects experiment with multiple bots before making a decision on adoption or switching. Factors such as generated noise and required adaptation in development practices are found to drive discussions about the adoption or removal of Devbots.
PEERJ COMPUTER SCIENCE
(2022)
Article
Computer Science, Information Systems
Di Cui, Lingling Fan, Sen Chen, Yuanfang Cai, Qinghua Zheng, Yang Liu, Ting Liu
Summary: This paper presents the first attempt to understand bug fixes from the perspective of dependencies. A systematic study on bug fixes collected from 157 Apache open source projects is conducted, revealing a relatively high proportion of bug fixes introducing dependency-level changes. These fixes are strongly correlated with high priority, large fixing churn, long fixing time, frequent bug reopening, and bug inducing. In addition, patched files with dependency-level changes consume much more maintenance costs compared to those without these changes.
SCIENCE CHINA-INFORMATION SCIENCES
(2022)
Article
Engineering, Manufacturing
Zach Zhizhong Zhou, Vidyanand Choudhary
Summary: The impact of competition from open source software on proprietary software providers is complex, sometimes leading to improvements in software quality and pricing by proprietary providers, but also potentially causing a decrease in social welfare.
PRODUCTION AND OPERATIONS MANAGEMENT
(2022)
Article
Computer Science, Software Engineering
Xiao Ling, Rishabh Agrawal, Tim Menzies
Summary: Different types of projects require tuning of prioritization approaches for effective detection and fixing of software faults.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Computer Science, Software Engineering
Apostolos Kritikos, Prodromos Polychroniadis, Ioannis Stamelos
Summary: This work presents Source-o-grapher, a tool for investigating the software resilience aspects of Open Source Software (OSS) projects. The tool evaluates OSS projects based on various metrics from the literature, and assesses them on four major dimensions: structural (source code), business and legal, integration, and social (community of the project). The tool automatically acquires many of these metrics from the project's Github repository, while some others are manually inputted by the expert conducting the analysis.
Article
Management
Nataliya Langburd Wright, Frank Nagle, Shane Greenstein
Summary: This study is the first to explore the relationship between open source software (OSS) and entrepreneurship on a global scale. Using cross-country data, the study shows that participation on the GitHub OSS platform has a positive impact on the founding of new technology ventures in a country. The study also finds that OSS contributions lead to ventures that are more mission- and global-oriented and of higher quality.
Article
Computer Science, Interdisciplinary Applications
Hans Friedrich Stabenau, Jonathan W. Waks
Summary: This article introduces an open-source software package called BRAVEHEART for scientific analysis of digital standard 12-lead ECGs. The software provides automatic processing of ECG and VCG signals, customizable measurements, and output of results. It aims to facilitate the development of ECG/VCG analysis and improve the reproducibility of future studies.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Engineering, Civil
Julien Lerat, Mark Thyer, David McInerney, Dmitri Kavetski, Fitsum Woldemeskel, Christopher Pickett-Heaps, Daeyhok Shin, Paul Feikema
JOURNAL OF HYDROLOGY
(2020)
Article
Environmental Sciences
David McInerney, Mark Thyer, Dmitri Kavetski, Richard Laugesen, Narendra Tuteja, George Kuczera
WATER RESOURCES RESEARCH
(2020)
Article
Environmental Sciences
E. Perret, B. Renard, J. Le Coz
Summary: A model accounting for transient changes due to vegetation was developed to manage stage-discharge relations at hydrometric stations affected by seasonal aquatic vegetation. The model estimates parameters and uncertainty through Bayesian inference and allows the use of qualitative observations on the plant growth state for validation. The case study showed significant improvements in predicting water discharge compared to a standard model with no vegetation module.
WATER RESOURCES RESEARCH
(2021)
Article
Multidisciplinary Sciences
Lukas Gudmundsson, Julien Boulange, Hong X. Do, Simon N. Gosling, Manolis G. Grillakis, Aristeidis G. Koutroulis, Michael Leonard, Junguo Liu, Hannes Muller Schmied, Lamprini Papadimitriou, Yadu Pokhrel, Sonia Seneviratne, Yusuke Satoh, Wim Thiery, Seth Westra, Xuebin Zhang, Fang Zhao
Summary: The study analyzed global river flow data from 7250 observatories and found that anthropogenic climate change has an impact on river flow. The research showed that some regions are consistently experiencing drying trends, while others are consistently experiencing wetting trends.
Article
Water Resources
Jerome Le Coz, Benjamin Renard, Vincent Vansuyt, Magali Jodeau, Alexandre Hauet
Summary: The development of video-based hydrometry requires orthorectification of images to ensure each pixel has the same physical size. Implicit and explicit calibration methods are commonly used to compute the coefficients of the transformation, which are beneficial in obtaining precise estimates.
