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Last papers                             

A Shape Calculus for Biological Processes


Model Checking Biological Oscillators


Learning and Detecting Emergent Behavior in Networks of Cardiac Myocytes


Modeling and Simulation of Cardiac Tissue using Hybrid I/O Automata


StonyCam: A Formal Framework for Modeling, Analyzing and Regulating Cardiac Myocytes


CellExcite: An Efficient Simulation Environment for Excitable Cells


Learning and Detecting Emergent Behavior in Networks of Cardiac Myocytes


BioWMS: a web-based Workflow Management System for bioinformatics


Biowep: a workflow enactment portal for bioinformatics applications


An Agent-based Multilayer Architecture for Bioinformatics Grids


Spatial Networks of Hybrid I/O Automata for Modeling Excitable Tissue


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University of Camerino
Department of Mathematics and Computer Science
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Oncology Over Internet
Litbio Project
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BioAgent Project
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".. I don’t know how I appear to the eyes of the world,
but to me I seem to be a kid who was playing on the beach
and sometimes had fun trying to find a smoother pebble,
a shell nicer than usual, while the great ocean of truth
would be extending unexplored in front of me.."

(I. Newton)

StudiesCourses & SchoolsScholarship awardsTeaching experiencesPubblicationsResearch interestsWorking positions


Studies:
Jan 2009PhD in Information Science and Complex Systems

Thesis: A Formal Framework for Modeling, Simulating
and Analyzing Network of Excitable Cells

Adviser: Prof. Flavio Corradini
Coadvisers: Prof. Radu Grosu & Prof. Scott A. Smolka

University of Camerino (MC) - Italy.
Apr 2005Master Degree in Bioinformatics
with full marks (110/110) and honors ("magna cum laude")

Thesis: "SISTEMA MULTI AGENTE PER LA PREDIZIONE, BASATA SU ORTOLOGIA, DELL' INTERAZIONE TRA PROTEINE."
Supervisors: Prof.ssa Emanuela Merelli & Prof. Mauro Angeletti
University of Camerino (MC) - Italy.

Courses:
Microbiology, Chemistry, Organic chemistry, Biochemistry, Biopolymers modeling, Neural nets, Chemistry physics, Genetics, Cellular biology, Molecular biology, Pharmacology, Analitical chemistry, Medical image analysis, Telemedicine, Proteomics, Genomics, Molecular modeling in pharmacology, Molecular genetics, Biological information theory, Structure of biological matter, Evolution and biodiversity.		Press Room
Sep 2002Bachelor's Degree in Computer Science
with full marks (110/110) and honors ("magna cum laude")

Thesis: "AIXO: Un wrapper generalizzato XML"
Supervisors: Prof.ssa Emanuela Merelli & Dr. Leonardo Mariani
University of Camerino (MC) - Italy.

Courses:
Programming languages, Mathematic analysis, Geometry, Algebra, Physics, Algorithms and data structures, Statistics and probability calculus, Operative systems, Algorithms and complexity, Logics, Operating research, Systems for elaboration of informations, Computer architectures, Database, Computer networks, Knowledge management.
Jul 1999Scientific High-School Degree
with marks (94/100)
Liceo Scientifico Serrani di Falconara M.ma (AN)- Italy


Courses & Schools:
Jun 20077th INTERNATIONAL SCHOOL ON FORMAL METHODS FOR THE DESIGN OF COMPUTER, COMMUNICATION AND SOFTWARE SYSTEMS: PERFORMANCE EVALUATION (SFM-07:PE)
Bertinoro Univ. Residential Center - Italy, 28 May - 2 June 2007
Performance Modelling and Markov Chains, Queueing Networks, Stochastic Petri Nets, Stochastic Process Algebras, Multi-paradigm Modelling, Behavioural Equivalences and Model Manipulations, Stochastic Model Checking, Fluid Approximations, Tackling Large State Spaces, Data Representation and Efficient Solution, Software Performance Evaluation, From Annotated Software Designs (UML SPT/MARTE) to Model Formalisms
May 2007Biomed Grid Summer School 2007
Villa Monastero, Via Polvani 2, Varenna, Italy 14-19/05/2007

New services and functionalities made available by middleware releases (gLite), The implementation of applications in the EGEE GRID environments, The development of high level interfaces for GRID and Web Services for data provision and management, Web Services, workflow technology and GRID services for Bioinformatics e Biomedical applications.
Jul 2006First International Summer School on Emerging Trends in Concurrency TiC'06
University of Bologna Residential Center Bertinoro, Italy 24-29/07/2006

