Page last modified 19:15, 22 Jun 2009 by davidla

Purdue Genomics Wiki > Archived Items > 2009 Summer Adv. Topics Seminar > Cellular Automata (for Biology)

1st of July 2009 - David La. Seems like I will be discussing Cellular Automata.

From the wikipedia: A **cellular automaton** (plural: **cellular automata**, abbrev. **CA**) is a discrete model studied in computability theory, mathematics, theoretical biology and microstructure modeling. It consists of a regular grid of **cells**, each in one of a finite number of *states*, such as "On" and "Off". The grid can be in any finite number of dimensions. For each cell, a set of cells called its **neighborhood** (usually including the cell itself) is defined relative to the specified cell.

Make sure to also check out a really cool example: Conway's Game of Life

- Ermentrout and Edelstein-Keshet. Cellular automata approaches to biological modeling. J Theor Biol (1993) vol. 160 (1) pp. 97-133
- Alber et al. On cellular automaton approaches to modeling biological cells. IMA VOLUMES IN MATHEMATICS AND ITS APPLICATIONS (2002)
- Kier et al. Modeling biochemical networks: a cellular-automata approach. Chem Biodivers (2005) vol. 2 (2) pp. 233-43

- Wolfram. A New Kind of Science. (2002) pp. 1197
- B. Kier et al. Cellular automata modeling of chemical systems: a textbook and laboratory manual. (2005) pp. 175
- Deutsch et al. Cellular automaton modeling of biological pattern formation .... (2005) pp. 331
- Keedwell and Narayanan. Intelligent bioinformatics: the application of artificial intelligence .... (2005) pp. 280 ) (Chapter 10 is good.)

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File | Size | Date | Attached by | |||
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IMA VOLUMES IN MATHEMATICS AND ITS APPLICATIONS 2002 Alber (1).pdf It's up to you if you want to read it. I recommend it. | 1286.38 kB | 18:09, 22 Jun 2009 | davidla | Actions | ||

J Theor Biol 1993 Ermentrout (2).pdf You might want to read this. | 1359.57 kB | 18:07, 22 Jun 2009 | davidla | Actions | ||

Kier_et_al.pdf It's up to you if you want to read it. I recommend it. | 257.3 kB | 18:11, 22 Jun 2009 | davidla | Actions |

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2. Since CA is a subcategory of AL (Artificial Life), can you give a very very very brief intro about AL, :)

3. What's the normal way they validate their model? Use ants trial as an example, how do they know it's a correct model?

4.What is the correspondence between CA and continuous systems?

Continuum descriptions may be given of many of the large-scale structures that occur in CA. Presumably in the limit of large spatial dimensionality, this approximation should become accurate. But in one or two dimensions, it is usually quite inadequate, and gives largely misleading results. Are there High-Dimensional CAs? I guess those are also computationally expensive edited 22:21, 30 Jun 2009

2. Also, there might be many cellular automata modeling a biological process using different parameters. What process do we use, if we want to compare the different models? Donâ€™t we need to have a uniform system-dependent methodology for comparing models?

3. Can cellular automata be used to study emergent properties of a system?

2. In deterministic CA, model derivation can be done in two ways. 1. simply abstract the observed phenomenon into few simple rules, without any analogous to full mathematical model 2. directly discretize the mathematical model.Which of these approaches is better. Is it more problem specific or is one approach performs better than the other always?

In a real biological system, if we wanted to see the effect of emergent properties of related pathways, I think it is becomes a more difficult problem because now you have to model different pathways at the same time.