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Bioinformatics Advance Access originally published online on August 29, 2006
Bioinformatics 2006 22(21):2709-2710; doi:10.1093/bioinformatics/btl456
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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 1,2,*

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

*To whom correspondence should be addressed.

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.

Contact: r.eils{at}dkfz.de

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

Received on June 11, 2006; revised on August 15, 2006; accepted on August 19, 2006

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