Systems Biology (Methods in Molecular Biology)

is organized and represented in a form of machine readable net-

work, which is the formalized representation of a large number of

individual experimental results. The network is then modeled with

suitable modeling formalisms, which after calibrating with experi-

mental data should recapitulate the biological phenomena under

consideration, is used to formulate or validate hypotheses, and is

used to support the design of new experiments. In this way, the

systems biology approach cycles into data-driven modeling and

model-driven experimentation. More specifically, we can divide

this approach into four main stages:

2.1.1 Setting the Context This step starts with the formulation of a biological question that is
investigated. For example, a general question could be what the
regulatory mechanism(s) underlying prostate tumor metastasis or
drug resistance are? This defines the project boundaries and gives
directions to collect information from the literature and databases.
This information is then converted into a machine readable format
(i.e.,in the form of network) for computational analysis. With the
help of domain experts or using computational methods, project-
specific network components or modules are then chosen.

Refine/Define

a question

Choose network

visualization

Specify &

hypothesize

mechanism(s)

Collect

information

Choose

network

components

Choose

type of

model

Design

new

experiments

Validate

model and refine

hypothesis

Analyze

the model

Specify

biochemical-

/physical

interaction

Mathematical

representation

Identify

parameter values

The

Systems Biology

Approach

Fig. 2The systems biology approach: an iterative process of data-driven modeling and model-driven
experimentation

250 Faiz M. Khan et al.