Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model.
BACKGROUND
The transformation of the embryo during development requires complex gene networks, cell signaling and gene-regulated cell behaviors (division, adhesion, polarization, apoptosis, contraction, extracellular matrix secretion, signal secretion and reception, etc.). There are several models of development implementing these phenomena, but none considers at the same time the very different bio-mechanical properties of epithelia, mesenchyme, extracellular matrix and their interactions.


RESULTS
Here, we present a new computational model and accompanying open-source software, EmbryoMaker, that allows the user to simulate custom developmental processes by designing custom gene networks capable of regulating cell signaling and all animal basic cell behaviors. We also include an editor to implement different initial conditions, mutations and experimental manipulations. We show the applicability of the model by simulating several complex examples of animal development.


METHODS
The source code can be downloaded from: http://www.biocenter.helsinki.fi/salazar/software.html.


BACKGROUND
isalazar@mappi.helsinki.fi


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Genetics, Universitat Autònoma de Barcelona, Edifici C. 08193, Spain and.
Miquel
M
Marin-Riera
Department of Genetics, Universitat Autònoma de Barcelona, Edifici C. 08193, Spain and.
Miguel
M
Brun-Usan
Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland.
Roland
R
Zimm
Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland.
Tommi
T
Välikangas
Department of Genetics, Universitat Autònoma de Barcelona, Edifici C. 08193, Spain and Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland.
Isaac
I
Salazar-Ciudad
D000818:Animals; D003198:Computer Simulation; D047108:Embryonic Development / Q000235:genetics; D004848:Epithelium / Q000196:embryology* / Q000502:physiology; D005109:Extracellular Matrix / Q000502:physiology; D053263:Gene Regulatory Networks; D008648:Mesoderm / Q000196:embryology / Q000502:physiology*; D008954:Models, Biological; D009024:Morphogenesis; D015398:Signal Transduction / Q000235:genetics; D012984:Software