Summary and conclusions

Bioscience computing draws inspiration from biology to solve computer sci-ence challenges and simultaneously uses new bio-inspired adaptive software to simulate biological systems. It is a rapidly emerging field for interdisciplinary

Biologists have a computational, process-oriented understanding of their subject — they think in terms of objects, interactions and processes: processes are more important than the end result; dynamic behaviour is more impor-cytoskeleton is intimately involved in the patterning of the cell wall and may

improved; e.g. the need to consider not only genetics but also environmental standing of the mechanism of the cytoskeleton during morphogenesis was

sciences.

research, with synergistic benefits for both computer science and the life Christopher D. Clack

17 tant than equilibrium; and behaviour and interactions ofindividualobjects are important. Computational simulation provides in-silico experiments as a pro-totyping technique for hypothesis formulation that more directly maps to the biologists’ understanding of their subject, and can more directly assist their thought processes. The process-oriented approach to simulating biological complexity leads to an increased understanding of dynamic emergence and regulatory interaction and control: this is a fundamental step towards a future theory of biology.

The artificial cytoskeleton has been presented as an example of the computa-tional simulation techniques of bioscience computing, illustrating real benefits accruing to both computer science and the life sciences.

Acknowledgements

research contributions of the following colleagues are nowledged: Katie Bentley (artifical cytoskeleton, PhD student), Cox (diatom morphology, NHM), Dr. Sylvia Nagl (oncology matical biology) and Manish Patel (model integration, PhD cs.ucl.ac.uk/research/bioscience).

References

Alberts, B., D. Bray, J. Lewis, M. Raff, K. Roberts, and J.D. Watson [1994].Molecular Biology of The Cell. Garland Publishing, 3rd edition.

Anderson, A.R.A., and M.A.J. Chaplain [1998]. Continuous and discrete mathematical models of tumour-induced angiogenesis.Bulletin of Mathematical Biology, 60:857–900.

Araujo, R., and D. McElwain [2004]. A history of the study of solid tumour growth: The con-tribution of mathematical modelling.Bulletin of Mathematical Biology, 66:1039–1091.

Bentley, K., and C.D. Clack [2004]. The artificial cytoskeleton for lifetime adaptation of mor-thesis of Living Systems (ALIFE IX), pages 13–16.

Bentley, K., and C.D. Clack [2005]. Morphological plasticity: Environmentally driven mor-phogenesis.Proceedings of the 8th European Conference on Artificial Life (ECAL 2005), Lecture Notes in Artificial Intelligence, 3630:118–127.

Bentley, K., E. Cox, and P. Bentley [2005]. Nature’s batik: A computer evolution model of diatom valve morphogenesis.Nanoscience and Nanotechnology Journal, 5(1):25–34.

Castellano, F., P. Chavrier, and E. Caron [2001]. Actin dynamics during phagocytosis.Seminars in Immunology, 13:347–355.

Condeelis, J. [2001]. How is actin polymerization nucleatedin vivo?TRENDS in Cell Biology, 11(7):288–293.

Davey, M.C., and R.M. Crawford [1986]. Filament formation in the diatom melosira granulata.

Journal of Phycology, 22:144–150.

Gatenby, R.A., and P.K. Maini [2003]. Mathematical oncology: Cancer summed up.Nature, 421:321–324.

The gratefully

ack-Dr. Eileen and mathe-student).

All are members of the UCL BioScience Computing Interest Group (www.

phology.SODANS Workshop proceedings of the 9th Intl. Conf. on the Simulation and Syn-Bioscience Computing and Computational Simulation in Biology

18

Giavitto, J-L., C. Godin, O. Michel, and P. Prusunkiewicz [2002].Modelling and Simulation of Biological Processes in the Context of Genomics, chapter Computational Models for Inte-grative and Developmental Biology. Hermes.

Glazier, J.A., and F. Graner [1993]. Simulation of the differential adhesion driven rearrangement of biological cells.Physical Review E, 47(3):2128–2154.

Holt, M.R., and A. Koffer [2001]. Cell motility: Proline-rich proteins promote protrusions.

TRENDS in Cell Biology, 11(1):38–46.

