Biocellion statistics

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Biocellion specifications

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Unique identifier OMICS_08774
Name Biocellion
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

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  • person_outline Biocellion <>

Publications for Biocellion

Biocellion in publications

 (5)
PMCID: 5863959
PMID: 29565975
DOI: 10.1371/journal.pone.0191089

[…] that the material properties of a biofilm both power and control wrinkle formation within biofilms in response to localized cell death. using an agent-based model and a high-performance platform (biocellion), we built a model that qualitatively reproduced wrinkle formation in biofilms due to cell death. through the use of computational simulations, we determined important relationships […]

PMCID: 5514506
PMID: 28716030
DOI: 10.1186/s12918-017-0443-z

[…] of enhancing anaerobic granulation, such as addition of positively charged ions and particles of polymers into the uasb system [, ]. to converge granulation model with reactor-like environment, a biocellion modelling environment can be used [, ]. possibility to parallelize computation load in biocellion would eliminate the main bottleneck of the cdynomics and allow development of a whole […]

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

[…] 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 examples […]

PMCID: 4373890
PMID: 25806784
DOI: 10.1371/journal.pone.0122192

[…] of agent-agent and agent-local environment interactions can challenge the parallelization of an abm, and there have been several specialized modeling platforms developed to provide this capability: biocellion [,], flame [,], and repast hpc [,]. however, despite their advantages in terms of lowering barriers to use and implementation on hpc environments, there are potential limitations […]

PMCID: 4385633
PMID: 25874228
DOI: 10.1155/2015/769471

[…] simulation of more complex biomolecular systems. namely, we are investigating the potential of the new distributed environment of mason, the dmason (http://www.isislab.it/projects/dmason/), and the biocellion framework []., abm is increasingly popular in biology due to its natural ability to represent multiple scales of system decomposition, intertwine complicated behaviours, and deal […]


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Biocellion institution(s)
Computational Biology and Bioinformatics Group, High-performance Computing Group, Pacific Northwest National Laboratory, Richland, WA, USA, Department of Computer Science, Utah State University, Logan, UT, USA and Institute for Systems Biology, Seattle, WA, USA

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