Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 
 

Evolving Systems with Multiple Functions

A system with multiple functions might reveal features of a complex system. Evolutionary methods were used to construct reaction networks with multiple functions. The networks were analyzed for modularity – regions in the network that are utilized by different functions. Individual molecular species were removed as well as perturbed to see how each species affects the rest of the network.

Reaction network capable of performing chemotaxis was also evolved in hopes to construct a complex network. The chemotaxis was given multiple functions to see whether that gives rise to modularity.



Research conducted by Deepak Chandran

Directed Evolution

Biological systems are inherently complex in nature. One can dissect this complexity by transforming a biological system in to an equivalent engineering system. Once we are done with this transformation we can use the well established engineering principles to gain a better understanding of the biological systems. So the problem now lies in identifying the components in biological systems akin to engineering systems. To address this problem we are constructing a library of biological motifs (e.g., oscillators, filters, toggle switches etc.) by using in silico evolution techniques.

Research conducted by Sri Rama Krishna Paladugu

Lakhesis

The program Lakhesis was developed to evolve chemical networks with the ability to perform simple mathematical computations. In the future the program will be used to develop novel networks and to investigate the evolution of regulated networks.

Read more: Lakhesis

Research conducted by Anastasia Deckard

Network Evolution C Library

A C based library specifically designed to evolve biochemical networks is under development. Further details can be found at:

Evolution Library

Source forge site itself:

Source Forge Site

Other Evolved Networks

Simple Mass-Action Based XOR Gate

This is a simple Jarnac script that models an evolved XOR gate based on a mass-action network. The solution involves 2 AND gates, 1 OR gate and 1 NOT gate (See http://www.art-sci.udel.edu/ghw/phys245/05S/classpages/logic-example.html for the circuit diagram). It is the most efficient design possible.

p = defn cell

   $x -> z; k0*x;
   $y -> z; k0*y;
   $x + $y -> w; k2*x*y;
   z + 2w -> 2w; k3*w^2*z;
   z -> $w1; k5 * z;
   w -> $w2; k6 * w;
end;

p.k0 = 2.0
p.k2 = 1.0
p.k3 = 0.1
p.k5 = 1.0
p.k6 = 1.0
p.x = 0;
p.y = 0;

// High level is indicated by a concentration of 10
// Low level by 0

m1 = p.sim.eval (0, 20, 100, [<p.Time>, <p.x>, <p.Y>, <p.z>]);
// Apply 0, 1
p.x = 0;
p.y = 10;
m2 = p.sim.eval (20, 40, 100, [<p.Time>, <p.x>, <p.Y>, <p.z>]);

// Apply 1, 0
p.x = 10;
p.y = 0;
m3 = p.sim.eval (40, 60, 100, [<p.Time>, <p.x>, <p.Y>, <p.z>]);

// Apply 1,1
p.x = 10;
p.y = 10;
m4 = p.sim.eval (60, 80, 100, [<p.Time>, <p.x>, <p.Y>, <p.z>]);

m = augr(m1,m2);
m = augr(m,m3);
m = augr(m,m4);

graph (m);

Network diagram is shown below. x and y are the inputs and z the output. The two our arcs collectively represent the OR function, the bimolecular reaction in the left center is the AND function and the bimolecular reaction to the right center is the NOT function.

Deepak Chandran

Simple Mass-Action Based Oscillator

p = defn cell
  s4 + s1 -> s4; s4*s1*2;
  s4 + s5 -> s6; s4*s5*1;
  s6 -> s1; s6*1;   
  s1 + s3 -> s6 + s5; s1*s3*1;
  s4 -> s3; s4*1;
  $n6 -> s4; n6*1;
end;

p.s1 = 0.0;
p.s3 = 0.0;
p.s4 = 0;
p.s5 = 0;
p.s6 = 0.5;
p.n6 = 4;

m = p.sim.eval (0, 100, 500, [<p.time>, <p.s1>, <p.s3>, <p.s4>, <p.s5>, <p.s6>]);
graph (m);

Other Papers

1. Construction of Oscillating Chemical Register Machines on Binary Numbers using Mass-Action Kinetics by Fasler et al.

http://users.minet.uni-jena.de/~hinze/piwmc2008-jena-proc2.pdf

2. EU Project devoted to this topic:

http://www.esignet.net/index.php?menuid=1

 
sysbio/evolcomputing.txt · Last modified: 2009/08/27 21:26 by hsauro
 

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