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To be of practical relevance for applications in systems biology, odeSD and odeSD mex are accessible via Matlab interfacesa, and we plan to make them more easily available through integrated modeling environments such as the SBToolbox2 [ 22] and COPASI [ 48], e.g. via the native C-language interface.
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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.
Interesting new developments include more refined non-polar solvation energy estimators, and implicit methods for modeling low-dielectric and heterogeneous environments such as membrane systems.
The enterprise models are represented in such modeling environment using unified modeling language (UML).
Such modeling environment comprises a central repository, model management system (MMS), translator, and standard application programming interface routines (APIs).
The standard GUI-based fMRI data processing environments, such as SPM, FSL [ 62] or AFNI [ 63], do not implement most of the modeling approaches described in this review.
Controlled environments, such as jails, are ideal.
Finally, we discuss the prospects for integration of these new representational techniques into existing modeling environments.
Today's modeling environments usually offer a variant of what we call amorphous heterogeneity to address this problem.
(iv)Many modeling environments are under continuous development.
This necessitates the use of suitably flexible modeling environments, though excessive flexibility can itself cause problems of overfitting.
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