HYDROLOGICAL PROCESSES
(2021)
Article
Environmental Sciences
M. Darienzo, B. Renard, J. Le Coz, M. Lang
Summary: The method proposed in the study utilizes a Bayesian framework and recursive segmentation to estimate shift times in stage-discharge rating curves, effectively separating observational changes from rating curve uncertainties.
WATER RESOURCES RESEARCH
(2021)
Article
Environmental Sciences
David McInerney, Mark Thyer, Dmitri Kavetski, Richard Laugesen, Fitsum Woldemeskel, Narendra Tuteja, George Kuczera
Summary: Sub-seasonal streamflow forecasts are crucial for water resource management, especially in predicting high and low flows. The study reveals that stratifying forecasts into high/low flow ranges can highlight significant under/over-estimations of forecast uncertainty. By introducing a flow-dependent component, the MuTHRE-FD model significantly improves the reliability of sub-seasonal forecasts for both high and low flows.
WATER RESOURCES RESEARCH
(2021)
Article
Water Resources
Ivan Horner, Jerome Le Coz, Benjamin Renard, Flora Branger, Mickael Lagouy
Summary: Streamflow data measured at hydrometric stations are influenced by uncertainty in water level measurements, which increases as the sensitivity of the stage-discharge controls decreases. The study demonstrates the importance of control sensitivity in reducing the uncertainty of streamflow, especially for low flows. Quantifying this uncertainty component is crucial for optimizing hydrometric station design.
HYDROLOGICAL PROCESSES
(2022)
Article
Engineering, Civil
Ruijie Liang, Mark A. Thyer, Holger R. Maier, Graeme C. Dandy, Michael Di Matteo
Summary: This study introduces a two-step method to minimize peak flows by optimizing the layout of distributed storages and their RTC strategies, showing that optimized layouts can achieve higher peak flow reductions than traditional end-of-system storage. The addition of optimized RTC can further reduce peak flows, with more significant effects on smaller storage volumes. Analysis of flood hydrographs indicates that peak flow reductions are achieved through attenuation at individual storages and delaying hydrographs to reduce coincidence at catchment confluences.
JOURNAL OF HYDROLOGY
(2021)
Article
Engineering, Civil
Jason Hunter, Mark Thyer, David McInerney, Dmitri Kavetski
Summary: This study demonstrates that using inconsistent objective functions in hydrological modeling can lead to poor-quality probabilistic predictions, while an enhanced error model can overcome this issue and achieve high-quality probabilistic predictions.
JOURNAL OF HYDROLOGY
(2021)
Article
Environmental Sciences
B. Renard, M. Thyer, D. McInerney, D. Kavetski, M. Leonard, S. Westra
Summary: This paper presents a Bayesian hierarchical framework for risk assessment of climate-sensitive systems. It models the joint distribution of multiple spatially distributed variables and their temporal variability by using hidden climate indices (HCIs) and Gaussian processes. The flexibility of the framework is demonstrated in a case study in Southeast Australia, which accurately reproduces intervariable and intersite dependencies.
WATER RESOURCES RESEARCH
(2022)
Article
Engineering, Civil
Emeline Perret, Benoit Camenen, Celine Berni, Kamal El Kadi Abderrezzak, Benjamin Renard
Summary: Our data indicates significant variation in the critical Shields stress values for initial sediment motion. The dispersal is mainly caused by differences in the methodological procedures for determining the onset of movement and the estimation of bed shear stress. The threshold for sediment motion is influenced by factors such as grain size, bed composition, arrangement, and slope. New models are proposed to estimate the critical Shields number, incorporating grain size, bed slope, or both. The best results are obtained with a four-parameter model based on grain size and bed slope, but there is still considerable model uncertainty, suggesting the need for additional input parameters.
JOURNAL OF HYDRAULIC ENGINEERING
(2023)
Article
Water Resources
Michel Lang, Matteo Darienzo, Jerome Le Coz, Benjamin Renard
Summary: A diagnosis of the safety of dikes from floods along the River Rhine downstream of Strasbourg was conducted by INRAE on behalf of DREAL Grand-Est. The flood discharge uncertainties of two long series in Basel and Maxau were analyzed using the BaRatin model. Statistical tests revealed heterogeneities in both series, which were partly caused by hydraulic developments on the Rhine in the past two centuries. The corrected series showed better quality, but there was still a step-change around 1966-1976 in Basel and Maxau, possibly due to a change in the climate circulation regime in Central Europe since the 1970s.
