The Logistics of Small Things - A Crossdisciplinary Feasibility Account

Lead Research Organisation: University of Nottingham
Department Name: School of Computer Science

Abstract

Nottingham's leading edge research at the interface of Computer Science and Operational Research (OR) is concerned with developing decision support systems for the optimal handling of large numbers (~ millions) of macroscopic objects, e.g., truck delivery, personnel rostering, space allocation, runway scheduling, etc. Nano and Bio sciences, on the other hand, deal with billions (or more) of micro/nano-scale objects. Very little research has been done on trying to bridge the gap between OR and NanoBio technologies for which scale reductions bring an explotion in objects' quantities. The Logistics of Small Things will be the conceptual umbrella under which the following research themes (and others) will be investigated:* Accelerating Nanoscience: Scanning Probe Microscopy is used to image and manipulate atom-sized objects. This process, a key-enabling technology for the nanosciences, is extremely laborious and time consuming. Can OR & decision support methodologies be brought to bear at the atom level? Can state-of-the-art planning and scheduling technologies be altered and developed to optimally build, atom-by-atom, complex matter? * Smart Drugs Automated Programming: Future smart drugs will be, at their core, distributed (nano-bio) information processing devices. Splitting up complex decision-making tasks (e.g. a given nano-capsule attaches to a specific cell, delivers its drug payload, monitors and reports progress) into myriads of simpler molecular processes is a critical bottleneck in patient-specific nanomedicine. Can decision support systems derived from, e.g., Genetic Programming, be used to automatically and optimally program Smart Drugs? * Optimising the life-cycle of Synthetic Biology Projects: Synthetic Biology aims at operating within an Engineering-like ethos. However, current practice lacks a rigorous and formal decision making process. That is, questions such as what is the most cost-effective path from design to implementation for a synthetic biology project? have no framework from where they could be systematically studied and answered. Can one define a Synthetic Biology project's life-cycle to minimise its costs?The Logistics of Small Things Cross-Disciplinary Feasibility account will seek to probe the interface between OR and the NanoBio Sciences. If the latter are to deliver practical applications soon, several logistics bottlenecks will need to be removed. This project will seek to identify where those bottlenecks reside and prototype their solutions

Planned Impact

According to the most recent report available from the World Health Organisation (WHO), infectious diseases are still a major cause of death, disability and social and economic upheaval for millions around the world, where they account for more than 11.9 million deaths a year (one in two deaths in developing countries) and are the main causes of mortality and morbidity worldwide (World Health Report, 2004 WHO). The quick raise on resistance to antibiotics has put pressure on the identification of new antimicrobials with novel mode of action. Moreover, recent public-health crisis such as bird flu and swine flu have brought to the fore, and in full force, the need for an optimal pathway from research to market for new vaccines as well as optimal strategies for vaccine distribution and stockpiling. By focusing on the operational bottlenecks behind nano-bio technology, throughout the life-span of this grant we will be alert to opportunities arising from new optimised products and procedures, new patents as well as the opportunities for more informed national health policies with a concomitant increase in the effectiveness of public services and policy. The beneficiaries of our research would thus be the public at large. Our research could also be of tremendous help to the pharma industry and any comercial entreprise where scanning probe microscopy plays a key role because even a modest optimisation in overall experimental costs through better logistics could potentially save millions of pounds in production costs. As part of our initiative to impact on the public understanding of science, a strong on-line presence for The Logistics of Small Things will be established where not only academic material will be made publicly available but also footage of meetings and projects' progress. We believe this will impact on the public's perception of the way real science is done and could help bridge the trust-gap between the tax payer and scientists.

Publications

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Description EPSRC
Amount £791,389 (GBP)
Funding ID EP/I031642/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start  
 
Title The Infobiotics Workbench 
Description The Infobiotics Workbench is a executable biology framework implementing multi-compartmental stochastic and deterministic simulation, formal model analysis and structural/parameter model optimisation for computational systems and synthetic biology. The Infobiotics Workbench is comprised of the following components: a modelling language based on P systems which allows modular and parsimonious multi-cellular model development where the outermost compartments can be positioned in 2-dimensional space to facilitate modelling at either extra-, inter- or intracellular levels of detail deterministic and stochastic simulator using algorithms optimised for large multi-compartmental systems (the simulator also accept a subset of SBML, allowing for visual model specification using tools such as CellDesigner) formal model analysis for the study of temporal and spatial model properties supported the model checkers PRISM and MC2 model structure and parameter optimisation using a variety of evolutionary and population-based algorithms to automatically generate models whose dynamics match specified target timeseries a user-friendly front-end for performing in-silico experiments, plotting and visualisation of simulations with many runs and compartments 
Type Of Technology Software 
Year Produced 2012 
Open Source License? Yes  
Impact -- 
URL http://ico2s.org/software/infobiotics.html