IBCell specifications


Unique identifier OMICS_09424
Name IBCell
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Katarzyna A. Rejniak <>

Publications for IBCell

IBCell in publications

PMCID: 5916489
PMID: 29689072
DOI: 10.1371/journal.pone.0196277

[…] 480 nm and emission at 570 nm., mitochondria from the renal cortex and hek293 cells were isolated as previously described with slight modifications []. briefly, tissue or cells were homogenized in ibcell buffer with a glass homogenizer driven by an electrically powered motor (wheaton overhead stirrer). the homogenates were centrifuged at 4°c at 600 g for 20 minutes. the supernatants […]

PMCID: 3627127
PMID: 23596570
DOI: 10.3389/fonc.2013.00087

[…] epithelial tissue behavior (newman, ; sandersius et al., ) and invasion (sandersius et al., ). another example of a well developed, off-lattice model is the immersed boundary framework (ibcell), introduced by rejniak (). the model has been applied to tumor modeling (anderson et al., ), together with two other cellular automata-like approaches (the hybrid discrete continuum model, […]

PMCID: 3820568
PMID: 24278670
DOI: 10.6064/2012/132978

[…] such as filled lumens or ductal disorganization, are among the first symptoms of the emerging epithelial tumors (carcinomas). using the previously developed biomechanical model of epithelial ducts: ibcell, we investigated how different signals and mechanical stimuli imposed on individual epithelial cells can impact the homeostatic (im)balance and integrity of the whole epithelial tissue. […]

PMCID: 3072361
PMID: 21490722
DOI: 10.1371/journal.pcbi.1002030

[…] below) clear mappings will be easier to establish and quantify., a good example of a project in which intracellular events are incorporated and to some degree mapped back to those in vitro, is the ibcell model , . it is a biomechanical model of mcf-10a cell cystogenesis in which proteins on the outer cell membrane and the extracellular matrix are specifically simulated. the ibcell model […]

PMCID: 2928778
PMID: 20865159
DOI: 10.1371/journal.pcbi.1000900

[…] when compared to regular epithelial monolayers enclosing the hollow lumen (acini). in order to shed light on phenotypic changes associated with tumor cells, we applied the bio-mechanical ibcell model of normal epithelial morphogenesis quantitatively matched to data acquired from the non-tumorigenic human mammary cell line, mcf10a. we then used a high-throughput simulation study […]

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IBCell institution(s)
Division of Mathematics, University of Dundee, Dundee, Scotland, UK

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