Welcome to Biological Networking

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 :

• ?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

• 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.

• 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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