OpenMicroBio

Project Title
A framework for computational simulation of cellular communities during BioProcess Engineering
Project Type
Nacional / Public
Funding Body
Funding Program
Reference
PTDC/BIO/69310/2006
Funding
  • CEB: 83 348,00
  • Total: 143 000,00
Start
01-07-2007
End
30-06-2010
Partnership
Universidade do Minho
External link
Internal link

Principal Investigator

Team Members - CEB

Abstract

This project is devoted to the development of High-End modeling strategies to describe the Saccharomyces colony dynamics based on individual cell models (ICM), using complex systems (holistic) approaches. It aims at obtaining a software platform to simulate bioprocess engineering from the mesoscale to the macroscale level, enabling to design several biotechnological processes with high accuracy and detail. The software framework is to be designed to simulate both colony dynamics under several scenario simulations, such as, production inside bio-reactors and growth in fermented foods, where the colony dynamics is affected also by external factors such as fluid dynamics, chemical and biochemical reactions, nutrient diffusion and electro-magnetic fields; all of which significantly affect production efficiency. It will be a framework tool to optimise and design new reactors (e.g. CSTR´s, micro-reactors), such as during flocculating yeast and the use of synergetic colonies for fermentations with greater product yields.Due to the large computational power needed and complexity of the models involved, the software will use the latest legacy computational technology, both hardware and software; as well as programming and system development technologies, such as the use of GPU workstations and distributed computing between these workstations. The project will use also the latest established technology in experimental apparatus. Experiments will comprise the use of batch/continuous bio-reactors, filming cellular growth and interactions at the microscope, detections of perturberations in the electro-chemica spectrum (electrophysiology) and spectroscopy (nutrient diffusion and chemical/biochemical reactions) . The OpenMicroBio will be a tool that opens the frontiers of mesoscale to macroscale computer assisted process design and prototyping, resulting in significant increases in productivity and development of new biotech products. The OpenMicroBio project will be coordenated by the BioEngineering Group (U. Minho - Braga), where the system and experimental tasks will be mostly developed. The Inst. Systems and Robotics (IST-Lisbon) will be mostly devoted to code developent and system simulations. The multidisciplinary characteristics of this project will enable the developent of an extremelly important software tool for the emergent Portuguese Biotech industry and services.