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Povzetek: Accurate, standardized, and comparable methods for estimating biodiversity are crucial in ecology to properly assess and monitor the health of communities. Special cases of generalized entropy are commonly used to estimate alpha diversity. The related concept of generalized divergence can be used to estimate the beta diversity. Using cross entropy notion, we propose a modular decomposition of gamma diversity by using entropy and divergence functions. We prove that if alpha is Shannon entropy and beta is Kullback-Liebler divergence, the classical Whittaker’s gamma diversity is mathematically decomposed via our proposed local gamma index. To show the ecological application of this index and its generalization we compute the local gamma of several orders using a real large biological dataset. The index is discussed in detail for two limit cases, one where the contribution of rare species is the highest and one where richness and evenness are balanced. The index defines a gradient from communities that are dominated by a few common species toward samples shared among several uncommon ones. Our findings support divergence-based measures as practical estimators of beta diversity. Also, the framework here proposed, based on entropy, divergences and cross-entropies, allows us to compute the classic gamma diversity while providing components that are independent, comparable, self-reliant and pointwise distributed.
Ključne besede: biodiversity, entropy, ecology, computational modelling
Objavljeno v DiRROS: 28.10.2025; Ogledov: 181; Prenosov: 100
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Povzetek: This paper surveys existing ontologies for visualization, which formally define and organize knowledge about visualization concepts, techniques, and tools. Although visualization is a mature field, the rapid growth of data complexity makes semantically rich frameworks increasingly essential for building intelligent and automated visualization systems. Current ontologies remain fragmented, heterogeneous, and inconsistent in terminology and modeling strategies, limiting their coverage and adoption. We present a systematic analysis of representative ontologies, highlighting shared themes and, most importantly, the gaps that hinder unification. These gaps provide the foundations for developing a comprehensive, generic ontology of visualization, aimed at unifying core concepts and supporting reuse across research and practice.
Ključne besede: semantic modelling, visualization types, domain gaps, domain challenges, ontology
Objavljeno v DiRROS: 24.10.2025; Ogledov: 173; Prenosov: 67
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Povzetek: This study investigates heat and mass transfer during energetic melt-coolant interactions, focusing on film boiling around a hot melt particle in subcooled convective flow. The considered conditions, free-flow velocities of a few m/s, melt particle temperatures of several thousand K, particle diameters of several tens of a μm, and liquid subcooling of several tens of a K, align with TREPAM experiments (CEA, France). A two-phase computational fluid dynamics framework, based on the Volume of Fluid method, is used. An improved phase-change model is implemented, combining Chen’s explicit formulation of the phase-change intensity factor with the robustness of the conventional Lee model. The approach reduces sensitivity to empirical parameters and enhances phase-change localisation. Additional constraints on the intensity factor ensure numerical stability under extreme thermal conditions relevant to vapour energetic melt-coolant interactions. Simulations of TREPAM experiments demonstrate improved heat flux predictions and enhanced flow dynamics capture. Analysis of the simulated velocity fields reveal secondary flows in the vapour wake, impacting heat and mass transfer and emphasizing the need to resolve vapor-phase flow conditions. To fully validate proposed modifications to phase-change model further numerical and experimental investigation is required, focusing on vapour film morphology and localized heat transfer intensity.
Ključne besede: film boiling, extreme thermal conditions, phase-change modelling, computational fluid dynamics, two-phase flow
Objavljeno v DiRROS: 16.09.2025; Ogledov: 238; Prenosov: 109
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Povzetek: The main goal of epidemic modelling is to support the epidemic management through forecasts and analyses of past developments. With this in mind a robust and intuitive SEIR (Susceptible, Exposed, Infectious, Recovered) type model has been developed, applied and verified during the multiple waves of the COVID-19 epidemics in Slovenia since March 2020. The model parameters were based on the general characteristics of the COVID-19 disease reported globally for the entire planet and refined with the aggregate data available mostly on a daily basis in Slovenia, as for example the number of confirmed cases, hospitalized patients, hospitalized patients in intensive care units and deceased. The Slovenian aggregate data was also used to estimate the degree of immunisation due to past infections and vaccination, which reduces the number of susceptible persons for the disease. Examples of the model application are presented to illustrate its robustness and intuitiveness in both the forecasts and analyses of past developments. The analyses of past developments provided specific estimates of modelling parameters for Slovenia and quantified the effects of pharmaceutical and non-pharmaceutical interventions and various events on the development of the epidemics as measured through the reproduction number R. This empirically obtained information was then applied in the forecasts. Accurate forecasts are a great support for decision makers and for hospitals to plan appropriate actions in advance. The inherent uncertainties in the model and data were quantified through intuitive sensitivity analyses represented as different scenarios. The observed accuracy of the forecasts was impressively good also in demanding conditions, when various complex processes influencing the spread of the disease were going on in parallel. This demonstrates the robustness and relevance of the proposed model.
Ključne besede: epidemic, COVID-19, modelling SEIR, reproduction number
Objavljeno v DiRROS: 11.04.2025; Ogledov: 579; Prenosov: 261
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Povzetek: Systems biology aims to understand living organisms through mathematically modeling their behaviors at different organizational levels, ranging from molecules to populations. Modeling involves several steps, from determining the model purpose to developing the mathematical model, implementing it computationally, simulating the model’s behavior, evaluating, and refining the model. Importantly, model simulation results must be reproducible, ensuring that other researchers can obtain the same results after writing the code de novo and/or using different software tools. Guidelines to increase model reproducibility have been published. However, reproducibility remains a major challenge in this field. In this paper, we tackle this challenge for physiologically-based pharmacokinetic (PBPK) models, which represent the pharmacokinetics of chemicals following exposure in humans or animals. We summarize recommendations for PBPK model reporting that should apply during model development and implementation, in order to ensure model reproducibility and comprehensibility. We make a proposal aiming to harmonize abbreviations used in PBPK models. To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of MATLAB code converted to Systems Biology Markup Language format using MOCCASIN. As directions for future improvement, more tools to convert computational PBPK models from different software platforms into standard formats would increase the interoperability of these models. The application of other systems biology standards to PBPK models is encouraged. This work is the result of an interdisciplinary collaboration involving the ELIXIR systems biology community. More interdisciplinary collaborations like this would facilitate further harmonization and application of good modeling practices in different systems biology fields.
Ključne besede: pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology
Objavljeno v DiRROS: 07.11.2024; Ogledov: 950; Prenosov: 515
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