LHB-HYDROSCIENCE JOURNAL
(2022)
Article
Computer Science, Interdisciplinary Applications
Jeffrey Wade, Christa Kelleher, Barret L. Kurylyk
Summary: This study developed a physically-based water temperature model coupled with the National Water Model (NWM) to assess the potential for water temperature prediction to be incorporated into the NWM at the continental scale. By evaluating different model configurations of increasing complexity, the study successfully simulated hourly water temperatures in the forested headwaters of H.J. Andrews Experimental Forest in Oregon, USA, providing a basis for integrating water temperature simulation with predictions from the NWM.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Shaun SH. Kim, Lucy A. Marshall, Justin D. Hughes, Lynn Seo, Julien Lerat, Ashish Sharma, Jai Vaze
Summary: A major challenge in hydrologic modelling is producing reliable uncertainty estimates outside of calibration periods. This research addresses the challenge by improving model structures and error models to more reliably estimate uncertainty. The combination of the RBS model and SPUE produces statistically reliable predictions and shows better matching performance in tests.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Juan Pedro Carbonell-Rivera, Javier Estornell, Luis Angel Ruiz, Pablo Crespo-Peremarch, Jaime Almonacid-Caballer
Summary: This study presents Class3Dp, a software for classifying vegetation species in colored point clouds. The software utilizes geometric, spectral, and neighborhood features along with machine learning methods to classify the point cloud, allowing for the recognition of species composition in an ecosystem.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Zhi Li, Daniel Caviedes-Voullieme, Ilhan Oezgen-Xian, Simin Jiang, Na Zheng
Summary: The optimal strategy for solving the Richards equation numerically depends on the specific problem, particularly when using GPUs. This study investigates the parallel performance of four numerical schemes on both CPUs and GPUs. The results show that the scaling of Richards solvers on GPUs is influenced by various factors. Compared to CPUs, parallel simulations on GPUs exhibit significant variation in scaling across different code sections, with poorly-scaled components potentially impacting overall performance. Nonetheless, using GPUs can greatly enhance computational speed, especially for large-scale problems.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Ludovic Cassan, Leo Pujol, Paul Lonca, Romain Guibert, Helene Roux, Olivier Mercier, Dominique Courret, Sylvain Richard, Pierre Horgue
Summary: Methods and algorithms for measuring stream surface velocities have been continuously developed over the past five years to adapt to specific flow typologies. The free software ANDROMEDE allows easy use and comparison of these methods with image processing capabilities designed for measurements in natural environments and with unmanned aerial vehicles. The validation of the integrated algorithms is presented on three case studies that represent the targeted applications: the study of currents for eco-hydraulics, the measurement of low water flows and the diagnosis of hydraulic structures. The field measurements are in very good agreement with the optical measurements and demonstrate the usefulness of the tool for rapid flow diagnosis for all the intended applications.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Mariia Kozlova, Robert J. Moss, Julian Scott Yeomans, Jef Caers
Summary: This paper introduces a framework for quantitative sensitivity analysis using the SimDec visualization method, and tests its effectiveness on decision-making problems. The framework captures critical information in the presence of heterogeneous effects, and enhances its practicality by introducing a formal definition and classification of heterogeneous effects.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Chad R. Palmer, Denis Valle, Edward V. Camp, Wendy-Lin Bartels, Martha C. Monroe
Summary: Simulation games have been used in natural resource management for education and communication purposes, but not for data collection. This research introduces a new design process which involves stakeholders and emphasizes usability, relevance, and credibility testing criteria. The result is a finalized simulation game for future research.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Tao Wang, Chenming Zhang, Ye Ma, Harald Hofmann, Congrui Li, Zicheng Zhao
Summary: This study used numerical modeling to investigate the formation process of iron curtains under different freshwater and seawater conditions. It was found that Fe(OH)3 accumulates on the freshwater side, while the precipitation is inhibited on the seaward side due to high H+ concentrations. These findings enhance our understanding of iron transformation and distribution in subterranean estuaries.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Grant Hutchings, James Gattiker, Braden Scherting, Rodman R. Linn
Summary: Computational models for understanding and predicting fire in wildland and managed lands are becoming increasingly impactful. This paper addresses the characterization and population of mid-story fuels, which are not easily observable through traditional survey or remote sensing. The authors present a methodology to populate the mid-story using a generative model for fuel placement, which can be calibrated based on limited observation datasets or expert guidance. The connection of terrestrial LiDAR as the observations used to calibrate the generative model is emphasized. Code for the methods in this paper is provided.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Saswata Nandi, Pratiman Patel, Sabyasachi Swain
Summary: IMDLIB is an open-source Python library that simplifies the retrieval and processing of gridded meteorological data from IMD, enhancing data accessibility and facilitating hydro-climatic research and analysis.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
Article
Computer Science, Interdisciplinary Applications
Pengfei Wu, Jintao Liu, Meiyan Feng, Hu Liu
Summary: In this paper, a new flow distance algorithm called D infinity-TLI is proposed, which accurately estimates flow distance and width function using a two-segment-distance strategy and triangulation with linear interpolation method. The evaluation results show that D infinity-TLI outperforms existing algorithms and has a low mean absolute relative error.
ENVIRONMENTAL MODELLING & SOFTWARE
(2024)
