24 papers · ranked by Valyu relevance
Xianni Zhong, Jihui Zhao, Liping Sun
A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging…
Balázs Szigeti, Yosef D. Roth, John A. P. Sekar, Arthur P. Goldberg + 2 more
Whole-cell models of human cells are a central goal of systems biology. Such models could help researchers understand cell biology and help physicians treat disease. Despite significant challenges, we believe that human whole-cell models are rapidly becoming feasible. To develop a plan for achieving human whole-cell…
Barak Raveh, Liping Sun, Kate L. White, Tanmoy Sanyal + 11 more
Comprehensive modeling of a whole cell requires an integration of vast amounts of information on various aspects of the cell and its parts. To divide-and-conquer this task, we introduce Bayesian metamodeling, a general approach to modeling complex systems by integrating a collection of heterogeneous input models. Each…
Eran Agmon, Ryan K Spangler
Building multiscale biological models requires the integration of independently developed submodels, which means moving shared variables between them and coordinating when each submodel runs. Existing tools typically address isolated biological mechanisms with specific numerical methods, rarely specify which variables…
J Kyle Medley, Kiri Choi, Matthias König, Lucian Smith + 4 more
The considerable difficulty encountered in reproducing the results of published dynamical models limits validation, exploration and reuse of this increasingly large biomedical research resource. To address this problem, we have developed Tellurium Notebook, a software system that facilitates building reproducible…
Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin
It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the…
Daniel Machado, Rafael S Costa, Miguel Rocha, Eugénio C Ferreira + 2 more
'Bruce Tidor' 'Isabel Rocha'] Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their…
Linda-Sophie Schneider, Patrick Krauß, Nadine Schiering, Christopher Syben + 2 more
Mathematical models are vital to the field of metrology, playing a key role in the derivation of measurement results and the calculation of uncertainties from measurement data, informed by an understanding of the measurement process. These models generally represent the correlation between the quantity being measured…
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…
Mingwang Shen, Yanni Xiao, Libin Rong
Since the re-emergence of Ebola in West Africa in 2014, comprehensive and stringent interventions have been implemented to decelerate the spread of the disease. The effectiveness of interventions still remains unclear. In this paper, we develop an epidemiological model that includes various controlling measures to…
Christopher W. Lorton, Joshua L. Proctor, Min K. Roh, Philip A. Welkhoff
The compartmental modeling software (CMS) is an open source computational framework that can simulate discrete, stochastic reaction models which are often utilized to describe complex systems from epidemiology and systems biology. In this article, we report the computational requirements, the novel input model…
Klaus‐Dieter Sommer, P M Harris, Sascha Eichstädt, Roland Füßl + 9 more
'Tanja Dorst' 'Andreas Schütze' 'Michael Heizmann' 'Nadine Schiering' 'Andreas Maier' 'Yuhui Luo' 'Christos Tachtatzis' 'Ivan Andonović' 'Gordon Gourlay'] - 1 Technische Universitaet Ilmenau, Germany - 2 National Physical Laboratory, Teddington, United Kingdom - 3 Physikalisch-Technische Bundesanstalt, Braunschweig and…
N. Furian, M. O’Sullivan, C. Walker, S. Vössner + 1 more
Conceptual Modeling (CM) is a fundamental step in a simulation project. Nevertheless, it is only recently that structured approaches towards the definition and formulation of conceptual models have gained importance in the Discrete Event Simulation (DES) community. As a consequence, frameworks and guidelines for…
Melissa Tomkins
Connecting multiple models as modules across spatial and temporal scales is a non-trivial undertaking. Even models written in the same language, as in Chew et al. (), require careful consideration and handling of time units, model parameters, and differences in the way the same variables are characterised in different…
Ahmed Abdelmonem Hemedan, Reinhard Schneider, Marek Ostaszewski
Computational modeling has emerged as a critical tool in investigating the complex molecular processes involved in biological systems and diseases. In this study, we apply Boolean modeling to uncover the molecular mechanisms underlying Parkinson’s disease (PD), one of the most prevalent neurodegenerative disorders. Our…
Authors not listed
Electrolyte wetting in a lithium-ion battery (LIB) cell is a time-intensive, quality-critical manufacturing step that determines the degree of homogeneity of lithium ion's transport within the electrode and separator pores, affecting ionic conductivity and current density. If the electrolyte is inadequately…
Gunther Eysenbach, Christine Hudak, Siobhan Hugh-Jones, Louise Freebairn + 8 more
Background Despite significant investment, mental health issues remain a leading cause of death among young people globally. Sophisticated decision analysis methods are needed to better understand the dynamic and multisector drivers of youth mental health. System modeling can help explore complex issues such as youth…
Mohit Agarwal, Parameshwaran Pasupathy, Xuehai Wu, Stephen S. Recchia + 1 more
'Stephen S. Recchia' 'Assimina A. Pelegri'] Herein, state-of-the-art multiscale modeling methods have been described. This research includes notable molecular, micro-, meso-, and macroscale models for hard (polymer, metal, yarn, fiber, fiber-reinforced polymer, and polymer matrix composites) and soft (biological…
John D. Jakeman, Lorena A. Barba, Joaquim R. R. A. Martins, Thomas O'Leary-Roseberry
"Thomas O'Leary-Roseberry"] Scientific machine learning (SciML) models are transforming many scientific disciplines. However, the development of good modeling practices to increase the trustworthiness of SciML has lagged behind its application, limiting its potential impact. The goal of this paper is to start a…
Adelinde M. Uhrmacher, Peter I. Frazier, Reiner Hähnle, Franziska Klügl + 8 more
'Franziska Klügl' 'Fabian Lorig' 'Bertram Ludäscher' 'Laura Nenzi' 'Cristina Ruiz-Martín' 'Bernhard Rumpe⋆' 'Claudia Szabo' 'Gabriel Wainer' 'Pia Wilsdorf'] Simulation has become, in many application areas, a sine-qua-non. Most recently, COVID-19 has underlined the importance of simulation studies and limitations in…
Peter Sagmeister, Lukas Melnizky, Jason Williams, C. Oliver Kappe
In modern pharmaceutical research, the demand for expeditious development of synthetic routes to active pharmaceutical ingredients (APIs) has led to a paradigm shift towards data-rich process development. Conventional methodologies en-compass prolonged timelines for reaction and analytical model developments. Both…
Authors not listed
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high…
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…
Authors not listed
Continuous manufacturing processes offer significant advantages over batch processes, including easier scalability, reduced costs, lower raw material and solvent consumption, and improved energy efficiency. A robust techno-economic assessment is therefore essential to evaluate and facilitate the adoption of such…