2024-03-28T19:37:42Z
http://eprints.biblio.unitn.it/cgi/oai2
oai:eprints.biblio.unitn.it:318
2012-02-28T14:16:05Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Applying Tropos Methodology to a real case study: Complexity and Criticality Analysis
Garzetti, Maddalena
Giorgini, Paolo
Mylopoulos, John
Sannicolò, Fabrizio
QA076.7 Programming Languages - Semantics
Currently in Requirements Engineering the attention is being focused more and more on the understanding of a problem by studying the existing organizational setting in which the system will operate. In this paper we present the application of the Tropos early requirements analysis to a real case study, the Ice Co. We introduce a new type of analysis for actor diagrams based on two different parameters, complexity and criticality, and we show the results we obtained during the case study.
2002-10
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/318/1/97.pdf
Garzetti, Maddalena and Giorgini, Paolo and Mylopoulos, John and Sannicolò, Fabrizio (2002) Applying Tropos Methodology to a real case study: Complexity and Criticality Analysis. UNSPECIFIED.
http://eprints.biblio.unitn.it/318/
oai:eprints.biblio.unitn.it:346
2013-01-29T14:54:44Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Proceedings of International Workshop "Global Computing: Programming Environments, Languages, Security and Analysis of Systems"
Priami, Corrado (eds.)
QA076.7 Programming Languages - Semantics
According to the IST/ FET proactive initiative on GLOBAL COMPUTING, the goal is to obtain techniques (models, frameworks, methods, algorithms) for constructing systems that are flexible, dependable, secure, robust and efficient.
The dominant concerns are not those of representing and manipulating data efficiently but rather those of handling the co-ordination and interaction, security, reliability, robustness, failure modes, and control of risk of the entities in the system and the overall design, description and performance of the system itself.
Completely different paradigms of computer science may have to be developed to tackle these issues effectively. The research should concentrate on systems having the following characteristics: • The systems are composed of autonomous computational entities where activity is not centrally controlled, either because global control is impossible or impractical, or because the entities are created or controlled by different owners.
• The computational entities are mobile, due to the movement of the physical platforms or by movement of the entity from one platform to another.
• The configuration varies over time. For instance, the system is open to the introduction of new computational entities and likewise their deletion.
The behaviour of the entities may vary over time.
• The systems operate with incomplete information about the environment.
For instance, information becomes rapidly out of date and mobility requires information about the environment to be discovered.
The ultimate goal of the research action is to provide a solid scientific foundation for the design of such systems, and to lay the groundwork for achieving effective principles for building and analysing such systems.
This workshop covers the aspects related to languages and programming environments as well as analysis of systems and resources involving 9 projects (AGILE , DART, DEGAS , MIKADO, MRG, MYTHS, PEPITO, PROFUNDIS, SECURE) out of the 13 founded under the initiative. After an year from the start of the projects, the goal of the workshop is to fix the state of the art on the topics covered by the two clusters related to programming environments and analysis of systems as well as to devise strategies and new ideas to profitably continue the research effort towards the overall objective of the initiative.
We acknowledge the Dipartimento di Informatica and Tlc of the University of Trento, the Comune di Rovereto, the project DEGAS for partially funding the event and the Events and Meetings Office of the University of Trento for the valuable collaboration.
Università degli Studi di Trento
Priami, Corrado
2003-02
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/346/1/03_006.pdf
Priami, Corrado (eds.) (2003) Proceedings of International Workshop "Global Computing: Programming Environments, Languages, Security and Analysis of Systems". Trento : Università degli Studi di Trento.
http://eprints.biblio.unitn.it/346/
oai:eprints.biblio.unitn.it:351
2012-02-28T14:16:14Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Extraction of pi-calculus specifications from UML sequence and state diagrams
Korenblat, Katerina
Priami, Corrado
QA076.7 Programming Languages - Semantics
We propose an automatic translation of UML specifications made up of sequence and state diagrams into pi-calculus processes. The central point of the proposed translation is the coherence of the two types of diagrams. An implicit result of the paper is also the definition of a formal semantics for UML sequence diagrams.
