Biomedical Engineering Reference
In-Depth Information
involving small numbers of reactant molecules such as occur in subcellular bio-
logical processes like genetic regulatory networks
13.
Virtual Cell
(http://www.nrcam.uchc.edu/) integrates biochemical and
electrophysiological data with microscopic images and has a web-based inter-
face.
14.
VLX Biological Modeler
(http://teranode.com/products/vlxbiological.
php) allows scientists to create and annotate visual models of complex biologi-
cal systems, perform simulations for exploring and predicting dynamic system
behaviors, analyze experimental data with models for hypothesis testing, and
effectively communicate their findings.
15.
E Cell
(http://www.e-cell.org) is a modeling and simulation environ-
ment from Keio University, Japan. The primary objective of the E-Cell group is
to create a dynamic quantitative model of metabolic and gene regulatory net-
works in lower and higher model organisms. However, the model building itself
involves a fair number of assumptions and rate constants. For example, to model
a random bi-bi reaction may incorporate 10 parameters for a single reaction,
without taking into consideration activation/inhibition by other molecules. Its
basic features are listed below.
E Cell (short for Electronic Cell) is a generic object-oriented environment
for modeling and simulating molecular processes of user-definable models,
equipped with graphical interfaces that allow observation and interaction. The E
Cell approach enables modeling of gene expression, signaling, and metabolism.
The first publicly released version of the E Cell simulation system was intro-
duced in 2001 under open source. E Cell is currently in its third version. Ver-
sions 1.0 and 3.0 are Linux-based, while version 2 is Windows-based (31).
E Cell 3.0 has been developed with an aim to providing a generic tool that
runs in a high-performance software environment. It has a geometry information
interface and a capability to integrate different simulation algorithms, including
approaches based on a variable-process model, differential equations, diffusion
reactions, and particle dynamics. One of the main features of E Cell is its ability
to integrate subsystems at different time scales. The modeling architecture is
tailored to individual modeling needs and allows users to add components to the
system. In addition, it is an integrated modeling environment and can simulate
both deterministic and stochastic models. Version 3 has been customized for
biologists with little or no programming knowledge.
The first application of E Cell was the creation of a virtual cell with 127
genes in silico (34). The
Mycoplasma
genomic raw material was used to con-
struct a virtual cell with "minimum cellular metabolism." This hypothetical cell
consumed glucose from the culture medium, generated ATP, and exported lac-
tate. Transcription and translation steps were modeled to biosynthesize proteins
within the cell. The cell also consumed glycerol and fatty acid, producing phos-
phatidyl glycerol for membrane structure. The cell was "self-supporting," but
incapable of proliferation.
Mycoplasma genitalium
was chosen for this virtual
