25 papers · ranked by Valyu relevance
Erik Butterworth, Bartholomew E. Jardine, Gary M. Raymond, Maxwell L. Neal + 1 more
JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter…
Maurice HT Ling
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such endeavors is worthwhile, exist to this day. Here, I argue that most of learning is…
Muffy Calder, Claire Craig, Dave Culley, Richard de Cani + 15 more
'Christl A. Donnelly' 'Rowan Douglas' 'Bruce Edmonds' 'Jonathon Gascoigne' 'Nigel Gilbert' 'Caroline Hargrove' 'Derwen Hinds' 'David C. Lane' 'Dervilla Mitchell' 'Giles Pavey' 'David Robertson' 'Bridget Rosewell' 'Spencer Sherwin' 'Mark Walport' 'Alan Wilson'] In order to deal with an increasingly complex world, we…
Nestor V. Torres, Guido Santos
In this communication, we introduce a general framework and discussion on the role of models and the modeling process in the field of biosciences. The objective is to sum up the common procedures during the formalization and analysis of a biological problem from the perspective of Systems Biology, which approaches the…
Reiner Jung, Sven Gundlach, Wilhelm Hasselbring
In this paper, we employ process modeling for analyzing scientific software development in ocean science to advance the state in engineering of ocean system models and to better understand how ocean system models are developed and maintained in ocean science. We interviewed domain experts in semi-structured interviews…
Chenxi Wang, Jihui Zhao, Jingjing Zheng, Barak Raveh + 2 more
Developing and optimizing models for complex systems poses challenges due to the inherent complexity introduced by multiple types of input information and sources of uncertainty. In this study, we utilize Bayesian formalism to analytically examine the propagation of probability in the modeling process and propose…
Julio Vera, Christopher Lischer, Momchil Nenov, Svetoslav Nikolov + 2 more
'Xin Lai' 'Martin Eberhardt'] In most disciplines of natural sciences and engineering, mathematical and computational modelling are mainstay methods which are usefulness beyond doubt. These disciplines would not have reached today’s level of sophistication without an intensive use of mathematical and computational…
Alexander L.R. Lubbock, Carlos F. Lopez
Computational modeling has become an established technique to encode mathematical representations of cellular processes and gain mechanistic insights that drive testable predictions. These models are often constructed using graphical user interfaces or domain-specific languages, with SBML used for interchange. Models…
Sabah Al‐Fedaghi
A conceptual model can be used to manage complexity in both the design and implementation phases of the system development life cycle. Such a model requires a firm grasp of the abstract principles on which a system is based, as well as an understanding of the high-level nature of the representation of entities and…
Vahid Moosavi
We discuss that how the majority of traditional modeling approaches are following the idealism point of view in scientific modeling, which follow the set theoretical notions of models based on abstract universals. We show that while successful in many classical modeling domains, there are fundamental limits to the…
Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Thierry Hoch + 3 more
There is currently an overwhelming increased interest in predictive biology and computational modelling. The development of reliable, reproducible and revisable simulation models in computational life sciences is often pointed out as a challenging issue. Population dynamics, including epidemiology, has not yet…
Authors not listed
Deriving versatile and robust mechanistic models from experimental data is a key challenge in engineering and natural sciences. This is especially true in chemical reaction engineering, where reactor manufacturers and operators increasingly pursue the development and maintenance of digital twins that rely on frequent…
Authors not listed
Kinetic modeling is essential for predicting changes in food quality during processing and storage. This study evaluates the application of physics-informed neural networks (PINN) for food kinetic modeling, integrating kinetic insights into neural network frameworks. Based on three case studies, namely seed drying…
Teegwendé V. Porgo, Susan L. Norris, Georgia Salanti, Leigh F. Johnson + 4 more
'Leigh F. Johnson' 'Julie A. Simpson' 'Nicola Low' 'Matthias Egger' 'Christian L. Althaus'] Mathematical modeling studies are increasingly recognised as an important tool for evidence synthesis and to inform clinical and public health decision-making, particularly when data from systematic reviews of primary studies do…
Marvin van Aalst, Oliver Ebenhöh, Anna Matuszyńska
Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies and disease evolution or transmission. Unfortunately, despite community efforts leading to the development of…
Anthony A. Hyman
Cell biologists are interested in how complexity arises from the interaction of different molecules. However, cells are many orders of magnitude larger than the protein-binding interfaces. To bridge these vast difference in scales, biologists construct hierarchies of organization of cellular structures. I describe how…
Luca Serena, Moreno Marzolla, Gabriele D’Angelo, Stefano Ferretti
—Multilevel modeling and simulation (M&S) is becoming increasingly relevant due to the benefits that this methodology offers. Multilevel models allow users to describe a system at multiple levels of detail. From one side, this can make better use of computational resources, since the more detailed and time-consuming…
Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran + 2 more
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in…
Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Reproducible, understandable models that can be reused and combined to true multi-scale systems are required to solve the present and future challenges of systems biology. However, many mathematical models are still built for a single purpose and reusing them in a different context can be challenging due to an…
Serdar Abut
Bilgisayar modellemesi ve simülasyonu, sistem davranışlarının analiz etmek ve tanımlayıcı veya tahmine dayalı modlarda işleyişindeki stratejileri değerlendirmek için kullanılmaktadır (Abar ve ark., 2017). Model kavramı, halihazırda var olan veya henüz planlanmış belirli bir gerçekliğin soyut ve basitleştirilmiş bir…
Muhammad Farman, Muhammad Farhan Tabassum, Muhammad Saeed, Nazir Ahmad Chaudhry
Hepatitis B is the main public health problem of the whole world. In epidemiology, mathematical models perform a key role in understanding the dynamics of infectious diseases. This paper proposes Padé approximation (Pa) with Differential Evolution (DE) for obtaining solution of Hepatitis-B model which is nonlinear…
Authors not listed
Accurate prediction of battery behavior under different dynamic operating conditions is critical for both fundamental research and practical applications. However, the diversity of emerging materials and cell architectures presents significant challenges to the generalizability of conventional prognostic approaches.…
Authors not listed
Accurate modeling of drug concentration--time (C--t) profiles is central to pharmacokinetics (PK) and plays a critical role in both early-stage compound selection and late-stage individualized dosing. Traditional PK model offer mechanistic interpretability but often rely on rigid assumptions, extensive…
Saer Samanipour, Jake O'Brien, Malcolm Reid, Kevin Thomas + 1 more
The European Chemicals Agency (ECHA) and US Environmental Protection Agency (EPA) have listed approximately 800k chemicals that must be further investigated for their potential environmental and/or human health risk. A significant number of these chemicals have large enough global volumes of consumption (e.g.…
Tianfan Jin, Brett M Savoie
Contemporary machine learning algorithms have largely succeeded in automating the development of mathematical models from data. Although this is a striking accomplishment, it leaves unaddressed the multitude of scenarios, especially across the chemical sciences and engineering, where deductive, rather than inductive…