CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks

CRNreals: a toolbox for distinguishability and identifiability analysis of chemical reaction networks USER GUIDE

Easy parameter identifiability analysis with COPASI

BACKGROUND AND SCOPE Differential equation systems modeling biochemical reaction networks can only give quantitative predictions, when they are in accordance with experimental data. However, even if a model can well recapitulate given data, it is often the case that some of its kinetic parameters can be arbitrarily chosen without significantly affecting the simulation results. This indicates a ...

Numerical modeling for nonlinear biochemical reaction networks

Nowadays, numerical models have great importance in every field of science, especially for solving the nonlinear differential equations, partial differential equations, biochemical reactions, etc. The total time evolution of the reactant concentrations in the basic enzyme-substrate reaction is simulated by the Runge-Kutta of order four (RK4) and by nonstandard finite difference (NSFD) method. A...

Integrating software packages for the analysis of biological pathway networks

Interactions at the cellular level are essential for maintaining the fundamental life processes in biological systems. The relationships that are established due to the biochemical reactions occurring within the cells often give rise to extremely complex network structures that may be conveniently represented by bipartite graphs; such networks are often known as biological pathway graphs (BPGs)...

Automated design of programmable enzyme-driven DNA circuits.

Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillato...