-
1
-
-
0037342537
-
The systems biology markup language (sbml): A medium for representation and exchange of biochemical network models
-
Hucka, M., et al. (2003) The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
-
2
-
-
84982130923
-
The systems biology markup language (sbml): Language specification for level 3 version 1 core
-
Hucka, M., Bergmann, F. T., Hoops, S., Keating, S. M., Sahle, S., Schaff, J. C., Smith, L. P., and Wilkinson, D. J. (2015) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integrat. Bioinf. 12, 266.
-
(2015)
J. Integrat. Bioinf
, vol.12
, pp. 266
-
-
Hucka, M.1
Bergmann, F.T.2
Hoops, S.3
Keating, S.M.4
Sahle, S.5
Schaff, J.C.6
Smith, L.P.7
Wilkinson, D.J.8
-
3
-
-
84982133324
-
Synthetic biology open language (sbol) version 2.0.0
-
Bartley, B., Beal, J., Clancy, K., Misirli, G., Roehner, N., Oberortner, E., Pocock, M., Bissell, M., Madsen, C., Nguyen, T., Zhang, Z., Gennari, J. H., Myers, C., Wipat, A., and Sauro, H. (2015) Synthetic Biology Open Language (SBOL) Version 2.0.0. J. Integrat. Bioinf. 12, 272.
-
(2015)
J. Integrat. Bioinf
, vol.12
, pp. 272
-
-
Bartley, B.1
Beal, J.2
Clancy, K.3
Misirli, G.4
Roehner, N.5
Oberortner, E.6
Pocock, M.7
Bissell, M.8
Madsen, C.9
Nguyen, T.10
Zhang, Z.11
Gennari, J.H.12
Myers, C.13
Wipat, A.14
Sauro, H.15
-
4
-
-
84902159136
-
The synthetic biology open language (sbol) provides a community standard for communicating designs in synthetic biology
-
Galdzicki, M., et al. (2014) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat. Biotechnol. 32, 545-550.
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 545-550
-
-
Galdzicki, M.1
-
5
-
-
84921345937
-
Proposed data model for the next version of the synthetic biology open language
-
Roehner, N., Oberortner, E., Pocock, M., Beal, J., Clancy, K., Madsen, C., Misirli, G., Wipat, A., Sauro, H., and Myers, C. J. (2015) Proposed Data Model for the Next Version of the Synthetic Biology Open Language. ACS Synth. Biol. 4, 57-71.
-
(2015)
ACS Synth. Biol
, vol.4
, pp. 57-71
-
-
Roehner, N.1
Oberortner, E.2
Pocock, M.3
Beal, J.4
Clancy, K.5
Madsen, C.6
Misirli, G.7
Wipat, A.8
Sauro, H.9
Myers, C.J.10
-
6
-
-
84939794173
-
Generating systems biology markup language models from the synthetic biology open language
-
Roehner, N., Zhang, Z., Nguyen, T., and Myers, C. J. (2015) Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language. ACS Synth. Biol. 4, 873-879.
-
(2015)
ACS Synth. Biol
, vol.4
, pp. 873-879
-
-
Roehner, N.1
Zhang, Z.2
Nguyen, T.3
Myers, C.J.4
-
7
-
-
80155212661
-
Controlled vocabularies and semantics in systems biology
-
Courtot, M., et al. (2011) Controlled vocabularies and semantics in systems biology. Mol. Syst. Biol. 7, 543.
-
(2011)
Mol. Syst. Biol
, vol.7
, pp. 543
-
-
Courtot, M.1
-
8
-
-
84864038026
-
Design and test of genetic circuits using iBioSim
-
Madsen, C., Myers, C., Patterson, T., Roehner, N., Stevens, J., and Winstead, C. (2012) Design and test of genetic circuits using iBioSim. IEEE Des. Test Comput. 29, 32-39.
-
(2012)
IEEE Des. Test Comput
, vol.29
, pp. 32-39
-
-
Madsen, C.1
Myers, C.2
Patterson, T.3
Roehner, N.4
Stevens, J.5
Winstead, C.6
-
9
-
-
84883221825
-
Biomodels database: A repository of mathematical models of biological processes
-
Chelliah, V., Laibe, C., and Le Nove?re, N. (2013) BioModels Database: A Repository of Mathematical Models of Biological Processes. Methods Mol. Biol. 1021, 189-199.
-
(2013)
Methods Mol. Biol
, vol.1021
, pp. 189-199
-
-
Chelliah, V.1
Laibe, C.2
Le Novere, N.3
-
10
-
-
84982111814
-
The systems biology markup language (sbml) level 3 package: Layout, version 1 core
-
Gauges, R., Rost, U., Sahle, S., Wengler, K., and Bergmann, F. T. (2015) The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core. J. Integrat Bioinf. 12, 267.
-
(2015)
J. Integrat Bioinf
, vol.12
, pp. 267
-
-
Gauges, R.1
Rost, U.2
Sahle, S.3
Wengler, K.4
Bergmann, F.T.5
-
11
-
-
84982133322
-
Sbml level 3 package: Hierarchical model composition, version 1 release 3
-
Smith, L. P., Hucka, M., Hoops, S., Finney, A., Ginkel, M., Myers, C. J., Moraru, I., and Liebermeister, W. (2015) SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. J. Integrat. Bioinf. 12, 268.
