The extended quadrature method of moments (EQMOM) for the solution of population balance equations (PBE) is implemented in the open-source computational fluid dynamic (CFD) toolbox OpenFOAM as part of the OpenQBMM project.
Here, we present Massively Parallel Dynamic Causal Modeling (mpdcm), a toolbox designed to address this bottleneck.
Simulation: the toolbox offers several dynamic simulation tasks (AMIGO_SModel, AMIGO_SObs and AMIGO_SData) to solve system dynamics under given values of model unknowns and given experimental schemes.
Thus, despite the very ancient origin of all proteasome regulators in eukaryotes, the "proteasome toolbox" appears as a dynamic adaptive machinery, whose requirement in eukaryotic cell physiology has greatly varied depending on species biology.
While many existing tools could benefit from improved brightness, higher dynamic range, and increased specificity, the current toolbox has nevertheless provided an unprecedented view of accessible metal pools in live cells and organisms.
In this regard, the recently developed toolbox DOTcvpSB [ 9] can handle the dynamic optimization of lumped systems (described in terms of ordinary differential equations), such as those related to biochemical processes (see the reviews by Banga et al. [ 7, 8, 10] and the works cited therein), or to biomedical systems [ 11- 16].
For integrating the dynamic model and optimal parameter estimation we used the MATLAB toolbox PottersWheel [ 43] including multi-experiment fitting.
Pure and mixed culture dynamic flux balance models were solved using the Mosek optimization toolbox (Mosek ApS, Denmark) to resolve the linear program for intracellular metabolism within Matlab (Mathworks, Natick, MA) [ 30].
Here, we describe a comprehensive quantitative biophysical toolbox which can be used for rigorous analysis of dynamic protein-nucleic acid complexes and is applied to the study of eukaryotic transcription initiation.
Banjo package (Smith et al., 2006): Bayesian ANalysis with Java Objects, Bayes Net Toolbox (Murphy, 2002) for Matlab with an extension for dynamic Bayesian networks inference using MCMC (Husmeier, 2003).
