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.
The following algorithm is implemented in version 2.8 of the freely available tool BIOCHAM, a modeling environment for the analysis of biological systems (Calzone et al., 2006).
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.
Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems.
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.
This necessitates the use of suitably flexible modeling environments, though excessive flexibility can itself cause problems of overfitting.
Higher program-representation levels include, beside the source-code level, languages of domain-specific modeling environments with automatic code generation.
The "Literature review" section presents key design principles guiding the integration of CT and science education in CTSiM, and reviews known challenges and scaffolds for CT-based environments and learning-by-modeling environments for science.