2003-02
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/351/1/03_007.pdf
Korenblat, Katerina and Priami, Corrado (2003) Extraction of pi-calculus specifications from UML sequence and state diagrams. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/351/
oai:eprints.biblio.unitn.it:409
2012-02-28T14:16:30Z
7374617475733D756E707562
7375626A656374733D51:5141:51413735
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A Semantic-Based Information Management System to Support Innovative Product Design
Ucelli, Giuliana
De Amicis, Raffaele
Conti, Giuseppe
Giunchiglia, Fausto
Noll, Stefan
QA075 Electronic computers. Computer science
QA076.7 Programming Languages - Semantics
International competition and the rapidly global economy, unified by improved communication and transportation, offer to the consumers an enormous choice of goods and services. The result is that companies now require quality, value, time to market and innovation to be successful in order to win the increasing competition. In the engineering sector this is traduced in need of optimization of the design process and in maximization of re-use of data and knowledge already existing in the company. The “SIMI-Pro” (Semantic Information Management system for Innovative Product design) system addresses specific deficiencies in the conceptual phase of product design when knowledge management, if applied, is often sectorial. Its main contribution is in allowing easy, fast and centralized collection of data from multiple sources and in supporting the retrieval and re-use of a wide range of data that will help stylists and engineers shortening the production cycle. SIMI-Pro will be one of the first prototypes to base its information management and its knowledge sharing system on process ontology and it will demonstrate how the use of centralized network systems, coupled with Semantic Web technologies, can improve inter-working activities and interdisciplinary knowledge sharing.
2003-05
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/409/1/020.pdf
Ucelli, Giuliana and De Amicis, Raffaele and Conti, Giuseppe and Giunchiglia, Fausto and Noll, Stefan (2003) A Semantic-Based Information Management System to Support Innovative Product Design. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/409/
oai:eprints.biblio.unitn.it:419
2012-02-28T14:16:35Z
7374617475733D7375626D6974746564
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Semantic coordination: a new approach and an application
Bouquet, Paolo
Serafini, Luciano
Zanobini, Stefano
QA076.7 Programming Languages - Semantics
Semantic coordination, namely the problem of finding an agreement on the meaning of heterogeneous semantic models, is one of the key issues in the development of the Semantic Web. In this paper, we propose a new algorithm for discovering semantic mappings across hierarchical classifications based on a new approach to semantic coordination. This approach shifts the problem of semantic coordination from the problem of computing structural similarities (what most other proposed approaches do) to the problem of deducing relations between sets of logical formulae that represent the meaning of concepts belonging to different models (here, classifications). We show why this is a significant improvement on previous approaches, and present the results of preliminary tests on two types of hierarchical classifications, namely web directories and catalogs.
2003-05
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/419/1/025.pdf
Bouquet, Paolo and Serafini, Luciano and Zanobini, Stefano (2003) Semantic coordination: a new approach and an application. UNSPECIFIED. (Submitted)
http://eprints.biblio.unitn.it/419/
oai:eprints.biblio.unitn.it:435
2012-02-28T14:16:40Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
7375626A656374733D51:5141:51413736
74797065733D746563687265706F7274
A Java implementation of Coordination Rules as ECA Rules
Kumar, K M Senthil
QA076 Computer software
QA076.7 Programming Languages - Semantics
This paper gives an insight in to the design and implementation of the coordination rules as ECA rules. The language specifications of the ECA rules were designed and the corresponding implementation of the same using JAVA as been partially done. The paper also hints about the future work in this area which deals with embedding this code in JXTA, thus enabling to form a P2P layer with JXTA as the back bone.
