Cannon at 08:44, 25 June 2010

2010-06-25T08:44:28Z

← Older revision		Revision as of 08:44, 25 June 2010
Line 2:		Line 2:
	[[Image:fish.jpg]]		[[Image:fish.jpg]]

	~~Next meeting... when?~~		Members:

	Members~~/interested~~:
	* [[Jonathan Cannon]]		* [[Jonathan Cannon]]
	* [[Gavin Fay]]		* [[Gavin Fay]]
	* [[Vanessa Weinberger]]		* [[Vanessa Weinberger]]
	* [[Borys Wrobel]]
	* [[Andrew Hein]]		* [[Andrew Hein]]

	~~We want to study~~ the ~~statistical properties of evolving networks (networks that change the number of nodes/connections/weights). What are the invariants? What properties change over~~ time?		In food webs, predation dynamics effect populations over the short time scale, but also affects network structure in the long term by the mechanism of extinction. Conversely, the couplings represented by the network structure constrain the short-term predation dynamics.

	~~For example~~, ~~for dynamic food webs (which interest [[Jonathan Cannon]]), a change may result from an adaptive modification of species diet~~ in ~~response to circumstance or~~ the ~~addition and~~ extinction ~~of species~~. ~~We will look for the structural and dynamic effects of these mechanisms~~, ~~including~~ the ~~formation of characteristic motifs and stabilization.~~

	~~For evolving gene regulatory networks, new regulatory units are created by duplications, destroyed~~ by ~~deletions, and~~ the weights can change due to point mutations. ([[Borys Wrobel]]) has built an artificial life platform (right now, it uses a genetic algorithm) that can generate a large number of gene regulatory networks that have evolved to perform certain computations (for example, process signals). Borys would be interested in investigating what are the statistical (or other) properties of these networks and how they change with time. Here is a paper that describes (a version) of the ~~[http://www.alifexi.org/papers/ALIFExi_pp297~~-~~304.pdf model].~~

	~~We are also interested in asking what is needed for a system~~ dynamics ~~to be preserved despite changes in network topology~~.

	~~For computing~~ the ~~properties~~, we are ~~thinking~~ of ~~using [http://igraph.sourceforge.net/ igraph]~~ and/or ~~[http://snap.stanford.edu/ snap]~~.		As new species are gradually introduced into a model food web, the network architecture and network dynamics interact, sometimes leading to large stable feeding networks and sometimes to massive extinction events. We are designing simulations to study the characteristic properties of stable, longitudinally-constructed food webs and the nature of the events that stabilize or destabilize them.

Cannon: New page: {{CSSS 2010 Santa Fe}} Image:fish.jpg Next meeting... when? Members/interested: * Jonathan Cannon * Gavin Fay * Vanessa Weinberger * Borys Wrobel * Andrew Hein ...

2010-06-11T19:54:57Z

New page: {{CSSS 2010 Santa Fe}} Image:fish.jpg Next meeting... when? Members/interested: * Jonathan Cannon * Gavin Fay * Vanessa Weinberger * Borys Wrobel * Andrew Hein ...

New page

{{CSSS 2010 Santa Fe}}
[[Image:fish.jpg]]

Next meeting... when?

Members/interested:
* [[Jonathan Cannon]]
* [[Gavin Fay]]
* [[Vanessa Weinberger]]
* [[Borys Wrobel]]
* [[Andrew Hein]]

We want to study the statistical properties of evolving networks (networks that change the number of nodes/connections/weights). What are the invariants? What properties change over time?

For example, for dynamic food webs (which interest [[Jonathan Cannon]]), a change may result from an adaptive modification of species diet in response to circumstance or the addition and extinction of species. We will look for the structural and dynamic effects of these mechanisms, including the formation of characteristic motifs and stabilization.

For evolving gene regulatory networks, new regulatory units are created by duplications, destroyed by deletions, and the weights can change due to point mutations. ([[Borys Wrobel]]) has built an artificial life platform (right now, it uses a genetic algorithm) that can generate a large number of gene regulatory networks that have evolved to perform certain computations (for example, process signals). Borys would be interested in investigating what are the statistical (or other) properties of these networks and how they change with time. Here is a paper that describes (a version) of the [http://www.alifexi.org/papers/ALIFExi_pp297-304.pdf model].

We are also interested in asking what is needed for a system dynamics to be preserved despite changes in network topology.

For computing the properties, we are thinking of using [http://igraph.sourceforge.net/ igraph] and/or [http://snap.stanford.edu/ snap].

Dynamic Architecture of Biological Networks - Revision history

Cannon at 08:44, 25 June 2010

Cannon: New page: {{CSSS 2010 Santa Fe}} Image:fish.jpg Next meeting... when? Members/interested: * Jonathan Cannon * Gavin Fay * Vanessa Weinberger * Borys Wrobel * Andrew Hein ...