HIGHLIGHTS

This article is 'Highly accessed'  (total accesses to this article since publication: 1197) relative to age  in  BioMed Central: Increasing risk behaviour can outweigh the benefits of antiretroviral drug treatment on the HIV incidence among men-having-sex-with-men in Amsterdam Shan Mei, Rick Quax, David VAN de Vijver, Yifan Zhu and P.m.a. Sloot BMC Infectious Diseases, 11:118   (11 May 2011)

As of August 27, the most downloaded/accessed paper in BMC Systems Biology is: D. van Dijk et al.: Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks, BMC Systems Biology, vol. 4, nr 1 pp. 96+17. 2010.

This paper received the ICCS best paper award 2010:
N. Zarrabi et al.: Modeling HIV-1 intracellular replication, Procedia Computer Science vol. 1, nr 1 pp. 555-564. Elsevier B.V., Amsterdam, May 2010.

The Project Consortium

The Project Consortium is an international, interdisciplinary team of researchers who are experts in the areas of, network science, virology and epidemiology, advanced ICT technologies, and computational science. The project employs a slim management structure (see WP1 description), implemented by the project coordinator, a management board, the WP leaders and a quality manager. The consortium of six partners reflects complementary competences and experiences critical to the proposed programme of research as described below:

  • Partner 1 (UvA, coordinator, WP1 lleader) is a European leader in computational science and well experienced in EC project management.
  • Partner 2 (ColBud, WP6 leader) is member of a Center for Excellence in Complex Systems and an acknowledged research site in network modeling as well as dynamical, qualitative and hybrid systems modeling and integration, with an experience in exploitation;
  • Partner 3 (USCS) is highly cited for works in HIV drug resistance epidemiology, interpretation and quantification;
  • Partner 4 (ISI) is an internationally leading member of network science with pioneering health applications;
  • Partner 5 (EMC, WP2 leader) is a high impact virology and epidemiology expert in HIV;
  • Partner 6 (ENS-Lyon, WP3 and WP5 leader) is a leading team on computer science, discrete mathematics and both theoretical and applied modeling of complex systems.
  • Partner 7 (WUT, WP4 leader) is a leading expert on graph theory and networks, as well as complex systems in general, with a particular emphasis on stochastic and highly nonlinear systems.
  • Partner 8 (PetaByte, WP6 leader)  is expert on complex systems, network science, large scale disaggregated modeling, integrated data management in experimental research, scientometrics and social media. In 2011 PetaByte succeeded ColBud (Partner 2) as leader of WP6.

All partners are engaged in education; the university partners (UvA, UCSC, EMC, ENS) are responsible for courses on using and developing new technologies addressed to students of medicine, science and engineering, thus creating an exceptional opportunity to apply the methodologies and systems developed in the Project. This is of great importance as the number of students in science and engineering in Europe is not increasing, despite a dramatic shortage of 700,000 scientists and engineers in Europe.
Several members of this Consortium have already successfully collaborated in the framework of EU Projects (CrossGrid, ViroLab,) as well as in events such as the European Grid Conference in 2005, e-Science'2006, Dagstuhl seminars, the International Conference on Computational Science (ICCS: www.iccs-meeting.org) and others. The consortium members have demonstrated that they are able to build communities around important subjects in which they are engaged.
 

Individual Participants

Partner 1: Universiteit van Amsterdam, UvA, the Netherlands

Description of the Institute
The Section Computational Science at the Universiteit van Amsterdam aims to be a worldwide key player in the school of thought on computational science in research and education. The section seeks to discover, through modeling and simulating, the way distributed information is being processed in complex information systems. The group focuses on cellular automata models. It addresses issues of how physical and biological problems can be formulated in this framework and how they can be mapped onto distributed computer architectures and grid systems. The applicability of this approach is validated through the development of high-performance, distributed problem solving environments for asynchronous natural processes stemming from Biomedicine.
The group is proactive with respect to e-Science virtual laboratories. Its work has strong theoretical foundations together with tight couplings to bio-medical applications. The UvA (P.M.A. Sloot) has an extensive experience in (the management of) EU Framework projects, including MARIE, CAMAS, DYNAMITE, HPCNET, CrossGrid, ACGT, Morphex, COAST, ViroLab, among others.

Qualifications and contribution to the project
The Section for Computational Science at UvA will provide a wealth of experience computational science and specifically in the Individual Based Modeling of mesoscopic biomedical systems. Their work on developing complex systems in general and complex networks in particular together with long experience in the application of Cellular Automata and Complex Networks methods will be crucial to this project. Also, in that respect, the simulation and visualization laboratory maintained at the group will be at the disposal of the project, while the presence of experts in bioinformatics and biostatistics will be invaluable to DYNANETS.

List of the principal scientific or technical personnel involved

 Name  Affiliation  Expertise
Prof. Dr. Peter Sloot Universiteit van Amsterdam Computational Science: Principal Investigator
Dr. Jaap Kaandorp Universiteit van Amsterdam Bioinformatics
Dr. R. Belleman Universiteit van Amsterdam Interactive high dimensional Visualization and Virtual Reality
Dr. Alfons Hoekstra Universiteit van Amsterdam Particle Based Modelling and Simulation
Dr. A. Boukhanovsky Universiteit van Amsterdam Biostatistics
Breanndán Ó Nualláin Universiteit van Amsterdam Information Theory and Knowledge Management
 

Postdoc or PhD student,

to be appointed

Universiteit van Amsterdam Information theory of Complex networks
PhD student to be appointed Universiteit van Amsterdam Individual Based models for HIV

 

Partner 2: Collegium Budapest (Institute for Advanced Study), Hungary

Description of the Institute
Collegium Budapest is the Institute for Advanced Study in Hungary and a Centre of Excellence in Complex Systems. It has been operating since 1992. The purpose of Collegium Budapest is to promote culture and the sciences by giving internationally recognized academics and young researchers an opportunity to pursue research of their choice in an international, intellectually stimulating environment. Following the model of the pioneering Princeton Institute for Advanced Study, the Wissenschaftskolleg in Berlin, the Netherlands Institute for Advanced Study in Wassenaar (NIAS) and other similar institutions, Collegium Budapest is the first IAS-type institute in the post-communist region.
As of academic year 2003/04, Collegium Budapest has instituted a new and productive selection mechanism. Half of its guests, called "Core Fellows", are invited to pursue their own research. Besides the above-mentioned core fellowships, COLBUD also hosts research projects. The interdisciplinary group of scholars who take part in these projects, called "Resident Scholars", usually follow a well-defined research agenda. Related to the framework of the proposed project, Collegium Budapest endeavours to host the team led by Professor George Kampis as Resident Scholar. The focus group's other Resident Scholars are Dr. Laszlo Gulyas and Dr. Ferenc Jordán

Qualifications and contribution to the project
The ColBud group's fundamental expertise is with networks, simulation models and methodologies. Accordingly the main thrust of the group is on WP6. ColBud also contributes to the development of theoretical tools in WP3 and WP4 and model validation tools (esp. intelligent scheduling and monitoring) as generalizations of operations central to interactive modelling methodology.
Professor Kampis, Dr. Gulyas and Dr. Jordan have been participating in a number of successful Framework projects as partners, among them the FP6 STREPs QosCosGrid, EMIL, and the FP6 IP ECAGENTS.

List of the principal scientific or technical personnel involved

 

 Name  Affiliation  Expertise
Prof. Dr. George Kampis Collegium Budapest Complex systems, modeling methodology, computational science
Dr. László Gulyás Collegium Budapest Network science, agent-based modeling and simulation, complex software systems
Dr. Ferenc Jordán Collegium Budapest Network sience, Theoretical ecology
Dr. Sándor Soós Institute for Research Organisation of the Hungarian Academy of Sciences Network science, data and text mining, trend analysis
Postdoc or PhD student to be appointed Collegium Budapest Networks and complex systems
PhD student to be appointed Collegium Budapest Individual based modeling
Person on temporary work contract Collegium Budapest Applied computer science