2003-06
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/435/1/037.pdf
Kumar, K M Senthil (2003) A Java implementation of Coordination Rules as ECA Rules. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/435/
oai:eprints.biblio.unitn.it:437
2012-02-28T14:16:40Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
C-OWL: Contextualizing ontologies
Bouquet, Paolo
Giunchiglia, Fausto
van Harmelen, Frank
Serafini, Luciano
Stuckenschmidt, Heiner
QA076.7 Programming Languages - Semantics
Ontologies are shared models of a domain that encode a view which is common to a set of dierent parties. Contexts are local models that encode a party's subjective view of a domain. In this paper we show how ontologies can be contextualized, thus acquiring certain useful properties that a pure shared approach cannot provide. We say that an ontology is contextualized or, also, that it is a contextual ontology, when its contents are kept local, and therefore not shared with other ontologies, and mapped with the contents of other ontologies via explicit (context) mappings. The result is Context OWL (C-OWL), a language whose syntax and semantics have been obtained by extending the OWL syntax and semantics to allow for the representation of contextual ontologies.
2003-07
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/437/1/038.pdf
Bouquet, Paolo and Giunchiglia, Fausto and van Harmelen, Frank and Serafini, Luciano and Stuckenschmidt, Heiner (2003) C-OWL: Contextualizing ontologies. UNSPECIFIED.
http://eprints.biblio.unitn.it/437/
oai:eprints.biblio.unitn.it:490
2012-02-28T14:16:52Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
7375626A656374733D51:5141:51413736
74797065733D746563687265706F7274
Preliminary Evaluation of Schema Matching Systems
Yatskevich, Mikalai
QA076 Computer software
QA076.7 Programming Languages - Semantics
This evaluation of the state-of-the-art schema matching approaches is based on a comprehensive testing of modern systems on various real-world schemas. The results obtained show that there is no matcher that performs best on all types of schemas used. The quality of mappings depends significantly on the approaches to schema matching used and on the tuning of the matcher to the particular schema type. The approach proposed in COMA that combines results of different schema matchers proved its effectiveness in our evaluation.
2003-11
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/490/1/028.pdf
Yatskevich, Mikalai (2003) Preliminary Evaluation of Schema Matching Systems. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/490/
oai:eprints.biblio.unitn.it:496
2012-02-28T14:16:53Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A semantics for abstraction
Ghidini, Chiara
Giunchiglia, Fausto
QA076.7 Programming Languages - Semantics
The goal of this paper is to propose a model-theoretic formalization of abstraction, where abstraction is modeled as two representations, the ground and the abstract representation, modeling the same phenomenon at different levels of detail. Using the framework of Local Models Semantics, the ground and abstract representations are modeled as two sets of (local) first order models, while the relations holding between them are captured by an appropriate "compatibility relation". The tuning of the compatibility relation allows for the definition of the many different kinds of abstraction.
2003-12
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/496/1/082.pdf
Ghidini, Chiara and Giunchiglia, Fausto (2003) A semantics for abstraction. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/496/
oai:eprints.biblio.unitn.it:520
2012-02-28T14:16:58Z
7374617475733D7375626D6974746564
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
NLP-Based Requirements Modeling: Experiments on the Quality of the models
Kiyavitskaya, Nadzeya
Zeni, Nicola
Mich, Luisa
Mylopoulos, John
QA076.7 Programming Languages - Semantics
Conceptual models are used in a variety of areas within Computer Science, including Software Engineering, Databases and AI. A major bottleneck in broadening their applicability is the time it takes to build a conceptual model for a new application. Not surprisingly, a variety of tools and techniques have been proposed for reusing conceptual models, e.g. ontologies, or for building them semi-automatically from natural language (NL) descriptions. What has been left largely unexplored is the impact of such tools on the quality of the models that are being created. This paper presents the results of three experiments designed to assess the extent to which a Natural-Language Processing (NLP) tool improves the quality of conceptual models, specifically object-oriented ones. Our main experimental hypothesis is that the quality of a domain class model is higher if its development is supported by a NLP system. The tool used for the experiment – named NL-OOPS – extracts classes and associations from a knowledge base realized by a deep semantic analysis of a sample text. Specifically, NL-OOPS produces class models at different levels of detail by exploiting class hierarchies in the knowledge base of a NLP system and marks ambiguities in the text. In our experiments, we had groups working with and without the tool, and then compared and evaluated the final class models they produced. The results of the experiments – the first on this topic – give insights on the state of the art of linguistics-based Computer Aided Software Engineering (CASE) tools and allow identifying important guidelines to improve their performance. In particular it was possible to highlight which of the linguistic tasks are more critical to effectively support conceptual modelling.
