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Number of citations per year for the bioinformatics software tool TinkerCell
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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

Versioning


No version available

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 citations

 (11)
library_books

Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis

2018
Sci Rep
PMCID: 5823942
PMID: 29472639
DOI: 10.1038/s41598-018-21840-w

[…] 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 autoregulat […]

library_books

Computational design of molecular motors as nanocircuits in Leishmaniasis

2017
F1000Res
PMCID: 5580435
PMID: 28928941
DOI: 10.5256/f1000research.11538.r19802

[…] 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 DN […]

library_books

Process based design of dynamical biological systems

2016
Sci Rep
PMCID: 5043446
PMID: 27686219
DOI: 10.1038/srep34107

[…] ines 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 of t […]

library_books

Improving Collaboration by Standardization Efforts in Systems Biology

2014
Front Bioeng Biotechnol
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 for the display […]

library_books

Photo sensitive degron variants for tuning protein stability by light

2014
BMC Syst Biol
PMCID: 4236813
PMID: 25403319
DOI: 10.1186/s12918-014-0128-9

[…] ctional also might include a term which characterizes an a priori information on the parameters (Additional file : Table S3). These information were obtained from cycloheximide chase simulations with TinkerCell and literature [,,-,,]. For each variant, parameters were chosen that approximated the experimental data. During parameter estimation, these approximations were then used as starting values […]

library_books

Computational Tools and Algorithms for Designing Customized Synthetic Genes

2014
Front Bioeng Biotechnol
PMCID: 4186344
PMID: 25340050
DOI: 10.3389/fbioe.2014.00041

[…] ic sequences that GenoCAD uses as biological parts are immutable, and no optimizations are applied in the creation of the constructs. Other circuit design tools include GEC (Pedersen and Phillips, ), TinkerCell (Chandran et al., ), and Clotho (Xia et al., ).In Section “,” we examine some of the most important objectives in synthetic gene design toward optimized expression, accompanied by a brief a […]


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

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