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The Cell in 2010: A Modeling Odyssey

How cell-centered models are adding fundamental insights into our understanding of cell behaviors

The cell is like our financial system: Even if you have a diagram of all the complex interactions going on, you still cannot intuit how the whole system will react when perturbed. Indeed, the cell...
Mar, 31, 2010
Agent-Based Virtual-Tissue Simulations
Cells have a limited repertoire of behaviors and interactions. They grow, divide, die, stick to each other, send and receive signals, change shape, polarize, differentiate (change behaviors), form...
Aug, 31, 2013
Bacteria with Byte

AgentCell is the first simulation program to model a biochemical network at the molecular, single cell, and population levels simultaneously.

When a bacterium swims toward food, it follows a chaotic path, alternating between spinning randomly and driving forward, or ‘tumbling’ and ‘running.’ Computer scientists at...
Aug, 31, 2005
Single-Cell Genomics: Can Bioinformatics Unlock its Potential?

The tools to sequence the genomes of individual cells yield data that’s noisy and somewhat unreliable. What bag of tricks can bioinformaticians use to address these challenges?

To study genomes, researchers have typically pooled the genetic material from thousands of cells together. But this approach can only get at “average genomes” or “average...
Mar, 31, 2016
3D Angiogenesis Modeled

CompuCell-3D models behaviors rather than genes

Researchers have successfully simulated how growing blood vessels affect the sizes and shapes of tumors using a 3-D model based solely on how cells behave—without reference to intracellular...
Dec, 31, 2009
The Biology of Interacting Things: The Intuitive Power of Agent-Based Models

Biomedical applications of ABMs are taking off.

In the early 1990s, when James A. Glazier, PhD, first became interested in using agent-based modeling to simulate biological phenomena, the field was so new that he had to borrow ideas...
Aug, 31, 2013
Simulating Cells in Context: Bringing Mechanics Into Play
Like humans, cells are affected by their physical environment, their neighbors, the context in which they exist. Much research has focused on the chemical signals that control cell behavior. But...
developmental biology
Aug, 31, 2011
The Physiome: Standardizing the Physiome

A closer look at the curation of models discussed in The Physiome: A Mission Imperative

Multi-scale quantitative models need to be validated and reproducible if they are to be useful for clinical workflows, says Hunter. The Physiome infrastructure developed by Hunter, Dr Poul Nielsen...
May, 31, 2010
Untangling Integrative Analysis

How researchers are combining disparate data types and simulating systems that contain many different moving parts

13 years ago Markus Covert, PhD, read a New York Times article that changed his life.  The article quoted a prominent microbiologist who suggested that the ultimate test of one’s...
Feb, 15, 2013
Tackling Tumors

Turning immune cells into cancer killers

Tumors often contain a hodgepodge of cells. Some cells have genetic glitches, others don’t; some obey normal growth rules, others divide out of control. Immune cells enter the mix as well,...
cancer, immuno-oncology
Nov, 01, 2016
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