2004-01
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/520/1/005.pdf
Kiyavitskaya, Nadzeya and Zeni, Nicola and Mich, Luisa and Mylopoulos, John (2004) NLP-Based Requirements Modeling: Experiments on the Quality of the models. UNSPECIFIED. (Submitted)
http://eprints.biblio.unitn.it/520/
oai:eprints.biblio.unitn.it:530
2012-02-28T14:17:00Z
7374617475733D696E7072657373
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Contextualizing Ontologies
Bouquet, Paolo
Giunchiglia, Fausto
van Harmelen, Frank
Serafini, Luciano
Stuckenschmidt, Heiner
QA076.7 Programming Languages - Semantics
Ontologies are shared models of a domain that encode a view which is common to a set of different parties. Contexts are local models that encode a party’s subjective view of a domain. In this paper we show how ontologies can be contextualized, thus acquiring certain useful properties that a pure shared approach cannot provide. We say that an ontology is contextualized or, also, that it is a contextual ontology, when its contents are kept local, and therefore not shared with other ontologies, and mapped with the contents of other ontologies via explicit (context) mappings. The results is Context OWL (C-OWL), a language whose syntax and semantics have been obtained by extending the OWL syntax and semantics to allow for the representation of contextual ontologies.
2004-02
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/530/1/013.pdf
Bouquet, Paolo and Giunchiglia, Fausto and van Harmelen, Frank and Serafini, Luciano and Stuckenschmidt, Heiner (2004) Contextualizing Ontologies. UNSPECIFIED. (In Press)
http://eprints.biblio.unitn.it/530/
oai:eprints.biblio.unitn.it:531
2012-02-28T14:17:00Z
7374617475733D696E7072657373
7375626A656374733D51:5141:51413736:514137362E37
7375626A656374733D51:5141:51413736
74797065733D746563687265706F7274
S-Match: an algorithm and an implementation of semantic matching
Giunchiglia, Fausto
Shvaiko, Pavel
Yatskevich, Mikalai
QA076 Computer software
QA076.7 Programming Languages - Semantics
We think of Match as an operator which takes two graph-like structures (e.g., conceptual hierarchies or ontologies) and produces a mapping between those nodes of the two graphs that correspond semantically to each other. Semantic matching is a novel approach where semantic correspondences are discovered by computing, and returning as a result, the semantic information implicitly or explicitly codified in the labels of nodes and arcs. In this paper we present an algorithm implementing semantic matching, and we discuss its implementation within the S-Match system. We also test S-Match against three state of the art matching systems. The results, though preliminary, look promising, in particular for what concerns precision and recall.
2004-02
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/531/1/015.pdf
Giunchiglia, Fausto and Shvaiko, Pavel and Yatskevich, Mikalai (2004) S-Match: an algorithm and an implementation of semantic matching. UNSPECIFIED. (In Press)
http://eprints.biblio.unitn.it/531/
oai:eprints.biblio.unitn.it:585
2012-02-28T14:17:16Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A Peer-to-Peer Database Management System
Roshelova, Albena
QA076.7 Programming Languages - Semantics
Peer-to-Peer Database Management Systems (PDBMS) are still in the beginning of their evolution. They rise up p2p technology to exploit the power of available distributed database management technologies. The proposed PDBMS will be completely autonomous and any notions of centralization as central server or creating a cost-based global schema will be absent. In this paper a number of potential research issues in the overlap between database and p2p systems is identified, and a vision for building a PDBMS is presented. The PDBMS is envisioned as a system that will be able to manage effectively at runtime semantic interdependences among databases in a decentralized, distributed and collaborative manner. The main focus of the proposed PhD work is the research of adaptive techniques for development of a database management system compatible with the p2p paradigm.
