Research

Main activities

Research activities are classified according to the following scientific fields

RESEARCH COMPUTER SCIENCE

The main activities of this department include the development of theoretical and technological solutions in the computer science domain for addressing the computational issues raised by the other research departments and our partners. The output will be mainly directed to the Applications Development department that will embed the proposed solutions into software modules. The core technologies adopted are related to programming language design, implementation and usage.

Molecular and cell biology

The main activities of this department include the study of the molecular machinery at the cell level and are centered around the basic mechanisms of the cell cycle and morphogenesis. Primary data will come from our partners, especially in the HFSP and NOBEL projects. The efforts of this team will also be devoted to contributing to the development of the models and to the study of the scientific problems raised by our partners as managed in the Technology Transfer department. Finally, this team will contribute to the development of novel conceptual and computational tools by providing clear and detailed requirements (through regular periodic meetings and reports) that will be implemented for enhancing life sciences research.

ECOLOGy

The main activities of this department include the study of the robustness and fragility of ecosystems to infer properties useful to biodiversity conservation and ecosystems management. We will select applications that are suitable for developing new methods and techniques that are scientifically interesting, data-rich and economically relevant. The primary data will come from our collaborators, which include existing, widely acknowledged online databases (e.g. NCEAS, Santa Barbara, CA, USA: www.nceas.org) and the literature that is very rich in undigested data. The efforts of this team will also be devoted to contributing to the development of models and to the study of the scientific problems raised by our partners as managed in the Technology Transfer department. Finally, this team will contribute to the development of novel conceptual and computational tools by providing clear and detailed requirements (through regular periodic meetings and reports) that will be implemented for enhancing life sciences research.

Molecular nutrition

The main activities of this department include the topological analysis of metabolic networks, the stochastic simulation of nutrient effects on gene expression, the identification of disease-related perturbations in network activities, the study of the food web architecture in natural and agro-ecosystems, and the investigation of the consequences of GMOs both on metabolic reactions and on biodiversity conservation. We will rely on and integrate genomics, proteomics, transcriptomics and metabolomics (starting from NuGo and integrating it with the main biological database). Fresh data will also be provided by our partners. The efforts of this team will also be devoted to contributing to the development of the models and to the study of the scientific problems raised by our partners as managed in the Technology Transfer department. Finally, this department will contribute to the development of novel conceptual and computational tools by providing clear and detailed requirements (through regular periodic meetings and reports) that will be implemented for enhancing life sciences research.

Inference and data manipulation

The main activities of this department include techniques for inferring parameters from wet lab data to feed the models (e.g., kinetic rates) and for inferring the overall structure of the interaction network. We will adopt data mining techniques to extract information from literature and databases and to import the relevant knowledge within the COSBI framework. We will also develop sensitivity analysis of the models produced to plan new experiments. The efforts of this team will additionally be devoted to contributing to the development of the models and to the study of the scientific problems raised by our partners as managed in the Technology Transfer department. Finally, this team will contribute to the development of novel conceptual and computational tools by providing clear and detailed requirements (through regular periodic meetings and reports) that will be implemented for enhancing life sciences research.