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Cell Collective specifications


Unique identifier OMICS_20159
Name Cell Collective
Interface Web user interface
Restrictions to use Academic or non-commercial use
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes



  • person_outline Tomas Helikar
  • person_outline Cell Collective Team

Additional information


Publications for Cell Collective

Cell Collective citations


A systems pharmacology model for inflammatory bowel disease

PLoS One
PMCID: 5841748
PMID: 29513758
DOI: 10.1371/journal.pone.0192949

[…] or IFNγ have the most complex pathways as can be seen in the corresponding Boolean equations ().With the aim of making the network model more accessible to the community it has been uploaded to “The Cell Collective” [,] platform (https://www.cellcollective.org/#cb963d7f-75cb-4b2e-8987-0c7592a9c21d). In addition, the supporting information document provides the network model in text format ready […]


ATLANTIS Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming

Sci Rep
PMCID: 5824948
PMID: 29476134
DOI: 10.1038/s41598-018-22031-3

[…] iously, several tools have been developed for construction,, visualization, and analyses, of logical networks. From amongst them, the leading tools for computing attractor states include BoolNet, The Cell Collective and CellNetAnalyzer. However, these tools fail to associate biologically relevant network states with emergent cell fates. It is the lack of this functionality which further impedes ce […]


Logical Reduction of Biological Networks to Their Most Determinative Components

Bull Math Biol
PMCID: 4993808
PMID: 27417985
DOI: 10.1007/s11538-016-0193-x

[…] to explore the Java software Naldi et al. () to actually perform network reduction preserving attractors and stability and use it to analyze dynamics of various signal transduction networks found in Cell Collective Helikar et al. () and Helikar et al. ().Finally, it would be of great interest to look further into other real networks to identify the possibility of reducing them to the most determi […]


Community Reviewed Biological Network Models for Toxicology and Drug Discovery Applications

PMCID: 4944831
PMID: 27429547
DOI: 10.4137/GRSB.S39076

[…] work visualization software. Edge information can be used to filter and compute on the networks.Other network resources that are geared toward a community-driven approach include WikiPathways and the Cell Collective. These resources do not have a calcium pathway appropriate for comparison, but like KEGG and Reactome, they are limited by less granular information about the nodes and edges compared […]


Logical Modeling and Dynamical Analysis of Cellular Networks

Front Genet
PMCID: 4885885
PMID: 27303434
DOI: 10.3389/fgene.2016.00094
call_split See protocol

[…] et al., ), the SBML Qual (for qualitative) package has been defined to store logical models (Chaouiya et al., , ). This format is currently supported by a number of software tools, including GINsim, Cell Collective, CellNOpt, the tools mentioned in this paper. Hence, models stored in the SBML qual format can be exchanged between these tools. Thanks to the LogicalModel library, GINsim also provide […]


Systems Perturbation Analysis of a Large Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics

Front Bioeng Biotechnol
PMCID: 4750464
PMID: 26904540
DOI: 10.3389/fbioe.2016.00010

[…] The Cell Collective platform was used to perform all computational simulations of the model. Although the model is built by using discrete mathematics the output activity levels (AL) can be continuous (ra […]


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Cell Collective institution(s)
Department of Mathematics, University of Nebraska at Omaha, Omaha, NE, USA
Cell Collective funding source(s)
Supported by the College of Arts and Sciences at the University of Nebraska at Omaha, the University of Nebraska Foundation, the Patrick J. Kerrigan and Donald F. Dillon foundations, the National Aeronautics and Space Administration Nebraska Space Grant Consortium, and National Institutes of Health grant no. 5R01DA030962.

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