Analytical techniques in computational cell biology such as kinetic parameter estimation, Metabolic Control Analysis (MCA) and bifurcation analysis require large numbers of repetitive simulation runs with different input parameters. The requirements for significant computational resources...

The thorough overview of the E‑Cell Simulation Environment in this chapter provides a foundation for understanding the systems biology research that uses the E‑Cell Simulation Environment presented within this book. To begin this inquiry, we open with the most general question possible:...

During cardiomyocyte development, early embryonic ventricular cells show spontaneous activity that disappears at a later stage. Dramatic changes in action potential are mediated by developmental changes in individual ionic currents. Hence, reconstruction of the individual ionic currents into...

The Myeloid Differentiation Primary‑Response Protein 88 (MyD88)‑dependent and—independent pathways induce proinflammatory cytokines when toll‑like receptor 4 (TLR4) is activated through lipopolysaccharide (LPS) stimulus. Recent studies have implicated a crosstalk mechanism between the...

Since a mature mammalian erthrocyte is enucleated and it is void of mitochondria, gene expression does not take place, while glycolysis is the only mechanism to produce ATP. This simplicity makes its metabolism unique from other cells. Due to its simple structure and the traceability of the...

Bacterial organisms like Escherichia coli have developed mechanisms to detect and direct cell movement toward substrate when starved. Such behavior is known as chemotaxis (15 for recent review). Some nutrition (amino acids, sugar, etc.) can be sensed by the chemotaxis signal transduction...

In this work, we used E‑Cell, a software package aiming at large‑scale modeling with full object‑oriented modeling support, to analyze the 70kDa heat shock protein (Hsp70) chaperone mediated protein folding. We analyzed the kinetic characteristics of this chaperone system during folding...

An offshoot of classical bioinformatics, whole cell modeling integrates information from metabolic pathways, gene regulation and expression. This new area of in‑silico biology converges disciplines as varied as mathematics, computers, physics and chemistry. Scientific advancements have...

While many inter‑organ and intra‑organ gene regulations have been found recently, raison d\'etre of such regulations are hardly explicated. We aimed liver ammonia detoxification as a prospective target because of its simple histological structure and adopted systems biology approach to...

Computer simulations can be used to predict the dynamic behaviour of metabolic pathways and to provide evidence in support of clinical treatments for metabolic disorders. Here, we performed dynamic kinetic simulations of mitochondrial energy metabolism using the E‑Cell Simulation...

The E‑Cell System is an advanced platform intended for mathematical modeling and simulation of well‑stirred biochemical systems. We have recently implemented the Spatiocyte method as a set of plug in modules to the E‑Cell System, allowing simulations of complicated multicompartment...