Afreen Nizar

BID - 19001

BID – 602 Systems Biology

Assignment – 6

1. What is Qualitative Model

Qualitative model formulation, then, is the conversion of an objective
statement and a set of hypotheses and assumptions into an informal,
conceptual model. This form does not contain explicit equations, but its
purpose is to provide enough detail and structure so that a consistent set of
equations can be written. The qualitative model does not uniquely determine
the equations, but does indicate the minimal mathematical components
needed. The purpose of a qualitative model is to provide a conceptual
framework for the attainment of the objectives. The framework summarizes
the modeler's current thinking concerning the number and identity of
necessary system components (objects) and the relationships among them.
Qualitative models can take any form (except mathematical), but diagrams
are the usual representation. Given our emphasis on differential equations
and compartment models, three important diagrammatic schemes are: block
structure diagrams (having origins in electrical engineering and analog
computers), Odum energy $ow diagrams (similar to block structure diagrams
but based on energy flow within ecosystems), and Forrester diagrams
(having origins in systems analysis and operations research). All three share
the ability to represent systems as a set of objects and their interrelations.
Qualitative model formulation is one of the sub-problems in the modeling
activity. We wish to discover the simplest description of a system that will
satisfy the objectives. This section describes a few basic principles that apply
to all attempts to formulate a qualitative compartment model using Forrester
diagrams. Many of the principles will also apply to other modeling
approaches. Based on the Forrester diagrams shown thus far, it should be
clear that the purpose of the principles is to help us:
Identify the state variables (levels)
Identify the flows among the state variables
Identify the controls on the flow rates
Identify the auxiliary and driving variables.
 Afreen Nizar
BID - 19001

2. What is Quantitative Model.

Qualitative model for a system is the one that specifies the objects; their
basic, qualitative interrelationships; and the underlying hypotheses. The next
step is to translate these ideas into mathematical equations.
The boxes of Forrester diagrams represent the objects of interest: the
variables whose dynamic quantities we wish to determine over time. For
each of these, we must supply a state (dynamic) equation that relates the
value of the variable at the next point in the future with the current value and
all of the inputs to and outputs from the variable's box. Inputs represent
absolute rates of gain, and outputs represent absolute rates of loss. Each of
the rates are, in general, calculated by complex, nonlinear equations that
combine the flow relations and control relations among system components.
The rate equations will therefore involve the parameters, auxiliary equations,
and driving variables as specified by the Forrester diagram. Summing all of
the rate equations for a given state variable yields the net rate of change for
that variable at the current point in time. After incrementing time, this
calculation is repeated using the state variable values from the previous
iteration until the necessary number of solutions is obtained. In the
remainder of this chapter, we will provide some general rules for the
specification of the rate equations.
3. Explain What is Biological feedback in Quantitative Model.
Feedback is pervasive in biological systems and is one of the fundamental
processes that is contained in almost all interesting models. It refers to the
relationship in which increases or decreases of the value of one or more
controlling variables affect the rate at which a process occurs. The action on
the rate can be direct or indirect and either positive or negative. The action is
direct when only the single variable affected is involved. The value of the
state variable influences its own rate of change. If the mechanism affecting
the state variable involves other state variables, then the feedback is indirect.
Positive and negative feedback are endpoints on a continuum of dynamical
relationships. The degree to which a feedback relation is positive or negative
depends on the function and parameters. Any given relation can be either
strongly or weakly negative or positive. The balance between the two
produces the possibility of sustained oscillations. The qualitative nature of
these relationships is revealed by loop analysis. The "+" or "-" symbols
attached to the arrows indicate the direction of the effect on the future values
 Afreen Nizar
BID - 19001

of the state variable (i.e., positive or negative, respectively). The basic test of
feedback direction on a state variable (e.g., A) is to determine whether A, if
it is increased in quantity, will decrease or increase as determined by
following the effects around a loop.
4. What is the use of Scientific Model
There are three primary, technical uses of models in science:
• Understanding - of either a real, physical system or of a system of
logic such as another scientific theory.
• Prediction - of the future or of some state that is currently unknown.
• Control - to constrain or manipulate a system to produce a desirable
condition
Three general problems that humans face with respect to any discipline or
body of knowledge are:
• Synthesis -use knowledge of inputs and outputs to infer system
characteristics.
• Analysis - use knowledge of the parts and their stimuli to account
for the observed responses.
• Instrumentation - design a system such that a specified output is the
result of an input.
Models can be used in each of these problem areas and when they are,
they allow us to understand, predict, and control systems. There are also
important secondary uses of scientific models that derive from the social
characteristics of science:
• Use as a conceptual framework for organizing or coordinating
empirical research (e.g., designing experiments or sampling
studies, allocating limited research dollars).
• Use as a mechanism to summarize or synthesize large quantities of
data (e.g., a simple linear regression equation y = mx + b to reduce
all of the x-y pairs of data to two parameters m and b).
• Identify areas of ignorance, especially when defining relations
between objects.