-
(2015)
J. Integrat. Bioinf
, vol.12
, pp. 268
-
-
Smith, L.P.1
Hucka, M.2
Hoops, S.3
Finney, A.4
Ginkel, M.5
Myers, C.J.6
Moraru, I.7
Liebermeister, W.8
-
12
-
-
84982113791
-
The systems biology markup language (sbml) level 3 package: Flux balance constraints
-
Olivier, B. G., and Bergmann, F. T. (2015) The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. J. Integrat. Bioinf. 12, 269.
-
(2015)
J. Integrat. Bioinf
, vol.12
, pp. 269
-
-
Olivier, B.G.1
Bergmann, F.T.2
-
13
-
-
84982145073
-
The systems biology markup language (sbml) level 3 package: Qualitative models, version 1, release 1
-
Chaouiya, C., Keating, S. M., Berenguier, D., Naldi, A., Thieffry, D., van Iersel, M. P., Nove?re, N. L., and Helikar, T. (2015) The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J. Integrat. Bioinf. 12, 270.
-
(2015)
J. Integrat. Bioinf
, vol.12
, pp. 270
-
-
Chaouiya, C.1
Keating, S.M.2
Berenguier, D.3
Naldi, A.4
Thieffry, D.5
Van Iersel, M.P.6
Novere, N.L.7
Helikar, T.8
-
15
-
-
79952074324
-
Standard biological parts knowledgebase
-
Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H. M., and Gennari, J. H. (2011) Standard Biological Parts Knowledgebase. PLoS One 6, e17005.
-
(2011)
PLoS One
, vol.6
, pp. e17005
-
-
Galdzicki, M.1
Rodriguez, C.2
Chandran, D.3
Sauro, H.M.4
Gennari, J.H.5
-
16
-
-
84867488931
-
Design, implementation and practice of JBEIICE: An open source biological part registry platform and tools
-
Ham, T. S., Dmytriv, Z., Plahar, H., Chen, J., Hillson, N. J., and Keasling, J. D. (2012) Design, implementation and practice of JBEIICE: An open source biological part registry platform and tools. Nucleic Acids Res. 40, e141 DOI: 10.1093/nar/gks531.
-
(2012)
Nucleic Acids Res
, Issue.40
, pp. e141
-
-
Ham, T.S.1
Dmytriv, Z.2
Plahar, H.3
Chen, J.4
Hillson, N.J.5
Keasling, J.D.6
-
17
-
-
85009124299
-
-
7th International Workshop on Bio-Design Automation; Seattle, Washington, August 20-21
-
Madsen, C., Misirli, G., Misirli, G., Hallinan, J., Wipat, A. SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs. 7th International Workshop on Bio-Design Automation; Seattle, Washington, August 20-21, 2015.
-
(2015)
SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs
-
-
Madsen, C.1
Misirli, G.2
Misirli, G.3
Hallinan, J.4
Wipat, A.5
-
18
-
-
77951969603
-
Standard virtual biological parts: A repository of modular modeling components for synthetic biology
-
Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., and Wipat, A. (2010) Standard virtual biological parts: A repository of modular modeling components for synthetic biology. Bioinformatics 26, 925-931.
-
(2010)
Bioinformatics
, vol.26
, pp. 925-931
-
-
Cooling, M.T.1
Rouilly, V.2
Misirli, G.3
Lawson, J.4
Yu, T.5
Hallinan, J.6
Wipat, A.7
-
19
-
-
84896831202
-
A methodology to annotate systems biology markup language models with the synthetic biology open language
-
Roehner, N., and Myers, C. J. (2014) A methodology to annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language. ACS Synth. Biol. 3, 57-66.
-
(2014)
ACS Synth. Biol
, vol.3
, pp. 57-66
-
-
Roehner, N.1
Myers, C.J.2
-
20
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
21
-
-
84953251562
-
Sbol visual: A graphical language for genetic designs
-
Quinn, J. Y., et al. (2015) SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biol. 13, e1002310.
-
(2015)
PLoS Biol
, vol.13
, pp. e1002310
-
-
Quinn, J.Y.1
-
22
-
-
84868619337
-
Genetic programs constructed from layered logic gates in single cells
-
Moon, T. S., Lou, C., Tamsir, A., Stanton, B. C., and Voigt, C. A. (2012) Genetic programs constructed from layered logic gates in single cells. Nature 491, 249-253.
-
(2012)
Nature
, vol.491
, pp. 249-253
-
-
Moon, T.S.1
Lou, C.2
Tamsir, A.3
Stanton, B.C.4
Voigt, C.A.5
-
23
-
-
85009143439
-
-
accessed on Dec 22, 2015
-
SBOL Designer. 2015. http://clarkparsia.github.io/sbol/(accessed on Dec. 22, 2015).
-
(2015)
SBOL Designer
-
-
|