Aaargh! Physicists!

Physics meets cancer: The disruptor
Nature 474, 20-22 (2011)

Paul Davies likes to ask big questions. But how did the freethinking cosmologist suddenly find himself probing the physics of cancer?

True, his naivety sometimes makes biologists grit their teeth. (“Aaargh! Physicists!” wrote Paul ‘PZ’ Myers, a biologist at the University of Minnesota, Morris, in a blog response to Davies’ proposal earlier this year that tumours are a reversion to primitive genetic mechanisms that pre-date the dawn of multicellular life.)

the comparatively new discipline of systems biology has been trying to take a more global view.
But even so, says Davies, few cancer biologists are familiar with nonlinear systems analysis, network theory or any of the other tools that have been developed by mathematicians and physicists over the past few decades to deal with complex systems.

The questions, he says, were “all very, very basic. My level of ignorance was embarrassing.”

In December 2008, the NCI outlined its plan to fund the 12 physics-oncology centres at roughly US$2 million apiece over five years, and invited applications to host them. Each one would look at cancer from one of four points of view: physics, evolution, biological-information processing or complex systems.

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COPASI: biochemical network simulator

COPASI: biochemical network simulator

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events can be included in such simulations.