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Synthetic Biology Circuit Design & In-Silico Prototyping Training | Genetic Circuits, SBOL & Design Automation

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Systems Biology, Network Modeling & Pathway Simulation >> Synthetic Biology Circuit Design & In-Silico Prototyping Training | Genetic Circuits, SBOL & Design Automation

Synthetic Biology Circuit Design & In-Silico Prototyping — Hands-on

Learn how to design and evaluate synthetic gene circuits using computational tools before going to the bench. This module walks through design abstractions (promoters, RBS, coding sequences, terminators) , logic gates and genetic toggles, modeling and simulation (deterministic and stochastic) , and in silico design workflows that use SBOL, Cello and circuit modeling platforms. By the end, you will implement a small design–build–test–learn style pipeline with publication ready circuit diagrams and simulation outputs.

Synthetic Biology Circuit Design & In-Silico Prototyping
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Session 1
Fee: Rs 8800
Synthetic Biology Foundations & Circuit Abstractions
  • Synthetic biology design abstractions
  • promoters, RBS, CDS, terminators logic gates & switches oscillators & feedback motifs
  • Circuit design principles
  • insulation & composability retroactivity & load effects (overview) host context & chassis choice
  • Toolchain & design workflow overview
  • SBOL descriptions Cello & related tools (overview) bench to model information flow
Session 2
Fee: Rs 11800
Circuit Modeling, Dynamics & Simulation
  • From circuit diagrams to models
  • Hill function based ODE models transcription and translation delays (overview) simple stochastic formulations
  • Simulating circuit behavior
  • switches, oscillators, logic gates input–output curves & thresholds noise & robustness checks
  • Circuit modeling tools
  • BioCRNpyler / Tellurium COPASI / iBioSim (overview) Python / R simulation notebooks
Session 3
Fee: Rs 14800
SBOL, Design Automation & In-Silico Prototyping
  • SBOL & standardization of circuit designs
  • SBOL entities & relationships linking sequence & function libraries & repositories
  • Logic synthesis & design automation
  • specification to circuit mapping (Cello style overview) constraints & objective functions screening candidate designs
  • In-silico prototyping workflows
  • from SBOL to executable models automated simulation pipelines ranking designs by performance
Session 4
Fee: Rs 18800
Mini Capstone: Design–Build–Test–Learn In-Silico Circuit
  • Case study: design a small genetic circuit in silico
  • Theory + Practical
  • Build & test loops in simulation
  • design variants & parameter sweeps performance metrics & specification checks iterative refinement of designs
  • Deliverables
  • PDF/HTML circuit design report SBOL files & model notebooks environment.yml / requirements.txt


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