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VirtualLeaf specifications

Information


Unique identifier OMICS_09422
Name VirtualLeaf
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Roeland M.H. Merks <>

Publications for VirtualLeaf

VirtualLeaf in publications

 (5)
PMCID: 5330541
PMID: 28192427
DOI: 10.1371/journal.pcbi.1005387

[…] model. a longer-term challenge is to extend such comparison studies across simulation tools, of which there is an increasing ecosystem, including compucell3d [], morpheus [], episim [], cellsys [], virtualleaf [], biocellion [], biofvm [], lbibcell [] and embryomaker []. we emphasize here the lack of ‘benchmarks’ on which to make such comparisons. we propose that the present study offers four […]

PMCID: 5264012
PMID: 28112150
DOI: 10.1038/ncomms13929

[…] molecular signalling, genetic regulation and structural changes to one another: ingeneue embeds gene networks in sheets of cells, but does not distinguish heterogeneous cell types or behaviours; virtualleaf and cellzilla both simulate the transport of chemical signals across a polygonal mesh of elastic compartments, the latter also allowing the specification of complex chemical networks, […]

PMCID: 3797531
PMID: 24137172
DOI: 10.3389/fpls.2013.00408

[…] et al., , ,; mjolsness, ), or at some level of geometric complexity with springs between polygonal vertices (rudge and haseloff, ; sahlin and johnsson, ), as is currently done by cellzilla. the virtualleaf (merks et al., ) provides an interesting hybrid that uses the cpm in combination with mechanical springs with a markovian relaxation algorithm to describe tissue growth. cellzilla […]

PMCID: 3264561
PMID: 22291882
DOI: 10.1371/journal.pone.0028762

[…] why we adapted this model type here. this model class was first applied to phyllotaxis –, and later extended to leaf venation patterning . we made use of an integrated model and the software package virtualleaf in which auxin transport and tissue growth are combined . for the present purposes we extended this model with auxin induced cell growth, cell differentiation to a provascular cell type, […]

PMCID: 3018162
PMID: 21179019
DOI: 10.1038/msb.2010.103

[…] root system maintenance, and de novo organ formation., for model description, parameters, sensitivity analysis, and simulation insets, we refer to . the model was based on a version of virtualleaf (; ), a cell-based simulation tool for modeling plant development. all simulations were run until steady-state patterns emerged. all figures were processed in adobe illustrator. , , , , […]


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VirtualLeaf institution(s)
Centrum Wiskunde & Informatica, Amsterdam, Netherlands; Netherlands Consortium for Systems Biology/Netherlands Institute for Systems Biology, Amsterdam, Netherlands; VIB, Department of Plant Systems Biology, and Department of Plant Biotechnology and Genetics, Ghent University, Ghent, Belgium; Department of Biology, University of Antwerp, Antwerp, Belgium

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