 

Partner 3: Università Cattolica del Sacro Cuore, UCSC, Italy 

Description of the Institute
The Institute of Clinical Infectious Diseases of the Università Cattolica del Sacro Cuore, is the fourth largest Infectious Diseases facility in Italy. It consists of three inpatient wards (40 beds), a day hospital, an ambulatory care service, a home care service for AIDS patients and a research laboratory. The outpatient unit cares for 1,700 HIV-infected patients (1,500 on antiretroviral therapy during 2007) with 6 staff physicians (ID specialists, all experts in antiretroviral treatment) and 5 nurses. The research lab consists of several staff (biologists, biotechnologists, physicians and a technician) and facilities for storage of patients samples (-80°C and liquid nitrogen) and molecular biology diagnostics, including genotypic HIV drug resistance testing. The research group consists of 5 Infectious Diseases Physicians (one with academical position) and 2 Computer Science Engineers.

Qualifications and contribution to the project
The group has several collaborations at the national and international level especially focusing on the knowledge-base for the interpretation of HIV drug resistance correlating genotypic results with therapeutic response data, on the role of viral replication capacity in influencing virological and immunological response and its correlation with drug resistance, the correlation between drug resistance and medication adherence as well as HIV drugs pharmacokinetics. The group's coordinator is member of several scientific research groups on HIV drug resistance in Italy (ICONA cohort, ARCA cohort, Mater cohort) and Europe (Eurosida virology group). The team's experience in the HIV field, including opportunistic infections and tumours dates >10 years. Since 1999 it is actively engaged in the HIV drug resistance research field. The team leader is member of the Organizing Committee of the Anuual European HIV Drug Resistance Workshop. Prof. A De Luca and Dr S Di Giambenedetto are partners in ViroLab (FP6).


List of the principal scientific or technical personnel involved

 Name  Affiliation  Expertise
Andrea De Luca Universita' Cattolica del Sacro Cuore Assistant Professor of Infectious Diseases, Infectious Diseases Physician, Clinical Infectious Diseases.
Simona Di Giambenedetto Universita' Cattolica del Sacro Cuore Expert in Antiretroviral Therapy efficacy and tolerability.
Bracciale Laura Universita' Cattolica del Sacro Cuore Data management. Epidemiology of HIV and of drug resistance interpretation.
Colafigli Manuela Universita' Cattolica del Sacro Cuore Data management and statistical analysis.
Fanti Iuri Universita' Cattolica del Sacro Cuore Computer Science Engineer. Expert in Data Management and Datawarehousing
Prosperi Mattia Virology Department of Istituto Nazionale Malattie Infettive L. Spallanzani Computer Science Engineer with expertise in biostatistics and mathematical modelling.

Partner 4: ISI - Institute for Scientific Interchange Foundation, Italy

Description of the Institute
The ISI Foundation (www.isi.it) is a private research institution located in Turin, Italy. It is founded and supported by the Regional Government, the Province of Turin, the City of Turin, and by the two major Bank Institutions in Piedmont – San Paolo and CRT Foundation. Its mission focuses on promoting scientific interchange and cooperation at the highest degree of quality, both in terms of creativity and originality of research. It aims to represent a pole of high level interdisciplinary training in the fields of Mathematics, Physics, Computer Science, and Life Sciences.
The ISI research unit participating to this project – the Complex Networks and Systems Group – gather an extensive range of scientific expertise both in the area of complex networks theory and models, and in the area of computational modelling of infectious diseases.  The research staff in the group has applied these skills in the study of transportation and mobility infrastructures, the collection and integration of demographic databases, the characterization and modelling of information networks, the study of the emergence and impact of complexity in social/behavioral networks, the development of data visualization techniques, the large scale simulation of infectious diseases. The international nature of the Institute allows the team to maintain ongoing collaborations with the National Institute of Health (INSERM) and the University of Paris-Sud in France, with the Queen Mary University and the Centre of Ecology and Hydrology in the UK, with the Indiana University and Boston University in the US, and with the Universitat Politecnica de Catalunya in Spain.

