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ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization

F. Pappalardo, M. D. Halling-Brown, N. Rapin, P. Zhang, D. Alemani, A. Emerson, P. Paci, P. Duroux, M. Pennisi, A. Palladini, O. Miotto, D. Churchill (+11 others)
2008 Briefings in Bioinformatics  
Originally trained as a computer scientist, he holds a masters and PhD in Bioinformatics and is currently involved with developing techniques for improvement of drug discovery for cancer.  ...  His major research area is on modeling immune system responses involved in several pathologies, including viral infections, tumors, multiple sclerosis and atherosclerosis. Mark D.  ...  Figure 3 : 3 An example of integration of system-level models for discovery, formulation, or optimization of vaccines.  ... 
doi:10.1093/bib/bbp014 pmid:19383844 fatcat:b6jsotye35g2tcpxwqftgsj7vm

The ImmunoGrid Simulator: How to Use It [chapter]

Francesco Pappalardo, Mark Halling-Brown, Marzio Pennisi, Ferdinando Chiacchio, Clare E. Sansom, Adrian J. Shepherd, David S. Moss, Santo Motta, Vladimir Brusic
2010 Lecture Notes in Computer Science  
In this paper we present the ImmunoGrid project, whose goal is to develop an immune system simulator which integrates molecular and system level models with Grid computing resources for large-scale tasks  ...  The ImmunoGrid project has proved that simulators can be used in conjunction with grid technologies for drug and vaccine discovery, demonstrating that it is possible to drastically reduce the developing  ...  The ImmunoGrid project goal is to address many specific vaccine questions thanks to the integration of molecular and system level models with Grid computing resources for large-scale tasks and databases  ... 
doi:10.1007/978-3-642-14571-1_1 fatcat:pvxsqk3jqzftphfr2pwul3o74m

Computational Simulations of the Immune System for Personalized Medicine: State of the Art and Challenges

Francesco Pappalardo, Ping Zhang, Mark Halling-Brown, Kaye Basford, Antonio Scalia, Adrian Shepherd, David Moss, Santo Motta, Vladimir Brusic
2008 Current Pharmacogenomics and Personalized Medicine  
The ImmunoGrid project integrates molecular and system level models of the immune system and processes for in silico studies of the immune function.  ...  This paper reviews the current developments in the field of computational simulation of the immune system. We use the ImmunoGrid project as a showcase for integration of immune system models.  ...  ImmunoGrid --an integrated immune system simulator The main objective of the ImmunoGrid project is the development of a human immune system simulator using common computational platform to help development  ... 
doi:10.2174/187569208786733839 fatcat:jrtcprovgvheno2mhlxgpwvdmy

ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale

M. Halling-Brown, F. Pappalardo, N. Rapin, P. Zhang, D. Alemani, A. Emerson, F. Castiglione, P. Duroux, M. Pennisi, O. Miotto, D. Churchill, E. Rossi (+13 others)
2010 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
The authors of this paper belong to the ImmunoGrid Consortium. The ImmunoGrid project has been funded by the EC contract FP6-2004-IST-4, No. 028069.  ...  The ultimate goal of ImmunoGrid is to develop a natural-scale model of the immune system.  ...  Keywords: systems biology; agent-based simulation; immunoinformatics; Grid computing; vaccine discovery Introduction The ImmunoGrid Consortium was funded by the European Commission in 2006 through the  ... 
doi:10.1098/rsta.2010.0067 pmid:20439274 fatcat:yzupqgvcxzdm7ndjj2lo37cq2q

GRIDUISS – A Grid Based Universal Immune System Simulator Framework [chapter]

Francesco Pappalardo, Marzio Pennisi, Ferdinando Chiacchio, Alessandro Cincotti, Santo Motta
2010 Lecture Notes in Computer Science  
GRIDUISS is a simulation framework to model the immune system using grid technologies. It integrates simulation engines, optimization techniques and other prediction models.  ...  GRIDUISS is then capable to reproduce general immune system behavior connected to several immune system response (to viruses, bacteria, tumors and auto-immune disease) and drug-induced immune system responses  ...  By adopting bit strings, many binding events can be simulated quickly, making it feasible to study large-scale properties of the immune system.  ... 
doi:10.1007/978-3-642-14922-1_36 fatcat:ytml2o4jsnb3rfdlhbblbhzswu

