Goksel Misirli's Outputs (5)

A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference (2018)
Journal Article
Misirli. (2018). A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS synthetic biology, 2812-2823. https://doi.org/10.1021/acssynbio.8b00201

A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer simulation in an... Read More about A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.

Harmonizing semantic annotations for computational models in biology (2018)
Journal Article
Misirli. (2018). Harmonizing semantic annotations for computational models in biology. Briefings in bioinformatics, bby087 - bby087. https://doi.org/10.1093/bib/bby087

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for... Read More about Harmonizing semantic annotations for computational models in biology.

A computational workflow for the automated generation of models of genetic designs (2018)
Journal Article
Misirli. (2018). A computational workflow for the automated generation of models of genetic designs. ACS synthetic biology, 1548-1559. https://doi.org/10.1021/acssynbio.7b00459

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modelling often requires expert knowledge and data to build models. Clearly, manual creation of models is no... Read More about A computational workflow for the automated generation of models of genetic designs.

Synthetic Biology Open Language (SBOL) Version 2.2.0. (2018)
Journal Article
Misirli. (2018). Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of Integrative Bioinformatics, https://doi.org/10.1515/jib-2018-0001

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long... Read More about Synthetic Biology Open Language (SBOL) Version 2.2.0..

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. (2018)
Journal Article
McLaughlin, J., Ofiteru, I., Goñi Moreno, A., Zundel, Z., Misirli, G., Zhang, M., Wipat, A., & Myers, C. (2018). SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS synthetic biology, 682-688. https://doi.org/10.1021/acssynbio.7b00403

The SynBioHub repository (synbiohub.org) is an open-source software project which facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical u... Read More about SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology..