Publications (5) View all
-
Article: ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale.
[show abstract] [hide abstract]
ABSTRACT: The ultimate aim of the EU-funded ImmunoGrid project is to develop a natural-scale model of the human immune system-that is, one that reflects both the diversity and the relative proportions of the molecules and cells that comprise it-together with the grid infrastructure necessary to apply this model to specific applications in the field of immunology. These objectives present the ImmunoGrid Consortium with formidable challenges in terms of complexity of the immune system, our partial understanding about how the immune system works, the lack of reliable data and the scale of computational resources required. In this paper, we explain the key challenges and the approaches adopted to overcome them. We also consider wider implications for the present ambitious plans to develop natural-scale, integrated models of the human body that can make contributions to personalized health care, such as the European Virtual Physiological Human initiative. Finally, we ask a key question: How long will it take us to resolve these challenges and when can we expect to have fully functional models that will deliver health-care benefits in the form of personalized care solutions and improved disease prevention?Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 06/2010; 368(1920):2799-815. · 2.77 Impact Factor -
Article: ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization.
[show abstract] [hide abstract]
ABSTRACT: Vaccine research is a combinatorial science requiring computational analysis of vaccine components, formulations and optimization. We have developed a framework that combines computational tools for the study of immune function and vaccine development. This framework, named ImmunoGrid combines conceptual models of the immune system, models of antigen processing and presentation, system-level models of the immune system, Grid computing, and database technology to facilitate discovery, formulation and optimization of vaccines. ImmunoGrid modules share common conceptual models and ontologies. The ImmunoGrid portal offers access to educational simulators where previously defined cases can be displayed, and to research simulators that allow the development of new, or tuning of existing, computational models. The portal is accessible at <igrid-ext.cryst.bbk.ac.uk/immunogrid>.Briefings in Bioinformatics 06/2009; 10(3):330-40. · 5.20 Impact Factor -
Article: High-pressure dissociation of crystalline para-diiodobenzene: optical experiments and Car-Parrinello calculations.
[show abstract] [hide abstract]
ABSTRACT: We have investigated the high-pressure properties of the molecular crystal para-diiodobenzene, by combining optical absorption, reflectance, and Raman experiments with Car-Parrinello simulations. The optical absorption edge exhibits a large red shift from 4 eV at ambient conditions to about 2 eV near 30 GPa. Reflectance measurements up to 80 GPa indicate a redistribution of oscillator strength toward the near-infrared. The calculations, which describe correctly the two known molecular crystal phases at ambient pressure, predict a nonmolecular metallic phase, stable at high pressure. This high-density phase is characterized by an extended three-dimensional network, in which chemically bound iodine atoms form layers connected by hydrocarbon bridges. Experimentally, Raman spectra of samples recovered after compression show vibrational modes of elemental solid iodine. This result points to a pressure-induced molecular dissociation process which leads to the formation of domains of iodine and disordered carbon.Journal of the American Chemical Society 04/2005; 127(9):3038-43. · 9.91 Impact Factor -
Article: ImmunoGrid - the virtual human immune system project.
[show abstract] [hide abstract]
ABSTRACT: ImmunoGrid is a 3 year project funded by the European Union which began in February 2006 and establishes an infrastructure for the simulation of the immune system that integrates processes at molecular, cellular and organ levels. It is designed for applications that support clinical outcomes such as the design of vaccines, immunotherapies and optimization of immunization protocols. The first phase of the project concentrated on improving and extending current models of the immune system. We are now entering the second phase which will design and implement a human immune system simulator. Since the new models are orders of magnitude more complex than the previous ones, grid technologies will be essential in providing the necessary computer infrastructure. The final phase of the project will validate the simulator with pre-clinical trials using mouse models.Studies in health technology and informatics 02/2007; 126:87-92. -
Conference Proceeding: Common Data Format for Program Sharing and Integration.
Computational Science - ICCS 2003, International Conference, Melbourne, Australia and St. Petersburg, Russia, June 2-4, 2003. Proceedings, Part II; 01/2003