Emerging Vaccine Informatics

Yongqun He, Rino Rappuoli, Anne S. De Groot, Robert T. Chen
2010 Journal of Biomedicine and Biotechnology  
Computational methods have also been used for development of immunization registries or immunization information systems, assessment of vaccine safety and efficacy, and immunization modeling.  ...  Vaccine informatics is an emerging research area that focuses on development and applications of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical, and postlicensure  ...  The authors wish to acknowledge the assistance of John Glasser and Gary Urquhart as reviewers for the sections on mathematical modeling and immunization information systems, respectively.  ... 
doi:10.1155/2010/218590 pmid:21772787 pmcid:PMC3134832 fatcat:jch6rfh4tbetbhga73oxp4cf7m

Understanding infectious agents from an in silico perspective

Joo Chuan Tong, Lisa F.P. Ng
2011 Drug Discovery Today  
and discuss their impact on the discovery of new therapeutics and controlling their spread.  ...  Knowledge of infectious diseases now emerging from genomic, proteomic, epidemiological and clinical data can provide insights into the mechanisms of immune function, disease pathogenesis and epidemiology  ...  Attempts have also been made to simulate the human immune system at the system level.  ... 
doi:10.1016/j.drudis.2010.10.007 pmid:20974283 pmcid:PMC7185741 fatcat:vf7f3ruebrc43ca6pyy2dz3co4

Vaccine protocols optimization: In silico experiences

Francesco Pappalardo, Marzio Pennisi, Filippo Castiglione, Santo Motta
2010 Biotechnology Advances  
Vaccines represent a special class of drugs, capable of stimulating immune system responses against pathogens and tumors.  ...  As the efficacy of a vaccine was demonstrated by biological/chemical investigations and pre-clinical studies, then a major problem is represented by the search for an optimal vaccination dosage.  ...  Acknowledgement This work was partially supported under the EC contract FP6-2004-IST-4, No.028069 (ImmunoGrid, and under EC contract FP6-2005-NEST-PATH, No.043241 (Complex-Dis  ... 
doi:10.1016/j.biotechadv.2009.10.001 pmid:19833190 fatcat:6of44cckene4zblqpabhen2j3i

Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment

Kerri-Ann Norton, Chang Gong, Samira Jamalian, Aleksander Popel
2019 Processes  
In this review, we summarize the state of the art in the applications of agent-based models (ABM) and hybrid modeling to the tumor immune microenvironment and cancer immune response, including immunotherapy  ...  Multiscale systems biology and systems pharmacology are powerful methodologies that are playing increasingly important roles in understanding the fundamental mechanisms of biological phenomena and in clinical  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pr7010037 pmid:30701168 pmcid:PMC6349239 fatcat:gnzbrq55crh43ethwn7olrlkmu


2006 Mathematical Models and Methods in Applied Sciences  
The aim of this paper is to discuss biological and computational models of tumor-immune system interactions.  ...  Finally we discuss a first approach to vaccine that prevent tumor onset from a biological point of view and we describe how to reproduce this phenomenon from a computational model.  ...  Acknowledgments This work was supported in part by IMMUNOGRID project, under EC contract  ... 
doi:10.1142/s0218202506001479 fatcat:mc4vxdkyjfhkfh3iegildprtau

The Strengths, Weaknesses, Opportunities and Threats (SWOT) Analysis of HIV Type-1

Babalola Michael Oluyemi
2012 IOSR Journal of Pharmacy (IOSRPHR)  
in the immune cells, antigenic mimicry and adoption of host derived glycan shield for immune evasion, HIV-1 strains harbor enhanced biological fitness upon recombination, HIV has exceptionally high rate  ...  The weaknesses of HIV are the internal attributes and requirements for survival of the virus that invariably present as opportunities and targets for elimination.  ...  The immunoGrid applications will provide tools for the clinicians and vaccine/ immunotherapy developers for identification of optimal immunization protocols.  ... 
doi:10.9790/3013-2440416 fatcat:oajepxznyvcsjam6g4japvgo2u