Ideker, T., and D. Lauffenburger [2003]. Building with a scaffold: emerging stategies for high-to low-level cellular modelling.Trends in Biotechnology, 21(6):255–262.

Kirkwood, T.B.L., R.J. Boys, C.S. Gillespie, C.J. Proctor, D.P. Shanley, and D.J. Wilkinson [2003]. Towards an e-biology of ageing: Integrating theory and data.Nature Reviews, Mole-cular Cell Biology, 4:243–249.

Noble, D. [2002]. The rise of computational biology.Nature Reviews, Molecular Cell Biology, 3:460–463.

Patel, M. [2004].Internal report. Department of Clinical Oncology, UCL.

Priami C. (ed.) [2003]. Proc. 1st Workshop Computational Methods in Systems Biology.

Springer.

Scalerandi, M., B. Capogrosso Sansone, C. Benati, and C.A. Condat [2002]. Competition effects in the dynamics of tumor cords.Physical Review E, 65(5 Pt 1):051918.

Succi, S., I.V. Karlin, and H. Chen [2002]. Colloquium: Role of the h theorem in lattice boltz-mann hydrodynamics simulations.Reviews of Modern Physics, 74:1203–1220.

Table 1.1. Glossary of biological terms.

term description

actin A protein that links into chains (polymers), forming microfilaments in muscle and other contractile elements in cells.

allele The precise sequence of nucleotides for a specified gene.

cellular secretion The escape of substances from a cell to its environment.

chemotaxis Migration of cells along a concentration gradient of an attractant.

chromosome The self-replicating genetic structure of cells containing the cellular DNA that contains the linear array of genes.

cytoplasm The contents of a cell (but not including the nucleus).

cytoskeleton A system of molecules within eukaryotic cells providing shape, in-ternal spatial organization, and motility, and may assist in communi-cation with other cells.

diatoms Microscopic algae with cell walls made of silicon and of two separat-ing halves.

eukaryote A cell or organism with a membrane-bound nucleus (and other sub-cellular compartments). Includes all organisms except viruses, bacte-ria, and bluegreen algae.

extracellular matrix (ECM)

Any material produced by cells and secreted into the surrounding medium. The properties of the ECM determine the properties of the tissue (e.g. bone versus tendon) and can also affect the behaviour of cells.

fibroblast A cell found in most tissues of the body, involved in wound repair and closure; they migrate towards the wound site via chemotaxis.

Christopher D. Clack

19

Glossary of biological terms.

term description

gene The fundamental unit of heredity; a sequence of nucleotides in a par-ticular position on a chromosome that encodes a specific functional product (e.g. a protein).

gene expression The process by which a gene’s coded information is translated into the structures present and operating in the cell (either proteins or RNA).

genome The set of different types of gene for a specified organism, distin-guished by allele type and position on the chromosome.

genotype The set of different gene alleles existing in an organism.

leukocyte A white blood cell, an important component of the body’s immune system.

macromolecule A molecule composed of a very large number of atoms. Includes proteins, starches and nucleic acids (e.g. DNA).

metabolic pathway A series of chemical reactions in a cell resulting in either a metabolic product to be used/stored by the cell or the initiation of another metabolic pathway.

morphogenesis The development and adaptation of the shape and form of an organ-ism.

nucleotide A subunit of DNA or RNA.

organelle A membrane-bound structure in a eukaryotic cell that partitions the cell into regions which carry out different cellular functions.

phagocytic cup An inward folding of the cell membrane creating an interior pocket, formed by an actin dependent process during phagocytosis.

phagocytosis The engulfment of a particle or a microorganism by leukocytes.

phenotype The physical characteristics of an organism.

physiome The functional behavior of the physiological state of an individual or species, describing the physiological dynamics of the normal intact organism.

PIP2 Phosphatidylinositol [4, 5]-biphosphate; formed and broken down in the cell membrane; mediates cell motility in fibroblast chemotaxis.

protist An organism with eukaryotic cells that is neither plant nor animal nor fungi.

protrusions Thin fingerlike extensions from the surface of a cell.

WASP Wiskott-Aldrich syndrome protein. Regulates the formation of actin chains.

Table 1.1 (contd).

Bioscience Computing and Computational Simulation in Biology

Chapter 2