Characterizing cell-type spatial relationships across length scales in spatially resolved omics data by Rafael dos Santos Peixoto, Brendan F. Miller, Maigan A. Brusko, Gohta Aihara, Lyla Atta, Manjari Anant, Mark A. Atkinson, Todd M. Brusko, Clive H. Wasserfall, Jean Fan

“…To quantify such multi-scale cell-type spatial relationships, we present CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package. To demonstrate the utility of such multi-scale characterization, recapitulate expected cell-type spatial relationships, and evaluate against other cell-type spatial analyses, we apply CRAWDAD to various simulated and real SRO datasets of diverse tissues assayed by diverse SRO technologies. …”
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Smell-ML: A Machine Learning Framework for Detecting Rarely Studied Code Smells by Esraa Hamouda, Abeer El-Korany, Soha Makady

“…We evaluated Smell-ML on a dataset composed of 13 open source Java projects with 125 versions per project. …”
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Analysis of archive formats and program solutions for compression of text files by Artem Perepelitsyn, Alona Chepelevych, Andrii Litvinov

“…The obtained research results allow to propose the use of the open source archive format zpaq for compressing text or a set of project versions and documentation to achieve a compression ratio that is twice better than for rar format, and two percent better than for 7z and txz formats.…”
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LINKS. A System for Historical Family Reconstruction in the Netherlands by Kees Mandemakers, Gerrit Bloothooft, Fons Laan, Joe Raad, Rick J. Mourits, Richard L. Zijdeman

“…We will discuss two matching systems, the first is the original querying system that runs within a MySQL database environment and the second is a newly developed system, called burgerLinker, which is based on knowledge graphs and which is designed as a system that can be used independently from LINKS and is made available as open source software. Finally, we present the most important releases of LINKS data so far: two national releases that link birth and parental marriage certificates, creating families and pedigrees and an integrated dataset of persons, families and family trees in four provinces. …”
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SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes by M. Eremeyeva, Y. Din, N. Shirokii, N. Serov

“…Results In this work, we develop a machine learning based open-source platform SequenceCraft allowing experimental scientists to perform DNAzyme exploratory analysis via quantitative observed rate constant (kobs) estimation as well as statistical and clustering data analysis. …”
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COVID-19 Fatality: Statistical Evidence to Engender the Need for Focal Shift from Air Pollutants to Multi-dimensional Intervention by Satya S. Patra, Subhasmita Panda, Trupti Das, Boopathy Ramasamy

“…Therefore, the current study aims to explore the statistical soundness of association of COVID-19 fatality with PM2.5, NO2, and O3 concentration levels across 463 air quality monitoring stations located in 35 selected cities from USA, India and European Regions (France, Germany and Italy). An aggregated open-source air quality data source was used to download the PM2.5, NO2, and O3 concentration for > 900 days in the selected cities. …”
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Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms by Marianne Bachmann Salvy, Luca Santuari, Emanuel Schmid-Siegert, Nikolaos Lykoskoufis, Ioannis Xenarios, Bulak Arpat

“…To address this methodological gap, we introduce Seq2scFv, a novel open-source toolkit designed for analyzing in vitro display libraries from long-read sequencing platforms. …”
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Application of a spatial dataset for monitoring invasive woody plant species in the forests of Transcarpathia, Ukraine by Andriy Mihaly, Vasyl Roman

“…The dataset was developed based on forest inventory data using the open source QGIS program, which performed digitisation of forest plantation plans of permanent forest users and overlay analysis. …”
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INSPIRE Datahub: A Pan-African Integrated Suite of Services For Harmonising Longitudinal Population Health Data Using OHDSI Tools. by Bhattacharjee, Tathagata, Kiwuwa-Muyingo, Sylvia, Kanjala, Chifundo, Maoyi, Molulaqhooa L., Amadi, David, Ochola, Michael, Kadengye, Damazo, Gregory, Arofan, Kiragga, Agnes, Amelia, Taylor, Greenfield, Jay, Slaymaker, Emma, Todd, Jim, INSPIRE Network8

