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...
Apr, 01, 2010
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...
Sep, 01, 2013
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...
Sep, 01, 2005
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...
Apr, 01, 2016
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...
Jan, 01, 2010
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...
Sep, 01, 2013
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...
Sep, 01, 2011
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, 16, 2013
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...
Jun, 01, 2010
Looking back, and looking forward.
Editor’s Note:
In addition to asking 10 experts to weigh in on Eric Jakobsson’s 2005 Top Ten Challenges for the field of biomedical computing (Top Ten Retrospective, in this issue),...
Jun, 18, 2014
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