Work Packages — Cosy-Bio

WP1 External controllers

investigate external controllers implementing various frameworks for modelling, state estimation and model predictive control
study their robustness and adaptability on a challenging control problem: balancing a toggle switch in E. coli and S. cerevisiae

WP2 Embedded controllers

Design new tools and methods for analysis and design of controllers in the presence of intracellular noise
Develop new strategies for designing robust embedded controllers that have a small footprint and low metabolic loads
Develop new theory and methods for building biological insulators that enable the modular connection of embedded biological systems in a noisy environment
Develop a theory for nonlinear system realization using biological components
Design and build embedded controllers for the E. coli and yeast toggle switches

WP3 Multicellular Control

The key goal of this work package is to study how to deploy control across cell populations to develop and demonstrate an integrated approach to create a synthetically engineered consortium where subpopulations of genetically engineered cells can respond to external reference inputs and self-regulate each other to exhibit a desired function

WP4 Automated microfluidics platform for quantitative modelling of biological processes

To design new model identification methods and tools for closed-loop modelling
To design new model based optimal experimental methods and tools for closed-loop model identification
To build an integrated platform for biomodel identification (BMID), optimal design of experiments (OED) and rapid prototyping of synthetic biology systems
To test and validate the performance of the rapid prototyping platform in three case study applications

WP5 Experimental applications in E. coli

WP6 Taking control of the cell cycle in yeast

Demonstrate that external and embedded control of gene expression can be used to drive the cell cycle in yeast

WP7 Management

To manage the project according to the approved plan, support the Participants in achieving the objectives, complete the milestones in time and convey the deliverables
To ensure that the required reports are made and delivered in a timely manner according to quality assurance standards and homogeneity
To monitor, track and control deviations due to progress, cost, financial and scheduling change
Manage the processes to properly protect intellectual property, including confidential information and patents

WP8 Communication, dissemination and exploitation of the results

Communication to stakeholders and the general public will be organized through workshops, summer schools, meetings, participation in media activities and via e-communication tools as part of the central interaction website
Dissemination and exploitation of the results