Modelling biological systems

Modelling biological systems

Modeling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modeling of biological systems. It involves the use of computer simulations of biological systems, like cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes.

Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.

Contents

Overview

It is understood that an unexpected emergent property of a complex system is a result of the interplay of the cause-and-effect among simpler, integrated parts (see biological organisation). Biological systems manifest many important examples of emergent properties in the complex interplay of components. Traditional study of biological systems requires reductive methods in which quantities of data are gathered by category, such as concentration over time in response to a certain stimulus. Computers are critical to analysis and modeling of these data. The goal is to create accurate real-time models of a system's response to environmental and internal stimuli, such as a model of a cancer cell in order to find weaknesses in its signaling pathways, or modeling of ion channel mutations to see effects on cardiomyocytes and in turn, the function of a beating heart.

A monograph on this topic summarizes an extensive amount of published research in this area up to 1987,[1] including subsections in the following areas: computer modeling in biology and medicine, arterial system models, neuron models, biochemical and oscillation networks, quantum automata, quantum computers in molecular biology and genetics, cancer modeling, neural nets, genetic networks, abstract relational biology, metabolic-replication systems, category theory[2] applications in biology and medicine,[3] automata theory, cellular automata, tessallation models[4][5] and complete self-reproduction, chaotic systems in organisms, relational biology and organismic theories.[6][7] This published report also includes 390 references to peer-reviewed articles by a large number of authors.[8][9][10]

Standards

By far the most widely accepted standard format for storing and exchanging models in the field is the Systems Biology Markup Language (SBML)[11] The SBML.org website includes a guide to many important software packages used in computational systems biology. Other markup languages with different emphases include BioPAX and CellML.

Particular tasks

Cellular model

Part of the Cell Cycle
Summerhayes and Elton's 1923 food web of Bear Island (Arrows represent an organism being consumed by another organism).
A sample time-series of the Lotka-Volterra model. Note that the two populations exhibit cyclic behaviour.

Creating a cellular model has been a particularly challenging task of systems biology and mathematical biology. It involves the use of computer simulations of the many cellular subsystems such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks to both analyze and visualize the complex connections of these cellular processes.

The complex network of biochemical reaction/transport processes and their spatial organization make the development of a predictive model of a living cell a grand challenge for the 21st century.

In 2006, the National Science Foundation (NSF) put forward a grand challenge for systems biology in the 21st century to build a mathematical model of the whole cell.[12] E-Cell Project aims "to make precise whole cell simulation at the molecular level possible".[13] CytoSolve developed by V. A. Shiva Ayyadurai and C. Forbes Dewey, Jr. of Department of Biological Engineering at the Massachusetts Institute of Technology, provided a method to model the whole cell by dynamically integrating multiple molecular pathway models.[14][15]

Membrane computing is the task of modeling specifically a cell membrane.

Protein folding

Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of a protein's tertiary structure from its primary structure. It is one of the most important goals pursued by bioinformatics and theoretical chemistry. Protein structure prediction is of high importance in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Every two years, the performance of current methods is assessed in the CASP experiment.

Human biological systems

Brain model

The Blue Brain Project is an attempt to create a synthetic brain by reverse-engineering the mammalian brain down to the molecular level. The aim of the project, founded in May 2005 by the Brain and Mind Institute of the École Polytechnique in Lausanne, Switzerland, is to study the brain's architectural and functional principles. The project is headed by the Institute's director, Henry Markram. Using a Blue Gene supercomputer running Michael Hines's NEURON software, the simulation does not consist simply of an artificial neural network, but involves a partially biologically realistic model of neurons.[16][17] It is hoped by its proponents that it will eventually shed light on the nature of consciousness. There are a number of sub-projects, including the Cajal Blue Brain, coordinated by the Supercomputing and Visualization Center of Madrid (CeSViMa), and others run by universities and independent laboratories in the UK, U.S., and Israel.

Model of the immune system

The last decade has seen the emergence of a growing number of simulations of the immune system.[18][19]

Tree model

Electronic trees (e-trees) usually use L-systems to simulate growth. L-systems are very important in the field of complexity science and A-life. A universally accepted system for describing changes in plant morphology at the cellular or modular level has yet to be devised.[20] The most widely implemented tree generating algorithms are described in the papers "Creation and Rendering of Realistic Trees", and Real-Time Tree Rendering

Ecological models

Ecosystem models are mathematical representations of ecosystems. Typically they simplify complex foodwebs down to their major components or trophic levels, and quantify these as either numbers of organisms, biomass or the inventory/concentration of some pertinent chemical element (for instance, carbon or a nutrient species such as nitrogen or phosphorus).

Modeling of infectious disease

It is possible to model the progress of most infectious diseases mathematically to discover the likely outcome of an epidemic or to help manage them by vaccination. This field tries to find parameters for various infectious diseases and to use those parameters to make useful calculations about the effects of a mass vaccination programme.

See also

Notes

  1. ^ http://en.scientificcommons.org/1857371
  2. ^ http://planetphysics.org/encyclopedia/BibliographyForCategoryTheoryAndAlgebraicTopologyApplicationsInTheoreticalPhysics.html
  3. ^ http://planetphysics.org/encyclopedia/BibliographyForMathematicalBiophysicsAndMathematicalMedicine.html
  4. ^ Modern Cellular Automata by Kendall Preston and M. J. B. Duff http://books.google.co.uk/books?id=l0_0q_e-u_UC&dq=cellular+automata+and+tessalation&pg=PP1&ots=ciXYCF3AYm&source=citation&sig=CtaUDhisM7MalS7rZfXvp689y-8&hl=en&sa=X&oi=book_result&resnum=12&ct=result
  5. ^ http://mathworld.wolfram.com/DualTessellation.html
  6. ^ Baianu, I. C. 1987, Computer Models and Automata Theory in Biology and Medicine., in M. Witten (ed.),Mathematical Models in Medicine, vol. 7., Ch.11 Pergamon Press, New York, 1513-1577. http://cogprints.org/3687/
  7. ^ http://www.kli.ac.at/theorylab/EditedVol/W/WittenM1987a.html
  8. ^ http://www.springerlink.com/content/w2733h7280521632/
  9. ^ Currently available for download as an updated PDF: http://cogprints.ecs.soton.ac.uk/archive/00003718/01/COMPUTER_SIMULATIONCOMPUTABILITYBIOSYSTEMSrefnew.pdf
  10. ^ http://planetphysics.org/encyclopedia/BibliographyForMathematicalBiophysics.html
  11. ^ Klipp, Liebermeister, Helbig, Kowald and Schaber. (2007). "Systems biology standards—the community speaks" (2007), Nature Biotechnology 25(4):390–391.
  12. ^ American Association for the Advancement of Science [1]
  13. ^ http://www.e-cell.org/ecell/
  14. ^ National Center for Biotechnology Information [2. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032229/]
  15. ^ Massachusetts Institute of Technology [2]
  16. ^ Graham-Rowe, Duncan. "Mission to build a simulated brain begins", NewScientist, June 2005.
  17. ^ Palmer, Jason. Simulated brain closer to thought, BBC News.
  18. ^ [3]
  19. ^ "Computer Simulation Captures Immune Response To Flu". http://www.sciencedaily.com/releases/2009/05/090518111729.htm. Retrieved 2009-08-19. 
  20. ^ "Simulating plant growth". http://www.acm.org/crossroads/xrds8-2/plantsim.html. Retrieved 2009-10-18. 

References

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Further reading

External links


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