Tumorcode

A framework to simulate vascularized tumors
Tips and Tricks

Abstract.

During the past years our group published several articles using computer simulations to address the complex interaction of tumors and the vasculature as underlying transport network. Advances in imaging and lab techniques pushed in vitro research of tumor spheroids forward and animal models as well as clinical studies provided more insights to single processes taking part in tumor growth, however, an overall picture is still missing. Computer simulations are a non-invasive option to cumulate current knowledge and form a quasi in vivo system. In our software, several known models were assembled into a multi-scale approach which allows to study length scales relevant for clinical applications. We release our code to the public domain, together with a detailed description of the implementation and several examples, with the hope of usage and futher development by the community. A justification for the included algorithms and the biological models was obtained in previous publications, here we summarize the technical aspects following the workflow of a typical simulation procedure.

Graphical abstract

Keywords

Tips and Tricks 

Supplementary material

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References

  1. 1.
    Peter Carmeliet, Rakesh K. Jain, Nature 407, 249 (2000)CrossRefGoogle Scholar
  2. 2.
    Heiko Rieger, Thierry Fredrich, Michael Welter, Eur. Phys. J. Plus 131, 31 (2016)CrossRefGoogle Scholar
  3. 3.
    Holger Perfahl, Barry D. Hughes, Toms Alarcn, Philip K. Maini, Mark C. Lloyd, Matthias Reuss, Helen M. Byrne, J. Theor. Biol. 414, 254 (2017)CrossRefGoogle Scholar
  4. 4.
    Roeland M.H. Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier, PLoS Comput. Biol. 4, e1000163 (2008)CrossRefGoogle Scholar
  5. 5.
    A.R.A. Anderson, M.A.J. Chaplain, Bull. Math. Biol. 60, 857 (1998)CrossRefGoogle Scholar
  6. 6.
    Paul Macklin, Steven McDougall, Alexander R.A. Anderson, Mark A.J. Chaplain, Vittorio Cristini, John Lowengrub, J. Math. Biol. 58, 765 (2009)MathSciNetCrossRefGoogle Scholar
  7. 7.
    Edoardo Milotti, Roberto Chignola, PLoS ONE 5, e13942 (2010)CrossRefGoogle Scholar
  8. 8.
    Luigi Preziosi, Andrea Tosin, J. Math. Biol. 58, 625 (2008)CrossRefGoogle Scholar
  9. 9.
    James Grogan, Anthony J. Connor, Bostjan Markelc, Ruth J. Muschel, Philip K. Maini, Helen M. Byrne, Joe M. Pitt-Francis, Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues, bioRxiv 105692,  https://doi.org/10.1101/105692 (2017)
  10. 10.
    Abbas Shirinifard, J. Scott Gens, Benjamin L. Zaitlen, Nikodem J. Popawski, Maciej Swat, James A. Glazier, PLoS ONE 4, e7190 (2009)ADSCrossRefGoogle Scholar
  11. 11.
    The HDF Group, Hierarchical Data Format, version 5, 1997. Google Scholar
  12. 12.
    Michael Heroux, Roscoe Bartlett, Vicki Howle Robert Hoekstra, Jonathan Hu, Tamara Kolda, Richard Lehoucq, Kevin Long, Roger Pawlowski, Eric Phipps, Andrew Salinger, Heidi Thornquist, Ray Tuminaro, James Willenbring, Alan Williams, An Overview of Trilinos, Technical Report SAND2003-2927 (Sandia National Laboratories, 2003)Google Scholar
  13. 13.
    Ralf Gödde, Haymo Kurz, Dev. Dyn. 220, 387 (2001)CrossRefGoogle Scholar
  14. 14.
    Cosmina S. Hogea, Bruce T. Murray, James A. Sethian, J. Math. Biol. 53, 86 (2006)MathSciNetCrossRefGoogle Scholar
  15. 15.
    Michael Welter, Thierry Fredrich, Herbert Rinneberg, Heiko Rieger, PLoS ONE 11, e0161267 (2016)CrossRefGoogle Scholar
  16. 16.
    A.R. Pries, B. Reglin, T.W. Secomb, Am. J. Physiol. - Heart Circul. Physiol. 284, H2204 (2003)CrossRefGoogle Scholar
  17. 17.
    Michael Welter, Heiko Rieger, PLoS ONE 8, e70395 (2013)CrossRefGoogle Scholar
  18. 18.
    A.R. Pries, T.W. Secomb, P. Gaehtgens, J.F. Gross, Circul. Res. 67, 826 (1990)CrossRefGoogle Scholar

Copyright information

© EDP Sciences, SIF, Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Thierry Fredrich
    • 1
  • Michael Welter
    • 2
  • Heiko Rieger
    • 1
  1. 1.Theoretical Physics and Center for Biophysics (ZBP)Saarland UniversitySaarbrückenGermany
  2. 2.TruPhysics GmbHStuttgartGermany

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