Biology Reference
In-Depth Information
generate novel insights into a system that could not be
otherwise obtained, to predict system behavior under
various conditions, and to perform in silico experiments for
node knockouts as well as gene over-expression.
The Boolean modeling framework can be readily
expanded to include more quantitative details. Multilevel
discrete dynamic models have more than two states
[20,
22
e
24]
, and continuous -Boolean hybrid models charac-
terize each component by two variables, a continuous vari-
able akin to a concentration and a discrete variable akin to an
activity
[64]
. The model can thus be adapted as new exper-
iments are conducted and more evidence is accumulated.
Such a process of trial and error, progress and adjustment
plays a vital role in the advancement of system biology.
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Table of System Biology Terms
Terms
Definitions
Node
A graphic representation of a component
of a biological system, such as a protein,
secondary messenger or small molecule
Edge
Any type of interaction that exists
between nodes, e.g., chemical reaction,
regulation or causal relationship
Node state
The value of the variable assigned to the
node. It can mean concentration,
activity, status. In Boolean modeling
there are two node states: ON, meaning
above threshold concentration or
activity, and OFF, meaning below
threshold concentration or activity
State of the system
An
is the
total number of nodes in the system. The
i
N-
dimensional vector where
N
th dimension is the state of the
i
th node
Fixed point or steady
state
A state vector of the system that is time-
invariant. If the system reaches a steady
state, it will stay in that state
State transition graph
A graph showing the evolution of the
state of the system. The system will
undergo state changes along the
direction of the arrows
Attractor
A set of connected states of the system.
Each state in the set has to be reachable
by the system after a sufficiently long
period of time. Fixed points (steady
states) are a subtype of attractors
Basin of attraction
A set of connected states of the system.
Given sufficiently long time, every state
in the set
reach a specific attractor of
the system. All such states that are able to
reach the same attractor form the basin
of attraction of
can
that
particular attractor