Role in the proposal
The ISI team brings skills and competence in the area of data and models integration as well as in Informatics and computational tools. The team has experience in theoretical and computational modelling of epidemics. The group is also active in the integration of transportation and demographic data in large scale epidemic stochastic models and is an expert in GIS interfaces and visualization algorithms. In this project the ISI team will have an active role in the WP2, WP3, WP4 and WP5. In addition, ISI foundation will coordinate the project and lead the management effort. The ISI team includes experts in complex networks theory and approaches, and in the modelling of infectious diseases. Alessandro Vespignani is also professor at the School of Informatics at Indiana University, half time resident scientists at ISI and will ensure the lead and supervision of the ISI team. V. Colizza was recently awarded a ERC grant on computational epidemiology.

List of the principal scientific or technical personnel involved

 Name  Affiliation  Expertise
Prof. Alessandro Vespignani ISI & Indiana University, USA

Theoretical and computational modelling of epidemics; characterization and modelling of information networks; study of transportation and mobility infrastructures;

Vittoria Colizza ISI Study of transportation and mobility infrastructures; collection and integration of societal databases; Geographic Information Systems
Alain Barrat ISI & CNRS, France Study of the emergence and impact of complexity in social/behavioral networks
Daniela Paolotti ISI Collection and integration of societal databases; epidemic data mining
Jose' J Ramasco ISI Study of transportation and mobility infrastructures
Paolo Bajardi ISI Collection and integration of societal databases

 

Partner 5: Erasmus MC, University Medical Centre Rotterdam, The Netherlands

Description of the Institute
The Erasmus MC, established in the city of Rotterdam, The Netherlands, is a university medical center in which (new) knowledge is both being generated and passed on to (future) professionals. This knowledge covers a broad field, ranging from illness to health, and from individual to community healthcare. The largest university medical center in the Netherlands (over 10,000 employees), Erasmus MC creates special opportunities for research, education and patient care.
The department of Virology of the Erasmus MC employs more than 110 employees of different disciplines and runs an extensive experimental research program on the epidemiology, pathogenesis, prevention and treatment of infections by human and animal viruses, including drug resistance to viruses such as HIV, herpes and influenza. It frequently publishes in high-impact journals such as Nature, Science, PNAS and the New England Journal of Medicine.
Prof Charles Boucher is a leading authority in the area of antiviral resistance. He has been among the first to describe the development of drug resistance and has been involved in the identification of several novel drug resistance mutations. Charles Boucher organizes several international conferences on HIV drug resistance such as the Annual international workshop on HIV drug resistance, as well as the European HIV drug resistance workshop. Prof. Boucher has been the coordinator of several EU-sponsored projects in the field of HIV drug resistance: SPREAD, EuropeHIVResistance and UNITE-More.
Dr. Van de Vijver has a PhD in epidemiology and has been involved in the collection and analysis of data of several landmark studies on the epidemiology of transmission of HIV drug resistance. He is a member of WHO's Working Group on Mutations for Surveillance of HIV Drug Resistance. Drs. Van de Vijver and Boucher are partner in ViroLab.

Role in the proposal
The ErasmusMC will be actively involved in the analysis of data. As such they will lead work-package 2. In particular they will:
•    Liaise with other networks on the epidemiology of HIV drug resistance
•    Provide data and knowledge about the epidemiology of transmission of drug resistance.
•    Statistical, mathematical and phylogenetic analysis of relevant data.
•    Actively involved in the case study on the epidemiology of drug resistant HIV.

