Tawny-SBOL: Using ontologies to design and constrain genetic circuits
(2017)
Presentation / Conference
Misirli. (2017, September). Tawny-SBOL: Using ontologies to design and constrain genetic circuits. Presented at International Conference on Biomedical Ontology 2017, Newcastle upon Tyne
Outputs (43)
Standard Enabled Model Generator for Genetic Circuit Design (2017)
Presentation / Conference
Myers, C., Wipat, A., Misirli, G., Nguyen, T., & McLaughlin, J. (2017, August). Standard Enabled Model Generator for Genetic Circuit Design. Presented at 9th International Workshop on Bio-Design Automation, Pittsburgh
A standard-enabled workflow for synthetic biology. (2017)
Journal Article
Mısırlı, G., Nguyen, T., Oberortner, E., Samineni, M., Wipat, A., Zhang, M., Zundel, Z., Madsen, C., McLaughlin, J., Myers, C., Beal, J., Gorochowski, T., & Kuwahara, H. (2017). A standard-enabled workflow for synthetic biology. Transactions, 793 - 803. https://doi.org/10.1042/BST20160347A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select... Read More about A standard-enabled workflow for synthetic biology..
Constructing Synthetic Biology Workflows in the Cloud (2017)
Journal Article
Misirli. (2017). Constructing Synthetic Biology Workflows in the Cloud. Engineering Biology, 61-65. https://doi.org/10.1049/enb.2017.0001The synthetic biology design process has traditionally been heavily dependent upon manual searching, acquisition and integration of existing biological data. A large amount of such data is already available from Internet-based resources, but data exc... Read More about Constructing Synthetic Biology Workflows in the Cloud.
The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. (2016)
Journal Article
Wipat, A., Hallinan, J., Madsen, C., McLaughlin, J., Mısırlı, G., Pocock, M., & Flanagan, K. (2016). The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. ACS synthetic biology, 487 - 497. https://doi.org/10.1021/acssynbio.5b00210Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange design... Read More about The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs..
Data Integration and Mining for Synthetic Biology Design. (2016)
Journal Article
Mısırlı, G., Hallinan, J., Pocock, M., Lord, P., McLaughlin, J., Sauro, H., & Wipat, A. (2016). Data Integration and Mining for Synthetic Biology Design. ACS synthetic biology, 1086 - 1097. https://doi.org/10.1021/acssynbio.5b00295One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existin... Read More about Data Integration and Mining for Synthetic Biology Design..
libSBOLj 2.0: A Java Library to Support SBOL 2.0 (2016)
Journal Article
Misirli. (2016). libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 34 - 37. https://doi.org/10.1109/LLS.2016.2546546The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic d... Read More about libSBOLj 2.0: A Java Library to Support SBOL 2.0.
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. (2015)
Journal Article
Gilfellon, O., Honorato-Zimmer, R., Pocock, M., Madsen, C., Waites, W., Cavaliere, M., Misirli, G., Zuliani, P., Danos, V., & Wipat, A. (2015). Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics, 908 - 917. https://doi.org/10.1093/bioinformatics/btv660MOTIVATION: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the for... Read More about Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization..
Composable Modular Models for Synthetic Biology. (2014)
Journal Article
Misirli. (2014). Composable Modular Models for Synthetic Biology. https://doi.org/10.1145/2631921Modelling and computational simulation are crucial for the large-scale engineering of biological circuits since they allow the system under design to be simulated prior to implementation in vivo. To support automated, model-driven design it is desira... Read More about Composable Modular Models for Synthetic Biology..
BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. (2014)
Journal Article
Röttger, R., Baumbach, J., Wipat, A., Misirli, G., & Hallinan, J. (2014). BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. Journal of Integrative Bioinformatics, 244 - ?. https://doi.org/10.2390/biecoll-jib-2014-244As high-throughput technologies become cheaper and easier to use, raw sequence data and corresponding annotations for many organisms are becoming available. However, sequence data alone is not sufficient to explain the biological behaviour of organis... Read More about BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species..