TinkerCell specifications

Information


Unique identifier OMICS_04790
Name TinkerCell
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Deepak Chandran <>

Information


Unique identifier OMICS_04790
Name TinkerCell
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Deepak Chandran <>

Publications for TinkerCell

TinkerCell in publications

 (10)
PMCID: 5823942
PMID: 29472639
DOI: 10.1038/s41598-018-21840-w

[…] protocols and minimum energy structures were exported from the trajectories for further analysis., the synthetic circuit with a laci negative autoregulatory loop was designed in tinker cell (www.tinkercell.com) and the chimeric pkc_ζα was coupled to it in such a way that its expression was under the transcriptional control of laci repressor protein. two odes depicting the negative […]

PMCID: 5580435
PMID: 28928941
DOI: 10.5256/f1000research.11538.r19802

[…] complexes attaches with this bound biotin, finally leading to internalization of complex ( )., the nanocircuit was designed using different biological parts available in tinker cell ( http://www.tinkercell.com/). the transcriptional repression processes were also indicated in the circuit. sequences for the different parts of the gene modules were obtained from various sources: the reporter […]

PMCID: 5043446
PMID: 27686219
DOI: 10.1038/srep34107

[…] the hyper-volume under the pareto front with the complexity of the model structure to obtain a single score used for ranking the candidate designs. the process-based design is closely related to tinkercell, which employs a hierarchical representation of domain knowledge, but, in contrast to our approach, limits its focus to manual resolution of the structural and parametric uncertainties […]

PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] which follows many traditional aspects. in order to display and draw similar maps, several programs have been developed, for instance, celldesigner (funahashi et al., ), jdesigner (sauro et al., ), tinkercell (chandran et al., ), vcell (resasco et al., ), or cytoscape (shannon et al., ) with its diverse plug-ins (könig et al., ; gonçalves et al., ). we now discuss recommendations […]

PMCID: 4236813
PMID: 25403319
DOI: 10.1186/s12918-014-0128-9

[…] type psd module (20 ± 1 min), although all three mutants showed decreased stability in darkness (table , additional file : figure s2 and s3)., previously, we used the computer-aided design software tinkercell [] to generate a model that simulated the behavior of the psd module []. among other things, the simulation and analysis functions of tinkercell can be used to predict the steady state […]


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TinkerCell institution(s)
Department of Bioengineering, University of Washington, Seattle, WA, USA

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