List of the principal scientific or technical personnel involved

 Name  Affiliation  Expertise
D.A.M.C. van de Vijver Erasmus MC

Epidemiology, HIV drug resistance

Prof. C.A.B. Boucher Erasmus MC HIV drug resistance, clinical virology
D. Frent Erasmus MC Epidemiology, HIV drug resistance
I. Schreuder Erasmus MC Epidemiology
M. Schutten Erasmus MC Molecular virology
Prof. A. Osterhaus Erasmus MC Virology

 

Partner 6: ENS-Lyon, Ecole Normale Superieure, Lyon, France

Description of the institute
ENS Lyon is one of the most active and incentive research and education centers in France. ENS Lyon (ens-lyon.eu) gathers 10 internationally renowned research laboratories covering nearly all exact sciences. Among them:

  • the Computer science laboratory (LIP, "Laboratoire de l'informatique du parallélisme", UMR 5668) which conduces active research in the field of complex systems through its studies in cellular automata and complexity theory (among its main subject of interest).
  • the Laboratory of Physics ("Laboratoire de Physique", UMR 5672) is active in a large spectrum of domains ranging from theoretical quantum computing, to signal processing and soft matter.

Eric Fleury is the head of the Computer Science department of ENS Lyon and is a professor at ENS Lyon, Computer Science Department since 2007. Eric Fleury is the scientific leader of the INRIA D-NET research team / INRIA Grenoble - Rhône-Alpes research centers . D-NET team is located at ENS Lyon and hosted by IXXI. Eric is also in the scientific board and in the steering comitee of the IXXI: Complex Systems Institute.
Dr. Pablo Jensen is a senior researcher (Directeur de Recherches) at CNRS. He was trained as a condensed-matter physicist at Ecole Normale Supérieure de Lyon and received his PhD in 1990. He has published more than 80 papers in international journals (Nature, Phys Rev Lett, Rev Mod Phys) which have gathered more than 2000 citations. He is now the head of IXXI (Complex systems institute). His current research interests focus on the use of quantitative tools to improve our knowledge of social systems. He is currently working on urban economics (rental housing markets, retail stores localization strategies...) and scientists' dissemination practices (are open scientists 'good' scientists?).

Qualifications and contribution to the project
Moreover, ENS Lyon has been at the origin of the initiative of creating in Lyon the interdisciplinary Complex Systems Institute (IXXI.fr) which federates complex systems research in region Rhône-Alpes. ENS Lyon has allocated to IXXI a 500 m2 building on its campus for hosting complex systems research and animation activities. IXXI, whose current director is Pablo Jensen, now federates 200 researchers from a broad spectrum of scientific fields.

List of the principal scientific or technical personnel involved:

 

 Name  Affiliation  Expertise
E. Fleury ENS / CNRS

Complex system design in software engineering.

P. Jensen ENS / CNRS Applying physics' methods to social systems.
Andrea Apoloni ENS System dynamics modeling.
Mathieu Maleterre ENS Advanced data structures and optimization.
Arnaud Guignard ENS Software architecture and system integration.

 

Partner 7: Warsaw University of Technology (WUT)

Description of the institute
Warsaw University of Technology (WUT) is a research intense, doctoral level academic institution focused on undergraduate and graduate programs in engineering, natural and social sciences. With 17 departments / faculties, over 30.000 students served by over 2000 professors and instructors, Warsaw University of Technology is the largest and the highest ranking engineering university in Poland. It maintains over 160 bilateral agreements of cooperation with many universities and scientific institutions from all over the world. Research teams of WUT have participated in over 130 Projects supported by European Union's Framework Programs.

Centre of Excellence for Complex Systems Research (CSR) and Division of Physics in Economy and Social Sciences belong to Faculty of Physics at WUT. The Centre was certified in 2002 and it continuously extends its interdisciplinary investigations on complex systems. It is directed by Prof. Janusz Hołyst (see below). The conducted studies cover statistical physics and its both traditional and non-traditional applications including: nonlinear dynamics, econophysics, sociophysics and biophysics. During the recent years the Centre has been involved in several EU funded projects (see below) on complex networks theory and interdisciplinary applications of this paradigm.