Lectures: X10: Computing at Scale, The design, implementation, and use of java.util.concurrent, Acute and HashCaml: Type-Safe and Version-Safe Distributed Programming, Process algebras, bisimulation (and logics), Atomicity analysis for concurrent software, Dissecting Transactional Semantics and Implementations, A Theoretical Basis of Communication-Centred Programming for Web Services, Adaptive Algorithms for new Parallel Supports, Java Memory Model, Highly Concurrent Data Structures.
Jun 2006PhD course on probabilistic model checking
University of Florence, Italy 7-9/06/2006

Lectures: DTMCs, probabilistic bisimulation, weak and simulation, Temporal logic (PCTL) and model checking of DTMCs, CTMCs, probabilistic bisimulation, weak and simulation, Temporal logic (CSL) and model checking of CTMCs, Cost-based extensions of Markov chains.
Jul 2003XV International School for Computer Science Researcher
"Algorithmics for Data Mining and Pattern Discovery"
Lipari (ME), Italia. 13-26/07/2003

Lectures: Economic and Game-Theoretic Aspects of Information Systems, Pattern Discovery in the Post Genomic Era, Search and Data Mining in the Internet Age, Authoritative Sources in a Hyperlinked Environment, A New Science of Discovery and the Algorithmics of Surprise, Activist Data Mining, Data Cleaning, Spectral Methods in Data Mining, Indexing Compressing and Searching Texts, Large Scale Text Indexing: Data Structures Algorithmic Design and Engineering, Post Genomic Data Mining: Discovering Patterns in Genomes Transcriptomes and Haplotypes, Network Expression Inference.


Scholarship awards:
2006PhD scholarship
2003-2004Fellowship in the Oncology Over Internet (O2I) project
2003Merit scholarship
Borsa di Merito "Università di Camerino: Piacere di Conoscere"
2001Merit scholarship
Borsa di Merito "Università di Camerino: Piacere di Conoscere"


Teaching experience:
2008/2009Teaching
Corso di Laurea in Informatica - Classe 26 - Università di Camerino
Laboratorio di Algoritmi e Strutture Dati
2007/2008Teaching
Corso di Laurea in Informatica - Classe 26 - Università di Camerino
Laboratorio di Algoritmi e Strutture Dati
2006/2007Teaching
Corso di Laurea in Informatica - Classe 26 - Università di Camerino
Laboratorio di Algoritmi e Strutture Dati
2005/2006Teaching
Corso di Laurea in Biotecnologie - Classe 1 - Università di Camerino
Fondamenti di Informatica I
mutuato con Informatica della Laurea Specialistica in Biologia - Classe 6/S
2005/2006Teaching assistant
Corso di Laurea in Informatica - Università di Camerino
Algoritmi e strutture dati (Prof.ssa Emanuela Merelli)
4 two-hours exercise lectures


Pubblications:
  1. A Shape Calculus for Biological Processes
    Ezio Bartocci, Maria Rita Di Berardini, Flavio Corradini, Merelli Emanuela, Luca Tesei.
    11th Italian Conference on Theoretical Computer Science. pp. 30-33. 2009.
    Bibtex

  2. Model Checking Biological Oscillators
    Ezio Bartocci, Flavio Corradini, Emanuela Merelli, Luca Tesei.
    In the proceedings of the 2th From Biology To Concurrency International Workshop (FBTC'08), Reykjavik, Island, July, 2008. pp. 41-58. Electronic Notes in Theoretical Computer Science vol. 229 no. 1. 2009.
    Bibtex

  3. Learning and Detecting Emergent Behavior in Networks of Cardiac Myocytes
    Radu Grosu, Scott A. Smolka, Anita Wasilewska, Flavio Corradini, Emilia Entcheva, Ezio Bartocci.
    Communication of ACM. pp. 97-105. vol. 52 no. 3. 2009.
    Bibtex pdf

  4. Modeling and Simulation of Cardiac Tissue using Hybrid I/O Automata
    Ezio Bartocci, Flavio Corradini, Maria Rita Di Berardini, Emilia Entcheva, Scott A. Smolka, Radu Grosu.
    Theoretical Computer Science. pp. In press. 2009.
    Bibtex

  5. StonyCam: A Formal Framework for Modeling, Analyzing and Regulating Cardiac Myocytes
    Ezio Bartocci, Flavio Corradini, Radu Grosu, Emanuela Merelli, Oliviero Riganelli, Scott A. Smolka.
    Concurrency, Graphs and Models. pp. 493-502. 2008.
    Bibtex

