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Mathematical Tools

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Introduction to Modeling for Biosciences

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Abstract

This chapter describes the use of the free, open-source computer algebra system Maxima. Maxima is a system similar to Maple and Mathematica. The use of Maxima is illustrated by a number of examples. Special emphasis is placed on practical advice on how the software can be used, and the reader is made aware of difficulties and pitfalls of Maxima. The chapter also demonstrates how to use Maxima in practice by walking the reader through a number of examples taken from earlier chapters of the book.

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Notes

  1. 1.

    http://www.maplesoft.com.

  2. 2.

    http://www.wolfram.com/products/mathematica.

  3. 3.

    http://www.mathworks.com/.

  4. 4.

    http://www.gnu.org/software/octave.

  5. 5.

    http://www.scilab.org.

  6. 6.

    http://ascend.cheme.cmu.edu.

  7. 7.

    http://www.r-project.org.

  8. 8.

    http://www.math.pitt.edu/~bard/xpp/xpp.html.

  9. 9.

    http://www.sagemath.org.

  10. 10.

    http://mathomatic.org.

  11. 11.

    http://maxima.sourceforge.net.

  12. 12.

    http://www.texmacs.org.

  13. 13.

    http://wxmaxima.sourceforge.net.

  14. 14.

    http://www.gnuplot.info.

  15. 15.

    In the remaining example sessions we will not explicitly write the quit() command any longer.

  16. 16.

    We have omitted much of the long output in line %o8.

  17. 17.

    The draw package including documentation can be found at: http://www.telefonica.net/web2/biomates/maxima/gpdraw.

  18. 18.

    This will only work if Gnuplot is used in X11 mode, which may not be the default setting on some systems.

  19. 19.

    In its widest sense, “terminal” is best thought of as Gnuplot-jargon for file format.

  20. 20.

    http://maxima.sourceforge.net.

References

  1. Cherry, J., Adler, F.: How to make a biological switch. Journal of Theoretical Biology 203(2), 117–133 (2000). doi:10.1006/jtbi.2000.1068

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Authors and Affiliations

  1. Computing Laboratory, University of Kent, Canterbury, Kent, CT2 7NF, UK

    David J. Barnes & Dr. Dominique Chu

Authors
  1. David J. Barnes
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  2. Dr. Dominique Chu
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Correspondence to David J. Barnes .

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© 2010 Springer-Verlag London Limited

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Barnes, D.J., Chu, D. (2010). Mathematical Tools. In: Introduction to Modeling for Biosciences. Springer, London. https://doi.org/10.1007/978-1-84996-326-8_5

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  • DOI: https://doi.org/10.1007/978-1-84996-326-8_5

  • Publisher Name: Springer, London

  • Print ISBN: 978-1-84996-325-1

  • Online ISBN: 978-1-84996-326-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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