Contribution to the project

CSR will contribute to the Project by its experience in stochastic and non-linear dynamics,  as well as in modelling and simulations of complex networks. The Centre possesses a wide expertise in collecting data on economic and social networks including public transport data, data on research collaboration (scientometrics) and economical network data. The CSR will be involved in WP2 providing data on research collaboration networks, in WP4 developing models and simulations tools for Stochastic Resonance in hierarchical complex networks and in WP5 integrating its results with other models of the Project

Qualifications 

The main researcher from the WUT is Professor Dr. Janusz A. Hołyst (*1955) . His current research field includes simulations of evolving networks, models of collective opinion formation, econophysics, non-equilibrium statistical physics, Stochastic Resonance, cellular automata, self-organized criticality and phase transitions. He is one of the pioneers in applying physical methods to economical and social systems. He was a scientific advisor of 8 completed Ph.D. thesis on interdisciplinary applications of nonlinear dynamics and complex systems. His list of publications includes around 120 papers (www.if.pw.edu.pl/~jholyst) in peer reviewed journals that have been cited over 800 times. Hołyst has organized or co-organized 15 international interdisciplinary workshop or conferences on complex systems. He acts as an Editor of European Journal of Physics B and as a Guest Editor or referee of  several  other journals. Hołyst maintains a close collaboration with many Institutes in Germany, France, Italy, UK, Switzerland, Japan and USA  where he spent over six years as a Visiting Professor,  Fellow of Humboldt Foundation or Guest Scientist. Hołyst is a coordinator of the EU FP7 ICT Integrated Project Collective Emotions in Cyberspace (CYBEREMOTIONS, 2009 – 2013), was a coordinator of  NEST Project Critical Events in Evolving Networks (CREEN, 2005-2008), a WP leader in the NEST Project Measuring and Modeling of Complex Networks Across Domains (MMCOMNET, 2005-2008), Vice-Chairman of the COST Action Physics of Risk and COST Action Physics of Competition and Conflicts. He is the President of KRAB (National Council for Research Projects Coordinators) and FENS (Physics in Economy and Social Sciences – Division of the Polish Physical Society).


List of the principal scientific or technical personnel involved:

 

Name Affiliation Expertise
Prof. Janusz Hołyst WUT

Professor of statistical physics, stochastic dynamics

Julian Sienkiewicz, Ph.D. WUT Evolving networks, sociophysics, public transport systems
Anna Chmiel, M.Sc. WUT Complex networks, sociophysics and random walks
Janusz Dębski M.Sc. WUT Technician

 

 

Partner 8: PetaByte Research Ltd, Hungary

Description of the Institute
PetyByte Research Ltd is a nonprofit research organization in Hungary, run by computational science professionals. They deal with complex systems, network science, large scale disaggregated modeling, integrated data management in experimental research, scientometrics and social media, to mention a few application areas. PetaByte's members participate in various RTD projects supported by national and international grant-giving organizations ranging from EC FP7 framework programs to Hungary's National Innovation Office (formerly NKTH).

Qualifications and contribution to the project
The PetaByte group's fundamental expertise is with networks, simulation models and methodologies. Accordingly the main thrust of the group is on WP6. PetaByte also contributes to the development of theoretical tools in WP3 and WP4 and model validation tools (esp. intelligent scheduling and monitoring) as generalizations of operations central to interactive modelling methodology.
Professor Kampis, Dr. Gulyas and Dr. Jordan have been participating in a number of successful Framework projects as partners, among them the FP6 STREPs QosCosGrid, EMIL, and the FP6 IP ECAGENTS.

List of the principal scientific or technical personnel involved

 

Name Affiliation Expertise
Prof. Dr. George Kampis PetaByte Complex systems, modeling methodology, computational science
Dr. László Gulyás PetaByte Network science, agent-based modeling and simulation, complex software systems
Dr. Sándor Soós Institute for Research Organisation of the Hungarian Academy of Sciences Network science, data and text mining, trend analysis
Balázs Bálint, M.Sc. PetaByte Applied computer science
Zalan Szakolci B.Sc. PetaByte Network science
Attila Palmai PetaByte Applied computer science

 

Real networks are dynamic

EU Grant Agreement

Number: 233847

BONUS Grant Number:

OMFB-00237/2010

FET Open

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