DNAr: An R Package to Simulate and Analyze CRN and DSD Networks
| Autor: | Omar P. Vilela Neto, Renan A. Marks, Maria C. O. Fonte Boa, Poliana A. C. Oliveira, Marcos V. Guterres, Daniel K. S. Vieira |
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| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0303 health sciences R language Artificial neural network Computer science Distributed computing Biomedical Engineering General Medicine DNA 01 natural sciences Biochemistry Genetics and Molecular Biology (miscellaneous) law.invention 03 medical and health sciences R package DNA computing law 010608 biotechnology Scalability Computer Simulation Algorithms Software 030304 developmental biology Dna strand displacement Abstraction (linguistics) |
| Zdroj: | ACS synthetic biology. 9(12) |
| ISSN: | 2161-5063 |
| Popis: | Chemical reaction networks (CRNs) have been proposed as an abstraction for molecular computing. DNA strand displacement (DSD) reactions are good candidates to realize this endeavor, since DNA strands can be wired to implement the desired dynamic behavior in a test tube. Specialists use simulators to help them design such chemical systems before experimental implementation. In this sense, we present the DNAr package, an alternative open-source tool, developed in R language, for users from multidisciplinary areas. The current version of our tool offers functions to simulate CRNs, convert a formal CRN into a DSD network, interpret results, export to Visual DSD, and create libraries. Here, we use the consensus CRN to show DNAr features and a neural network model to demonstrate scalability, simulating more than 600 chemical reactions in a few minutes. |
| Databáze: | OpenAIRE |
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