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CellSys specifications


Unique identifier OMICS_09423
Name CellSys
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes


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  • person_outline Stefan Hoehme

Publication for CellSys

CellSys citations


High Performance Agent Based Modeling Applied to Vocal Fold Inflammation and Repair

Front Physiol
PMCID: 5906585
PMID: 29706894
DOI: 10.3389/fphys.2018.00304

[…] running multiple non-interacting single-cell instances concurrently on massively parallel computers. More examples include HPC ABM frameworks for multi-core CPUs such as CompuCell3D (Swat et al., ,), CellSys (Hoehme and Drasdo, ), and Morpheus (Starruß et al., ). These frameworks target multi-core CPU acceleration on a single compute node using OpenMP. In addition, other techniques have been propo […]


PhysiCell: An open source physics based cell simulator for 3 D multicellular systems

PLoS Comput Biol
PMCID: 5841829
PMID: 29474446
DOI: 10.1371/journal.pcbi.1005991

[…] s with graphical model editors, integrated ODE and PDE solvers, and support for molecular-scale sub-models, but they currently cannot scale to large numbers (105 or more) of cells. TiSim (part of the CellSys package []) can simulate many more cells by using a cell-centered, off-lattice approach. However, it is currently closed source, and its executables are restricted to a limited set of simulati […]


Comparing individual based approaches to modelling the self organization of multicellular tissues

PLoS Comput Biol
PMCID: 5330541
PMID: 28192427
DOI: 10.1371/journal.pcbi.1005387

[…] of cell-based 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 of […]


Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis

PMCID: 3996365
PMID: 24748404
DOI: 10.1007/s00204-014-1243-5

[…] In the upcoming open-source software framework CellSys, the quantifications obtained from TiQuant can directly be used as an input for the CellSys modelling engine. As an illustration of this application of the processing pipeline, we refer to a m […]

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CellSys institution(s)
Interdisciplinary Centre for Bioinformatics, University of Leipzig, Germany; Institut National de Recherche en Informatique et en Automatique (INRIA) Unit Rocquencourt, Le Chesnay, France
CellSys funding source(s)
German Federal Ministry of Education and Research [HepatoSys 0313081F, LungSys 0315415F and VirtualLiver 0315735, in part]; European Union [CancerSys HEALTH-F4-2008-223188, Passport: 223894, in part]

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