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Methodologies, like co-simulation which allows for parallel simulation at different time-scales in different modules, and modeling environments for integrative models including different types of equations (ODEs, PDEs, SDEs etc) were discussed and evaluated.
The more comprehensive modeling environments for systems biology, such as CellDesigner [ 3], COPASI [ 4], Virtual Cell [ 5] and others, have been gradually enriched and now offer a wealth of features for modelers.
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Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems.
It also describes the modeling environment for software and hardware (MESH) environment for hardware and software modeling.
Using a Cellular Automaton (CA) as a modeling environment for discrete systems with local dynamics, we study the boundary conditions for such pattern-dependent genetic erosion.
A graphical user interface, Piraña, was developed that offers a complete modeling environment for NONMEM, enabling both novice and advanced users to increase efficiency of their workflow.
A comparative transient simulation analysis for domestic buildings with a floor-embedded heating system coupled to a modern air source heat-pump (ASHP) has been carried out using the TRNSYS numerical modeling environment for various UK locations.
As the first, fully integrated and quantitative modeling environment for the study of ion transport dynamics in a plant cell, OnGuard offers a unique tool for exploring homeostatic properties emerging from the interactions of ion transport, both at the plasma membrane and tonoplast in the guard cell.
In this work we describe and assess the performance of Nanotools, a feature of the MoDena software we are currently developing in the framework of a granted EU project devoted to the implementation of a multiscale modeling environment for nanomaterials and systems by design.
A company called Adaptive Computing started in 2001 as a scheduling and modeling environment for large-scale, high-performance computing environments.
NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com