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Bioinformatics Advance Access published online on August 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl456
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© 2006 The Author(s)
Received June 11, 2006
Revised August 15, 2006
Accepted August 19, 2006

Applications note

Tropical - parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images

Markus Ulrich 1 {dagger}, Constantin Kappel 1 {dagger}, Joel Beaudouin 1, Stefan Hezel 1, Jochen Ulrich 1, and Roland Eils 2 *

1 Department of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg
2 Department of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg; Institute for Pharmacy and Molecular Biology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg

* To whom correspondence should be addressed.
Roland Eils, E-mail: r.eils{at}dkfz.de


  Abstract

Summary: Tropical is a software for simulation and parameter estimation of reaction-diffusion models. Based on spatio-temporal microscopy images, Tropical estimates reaction and diffusion coefficients for user-defined models. Tropical allows the investigation of systems with an inhomogeneous distribution of molecules, making it well suited for quantitative analyses of microscopy experiments such as fluorescence recovery after photobleaching (FRAP).

Availability: Tropical is available free of charge for academic use at http://www.dkfz.de/tbi/projects/modellingAndSimulationOfCelluarSystems/tropical.jsp after signing a material transfer agreement.

Supplementary information: http://www.dkfz.de/tbi/projects/modellingAndSimulationOfCelluarSystems/tropical.jsp.

Associate Editor: Alfonso Valencia

{dagger} The authors contributed equally to this work.


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