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From Data to Models: New Bioinformatics Methods and Tools for Data-Driven Predictive Dynamic Modelling in Biotechnological Applications

Objective

Currently, biologists are collecting enormous amounts of ‘omics’ data in a vast number of different databases. Predictive, data-driven computational models are needed to understand the complex, multi-scale biological networks underlying these high-throughput datasets. Such models are non-linear and contain many parameters, which are difficult (or impossible) to measure directly. Instead, parameters need to be inferred from data. This approach is called reverse-engineering. It has tremendous potential for several areas, such as biotechnology and systems biology, since it allows us to develop models with unprecedented accuracy and predictive power. This is achieved through an iterative refinement of our models compared to quantitative ‘omics’ data, a process called the systems-biology modelling cycle. Many methods have been developed that deal with specific steps in this cycle (data analysis, model building/discrimination, parameter estimation/identifiability analysis, uncertainty quantification, and optimal experimental design), but we still lack an over-arching, easy-to-use software framework that supports the modelling cycle in its entirety, allowing its widespread application. This project aims at improving accessibility of the data, and developing novel algorithms and tools implemented in such a general framework, which will enable the efficient transfer of cutting-edge modelling and optimisation methods from an academic research setting to private biotechnology partners. We will use representative biological and biotechnological applications as benchmark problems to develop robust and generally applicable methodology. The availability of such tools to the biotechnology sector (and other industries) will greatly enhance our ability to design and optimise complex production processes, especially those of nutraceuticals, biopharmaceuticals, or fine chemicals based on engineered organisms such as bacteria, yeast or plants.

Field of science

  • /medical and health sciences/health sciences/public and environmental health/epidemics prevention/modeling of disease spread

Call for proposal

FP7-KBBE-2011-5
See other projects for this call

Funding Scheme

CP-TP - Collaborative Project targeted to a special group (such as SMEs)

Coordinator

FUNDACIO CENTRE DE REGULACIO GENOMICA
Address
Carrer Doctor Aiguader 88
08003 Barcelona
Spain
Activity type
Research Organisations
EU contribution
€ 477 987
Administrative Contact
Stefan Pönisch (Mr.)

Participants (11)

AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS
Spain
EU contribution
€ 320 145
Address
Calle Serrano 117
28006 Madrid
Activity type
Research Organisations
Administrative Contact
Eusebio Jimenez Arroyo (Mr.)
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Germany
EU contribution
€ 171 931
Address
Meyerhofstrasse 1
69117 Heidelberg
Activity type
Research Organisations
Administrative Contact
Tom Ratcliff (Mr.)
UNIVERSITEIT VAN AMSTERDAM
Netherlands
EU contribution
€ 307 242
Address
Spui 21
1012WX Amsterdam
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Vanessa Wolters (Ms.)
STICHTING CENTRUM VOOR WISKUNDE EN INFORMATICA
Netherlands
EU contribution
€ 267 428
Address
Science Park 123
1098XG Amsterdam
Activity type
Research Organisations
Administrative Contact
Margriet Brouwer (Ms.)
FONDAZIONE TELETHON
Italy
EU contribution
€ 115 200
Address
Via Varese 16/B
00185 Roma
Activity type
Research Organisations
Administrative Contact
Irene Mearelli (Ms.)
THE UNIVERSITY OF MANCHESTER
United Kingdom
EU contribution
€ 257 853
Address
Oxford Road
M13 9PL Manchester
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Liz Fay (Ms.)
THE UNIVERSITY OF SHEFFIELD
United Kingdom
EU contribution
€ 291 240
Address
Firth Court Western Bank
S10 2TN Sheffield
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Joanne Watson (Ms.)
COSMO TECH
France
EU contribution
€ 282 000
Address
Passage Du Vercors 5 Le Vercors
69007 Lyon
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Visnia Boccon-Gibod (Ms.)
INSILICO BIOTECHNOLOGY AG
Germany
EU contribution
€ 259 200
Address
Meitnerstrasse 9
70563 Stuttgart
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Klaus Mauch (Mr.)
FLUXOME SCIENCES A/S

Participation ended

Denmark
EU contribution
€ 137 376
Address
Diplomvej 378
2800 Lyngby
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Sarah Barret (Ms.)
EVOLVA AG
Switzerland
EU contribution
€ 112 398
Address
Duggingerstrasse 23
4153 Reinach
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Jakob Dynnes Hansen (Mr.)