“…Methods: The INSPIRE datahub, part of the Implementation Network for Sharing Population Information from Research Entities (INSPIRE), employs the Observational Health Data Sciences and Informatics (OHDSI) open-source stack of tools and the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to harmonize data from African longitudinal population studies. …”
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Shear Wave Velocity Prediction with Hyperparameter Optimization by Gebrail Bekdaş, Yaren Aydın, Umit Işıkdağ, Sinan Melih Nigdeli, Dara Hajebi, Tae-Hyung Kim, Zong Woo Geem

“…The dataset used in this study is an open-source dataset, and the soil data are from the Taipei Basin. …”
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Detectability of Emission from Exoplanet Outflows Calculated by pyTPCI, a New 1D Radiation-hydrodynamic Code by Riley Rosener, Michael Zhang, Jacob L. Bean

“…We introduce pyTPCI, a new, open-source self-consistent 1D radiative-hydrodynamics code that is an improved version of The PLUTO-CLOUDY Interface. …”
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The NeuroML ecosystem for standardized multi-scale modeling in neuroscience by Ankur Sinha, Padraig Gleeson, Bóris Marin, Salvador Dura-Bernal, Sotirios Panagiotou, Sharon Crook, Matteo Cantarelli, Robert C Cannon, Andrew P Davison, Harsha Gurnani, Robin Angus Silver

“…It has enabled the development of a large ecosystem of interoperable open-source software tools for the creation, visualization, validation, and simulation of data-driven models. …”
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Practical analysis of using PPPH and raPPPid for Precise Point Positioning in Europe by Saber Mohamed, El-Mewafi Mahmoud, Awad Ahmed

“…Assessing the reliability of using open-source software packages for post-processing of the Global Navigation Satellite System (GNSS) is essential since GNSS modernization has the potential to assist satellite navigation users. …”
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Credit Cycles: Econometric Analysis and Evidence for Russia by N. V. Artamonov, D. V. Artamonov, V. A. Artamonov

“…All estimations are made in gretl, an open-source multiplatform econometric software.…”
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NIRS-BIDS: Brain Imaging Data Structure Extended to Near-Infrared Spectroscopy by Robert Luke, Robert Oostenveld, Helena Cockx, Guiomar Niso, Maureen J Shader, Felipe Orihuela-Espina, Hamish Innes-Brown, Stephen Tucker, David Boas, Meryem A. Yücel, Remi Gau, Taylor Salo, Stefan Appelhoff, Christopher J. Markiewicz, David McAlpine, The BIDS Maintainers, Luca Pollonini

“…Although the fNIRS community has been successful in disseminating open-source processing tools and a standard file format (SNIRF), reproducible research and sharing of fNIRS data amongst researchers has been hindered by a lack of standards and clarity over how study data should be organized and stored. …”
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Self-sovereign management scheme of personal health record with personal data store and decentralized identifier by Tong Min Kim, Taehoon Ko, Byoung Woo Hwang, Hyung Goo Paek, Wan Yeon Lee

“…We developed a prototype using the Solid open-source library and Hyperledger Aries protocol. …”
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Cost-Effective Autonomous Drone Navigation Using Reinforcement Learning: Simulation and Real-World Validation by Tomasz Czarnecki, Marek Stawowy, Adam Kadłubowski

“…It involves using commercially available, cost-effective drones and open-source or free simulation tools, significantly reducing entry barriers for potential users. …”
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The Switchmaze: an open-design device for measuring motivation and drive switching in mice by Hartmann, Clara, Mahajan, Ambika, Borges, Vinicius, Razenberg, Lotte, Thönnes, Yves, Karnani, Mahesh Miikael

“…We designed an automated extended home-cage, the Switchmaze, using open-source hardware and software. In this study, we use it to establish a behavioural assay of motivational switching in mice. …”
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EzSkiROS: enhancing robot skill composition with embedded DSL for early error detection by Momina Rizwan, Christoph Reichenbach, Ricardo Caldas, Matthias Mayr, Volker Krueger

“…We describe design patterns suitable for robot programming and show how to use these design patterns for DSL embedding in Python, using two case studies on an open-source robot skill platform SkiROS2, designed for the composition of robot skills. …”
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An Object-Oriented Systems Engineering Point of View to Develop Controllers of Quadrotor Unmanned Aerial Vehicles by Ngo Van Hien, Van-Thuan Truong, Ngoc-Tam Bui

“…The detailed PIM is subsequently transformed into the PSM by open-source platforms to rapidly implement and deploy the Q-UAV controller. …”
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