摘要：SummarySynthetic biology has the potential to revolutionize the biotech industry and our everyday lives and is already making an impact. Developing synthetic biology applications requires several steps including design and modeling efforts which may be performed byin silicotools. In this work, we have developed two such tools,EukaryoticGeneticCircuitDesign (EuGeneCiD) andModeling (EuGeneCiM), which use optimization concepts and bioparts including promotors, transcripts, and terminators in designing and modeling genetic circuits. EuGeneCiD and EuGeneCiM preclude problematic designs leading to future synthetic biology application development pipelines. EuGeneCiD and EuGeneCiM are applied to developing 30 basic logic gates as genetic circuit conceptualizations which respond to heavy metal ions pairs as input signals forArabidopsis thaliana. For each conceptualization, hundreds of potential solutions were designed and modeled. Demonstrating its time-dependence and the importance of including enzyme and transcript degradation in modeling, EuGeneCiM is used to model a repressilator circuit.Graphical abstractDisplay OmittedHighlights•Anin silicoEukaryotic Genetic Circuit Design (EuGeneCiD) tool is introduced•A complimentary Eukaryotic Genetic Circuit Modeling (EuGeneCiM) tool is developed•In a unified workflow, these tools generated thousands of designs and modeled them•The EuGeneCiM tool is also used to model a dynamic repressilator circuitBiotechnology; Systems biology; Synthetic biology
