Automated Biocircuit Design with SYNBADm

SYNBADm is a Matlab toolbox for the automated design of biocircuits using a model-based optimization approach. It enables the design of biocircuits with pre-defined functions starting from libraries of biological parts. SYNBADm makes use of mixed integer global optimization and allows both single and multi-objective design problems. Here we describe a basic protocol for the design of synthetic gene regulatory circuits. We illustrate step-by-step how to solve two different problems: (1) the (single objective) design of a synthetic oscillator and (2) the (multi-objective) design of a circuit with switch-like behavior upon induction, with a good compromise between performance and protein production cost.

Optimal design of multiple-objective Lot Quality Assurance Sampling (LQAS) plans

Lot Quality Assurance Sampling (LQAS) plans are widely used for health monitoring purposes. We propose a systematic approach to design multiple-objective LQAS plans that meet user-specified type 1 and 2 error rates and targets for selected diagnostic accuracy metrics. These metrics may include sensitivity, specificity, positive predictive value, and negative predictive value in high or low anticipated prevalence rate populations. We use Mixed Integer Nonlinear Programming (MINLP) tools to implement our design methodology. Our approach is flexible in that it can directly generate classic LQAS plans that control error rates only and find optimal LQAS plans that meet multiple objectives in terms of diagnostic metrics. We give examples, compare results with the classic LQAS and provide an application using a malaria outcome indicator survey in Mozambique.