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What do
we do?
The "System" as the
"Network".......
Biological systems can be envisioned to be
a complex network of
physical objects (example: molecules, ions, and bacteria) through the
different signaling methods (example: reactions/binding through
diffusions and transportation). This "networking"
is responsible for driving the wide variety of structure and form found
in living organisms, spreading of diseases and evolution of the species.
The network can be extended from the
interaction of the genes, to the proteins,
moving into higher scales - interaction between cells, tissues and
finally to that of organs manifesting itself in 'Life'.
A holistic
understanding of this complex biological network can play a key role in
comprehending Natures' choreography of 'Life'.
In this laboratory, we are focused on a
network-centric systems
engineering approach
to unravel the dynamics of this complex network. A biological
process and system can be abstracted as multi-layered physical network
inter-working with each other to create a total biological system. This
abstraction can be realized by modeling a cell as a node of the biological
network.. From the cell then the specialized tissue and organ models can
be established as a distributed network of cells. And from tissue, we
should be able to abstract the organ and process models of the biological
system as a layered view of this distributed network architecture.
Our work is centered around three key
areas :
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?Knowledge
Extraction and Pathway Construction :
In
this work, we are focused on extracting knowledge from existing
databases and literatures to build the molecular interaction maps of
various biological processes
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Stochastic Modeling of biological processes :
One of the primary component of our research is focused
on developing stochastic models for various biological processes and
sub-processes. We have developed stochastic models for some key
cellular processes, the details of which are available
here.
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Discrete Event Simulation
:
The dynamics of a cellular process are captured based on an 'in
silico' discrete event based simulation. The simulation platform uses
pathway intelligence in conjunction with stochastic modeling knowledge
for simulating the temporal dynamics of various sub-processes in a
complex biological system. Details on our simulation methodology and
software are available in projects.
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