Software engineering for computational science: Past, present, future

A Johanson, W Hasselbring - Computing in Science & …, 2018 - ieeexplore.ieee.org
Despite the increasing importance of in silico experiments to the scientific discovery process,
state-of-the-art software engineering practices are rarely adopted in computational science …

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

DJ Klionsky, AK Abdel-Aziz, S Abdelfatah, M Abdellatif… - autophagy, 2021 - Taylor & Francis
In 2008, we published the first set of guidelines for standardizing research in autophagy.
Since then, this topic has received increasing attention, and many scientists have entered …

[HTML][HTML] Guidelines for the use and interpretation of assays for monitoring autophagy 1

DJ Klionsky, AK Abdel-Aziz, S Abdelfatah… - …, 2021 - pmc.ncbi.nlm.nih.gov
In 2008, we published the first set of guidelines for standardizing research in autophagy.
Since then, this topic has received increasing attention, and many scientists have entered …

Best practices for making reproducible biochemical models

VL Porubsky, AP Goldberg, AK Rampadarath… - Cell systems, 2020 - cell.com
Like many scientific disciplines, dynamical biochemical modeling is hindered by
irreproducible results. This limits the utility of biochemical models by making them difficult to …

Domain-specific architectures: Research problems and promising approaches

A Krishnakumar, U Ogras, R Marculescu… - ACM Transactions on …, 2023 - dl.acm.org
Process technology-driven performance and energy efficiency improvements have slowed
down as we approach physical design limits. General-purpose manycore architectures …

[KNIHA][B] Towards Bayesian model-based demography: Agency, complexity and uncertainty in migration studies

J Bijak - 2022 - library.oapen.org
This open access book presents a ground-breaking approach to develo** micro-
foundations for demography and migration studies. It offers a unique and novel methodology …

Validity frame–enabled model-based engineering processes

B Van Acker, P De Meulenaere, H Vangheluwe… - …, 2024 - journals.sagepub.com
Model-based systems engineering (MBSE) focuses on using models to support the design,
optimization, simulation, and ultimately deployment of complex cyber-physical systems …

Tellurium notebooks—an environment for reproducible dynamical modeling in systems biology

JK Medley, K Choi, M König, L Smith, S Gu… - PLoS computational …, 2018 - journals.plos.org
The considerable difficulty encountered in reproducing the results of published dynamical
models limits validation, exploration and reuse of this increasingly large biomedical …

Context, Composition, Automation, and Communication: The C2AC Roadmap for Modeling and Simulation

AM Uhrmacher, P Frazier, R Hähnle, F Klügl… - ACM Transactions on …, 2024 - dl.acm.org
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 current practices …

Trustworthy agent-based simulation: the case for domain-specific modelling languages

S Zschaler, FAC Polack - Software and Systems Modeling, 2023 - Springer
Simulation is a key tool for researching complex system behaviour. Agent-based simulation
has been applied across domains, such as biology, health, economics and urban sciences …