  6. CellExcite: An Efficient Simulation Environment for Excitable Cells
    Ezio Bartocci, Flavio Corradini, Emilia Entcheva, Radu Grosu, Scott A. Smolka.
    BMC Bioinformatics. pp. S1-S13. vol. 9 no. Suppl. 2. 2008. Abstract
    Bibtex 1471-2105-9-S2-S3.pdf S3

  7. Learning and Detecting Emergent Behavior in Networks of Cardiac Myocytes
    Radu Grosu, Ezio Bartocci, Flavio Corradini, Emilia Entcheva, Scott A. Smolka, Anita Wasilewska.
    In the proceedings of the 11th International Conference on Hybrid Systems: Computation and Control (HSCC'08), St. Louis, USA, April, 2008. pp. 229-243. Lectures Notes in Computer Science vol. 4981. Springer. 2008. Abstract
    Bibtex

  8. BioWMS: a web-based Workflow Management System for bioinformatics
    Ezio Bartocci, Flavio Corradini, Emanuela Merelli, Lorenzo Scortichini.
    BMC Bioinformatics. pp. S2. vol. 8 no. Suppl 1. 2007. Abstract
    Bibtex S2

  9. Biowep: a workflow enactment portal for bioinformatics applications
    Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Domenico Marra, Giancarlo Mauri, Emanuela Merelli, Luciano Milanesi.
    BMC Bioinformatics. pp. S19. vol. 8 no. Suppl 1. 2007. Abstract
    Bibtex S19

  10. An Agent-based Multilayer Architecture for Bioinformatics Grids
    Ezio Bartocci, Diletta Cacciagrano, Nicola Cannata, Flavio Corradini, Emanuela Merelli, Luciano Milanesi, Paolo Romano.
    IEEE transactions on Nanobioscience. pp. 142-148. vol. 6 no. 2. 2007. Abstract
    Bibtex

  11. Spatial Networks of Hybrid I/O Automata for Modeling Excitable Tissue
    Ezio Bartocci, Flavio Corradini, Maria Rita Di Berardini, Emilia Entcheva, Radu Grosu, Scott A. Smolka.
    In the proceedings of FBTC'07 From Biology to Concurrency and Back International Workshop co-sited with CONCUR conference. pp. 86-102. Electronic Notes in Theoretical Computer Science vol. 194 no. 3. Elsevier. 2007. Abstract
    Bibtex

  12. Enacting Proactive Workflows Engine in e-Science.
    Ezio Bartocci, Flavio Corradini, Emanuela Merelli.
    International Conference on Computational Science (3). pp. 1012-1015. 2006. Abstract
    Bibtex fulltext.pdf

  13. Model driven design and implementation of activity-based applications in Hermes.
    Ezio Bartocci, Flavio Corradini, Emanuela Merelli, Leonardo Vito.
    WOA. 2006.
    Bibtex

  14. Building a Multiagent System from a User Workflow Specification.
    Ezio Bartocci, Flavio Corradini, Emanuela Merelli.
    WOA. 2006.
    Bibtex

  15. A GRID-based multilayer architecture for bioinformatics
    Ezio Bartocci, Diletta Cacciagrano, Nicola Cannata, Flavio Corradini, Emanuela Merelli, Luciano Milanesi, Paolo Romano.
    In the proceedings of NETTAB'06 Network Tools and Applications in Biology. 2006.
    Bibtex

  16. An XML View of the "World".
    Emanuela Merelli, Leonardo Mariani, Ezio Bartocci.
    ICEIS (1). pp. 19-27. 2003.
    Bibtex

  17. Expressionview: visualization of quantitative trait loci and gene-expression data in Ensembl
    Gertrud Fischer, Saleh Ibrahim, Gudrun Brockmann, Jens Pahnke, Ezio Bartocci, Hans-Jürgen Thiesen, Steffen Möller, Pablo Serrano-Fernández.
    Genome Biology. pp. R77. vol. 4 no. 11. 2003.
    Bibtex R77




Research interests:
Formal Methods for in-silico biology, Spatial Properties Analysis, Chaos and Fractals, Image anlysis, Computational models in systems biology, simulation, model checking, workflow management systems, Agent-based technology.


Past projects:
Ott 2005/Dic 2005Collaboration Contract in the Oncology Over Internet (O2I) project
Camerino (MC) - Italy
Giu 2003/Feb 2004Fellowship in the Oncology Over Internet (O2I) project
Camerino (MC) - Italy

Sep 2002/Dic 2002Collaboration with the Proteum-Zentrum of Rostock University
Rostock - Germany