2004-06
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/585/1/albena.pdf
Roshelova, Albena (2004) A Peer-to-Peer Database Management System. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/585/
oai:eprints.biblio.unitn.it:715
2012-02-28T14:17:51Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Textual Article Clustering in Newspaper Pages
Aiello, Marco
Pegoretti, Andrea
QA076.7 Programming Languages - Semantics
In the analysis of a newspaper page an important step is the clustering of various text blocks into logical units, i.e., into articles. We propose three algorithms based on text processing techniques to cluster articles in newspaper pages. Based on the complexity of the three algorithms and experimentation on actual pages from the Italian newspaper L’Adige, we select one of the algorithms as the preferred choice to solve the textual clustering problem.
2004
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/715/1/aiello%2Dpegoretti.pdf
Aiello, Marco and Pegoretti, Andrea (2004) Textual Article Clustering in Newspaper Pages. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/715/
oai:eprints.biblio.unitn.it:717
2012-02-28T14:17:52Z
7374617475733D696E7072657373
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Efficient Semantic Matching
Giunchiglia, Fausto
Yatskevich, Mikalai
Giunchiglia, Enrico
QA076.7 Programming Languages - Semantics
We think of Match as an operator which takes two graph-like structures and produces a mapping between semantically related nodes. We concentrate on classifications with tree structures. In semantic matching, correspondences are discovered by translating the natural language labels of nodes into propositional formulas, and by codifying matching into a propositional unsatisfiability problem. We distinguish between problems with conjunctive formulas and problems with disjunctive formulas, and present various optimizations. For instance, we propose a linear time algorithm which solves the first class of problems. According to the tests we have done so far, the optimizations substantially improve the time performance of the system.
2004-12
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/717/1/112.pdf
Giunchiglia, Fausto and Yatskevich, Mikalai and Giunchiglia, Enrico (2004) Efficient Semantic Matching. UNSPECIFIED. (In Press)
http://eprints.biblio.unitn.it/717/
oai:eprints.biblio.unitn.it:751
2012-02-28T14:17:58Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Simple methods for peak and valley detection in time series microarray data
Sboner, A.
Romanel, A.
Malossini, A.
Ciocchetta, F.
Demichelis, F.
Azzini, I.
Blanzieri, E.
Dell'Anna, R.
QA076.7 Programming Languages - Semantics
Given a set of gene expression time series obtained by a microarray experiment, this work proposes a novel quality control procedure, which exploits some analytical methods enabling the identification of genes which spike expressions within narrow time-windows and over a chosen amplitude threshold. The procedure automatically provides a list of genes and time points in which abrupt variations have been detected. The quality control has to be performed by a biologist, who assesses those spikes as bearing biology relevance or being artifacts. In the latter case spikes have to be substituted by a smoothing procedure. In particular, we focused on transcriptome of Plasmodium falciparum Intraerythrocytic Developmental Cycle. Assuming that spikes detected in this set have been labeled as artifacts by a biologist, in the second part of this paper we discuss the effects of smoothing on subsequent different types of analyses.
2005-03
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/751/1/dit%2D05%2D015_final.pdf
Sboner, A. and Romanel, A. and Malossini, A. and Ciocchetta, F. and Demichelis, F. and Azzini, I. and Blanzieri, E. and Dell'Anna, R. (2005) Simple methods for peak and valley detection in time series microarray data. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/751/
oai:eprints.biblio.unitn.it:888
2012-02-28T14:18:39Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A Multi-Agent System that Facilitates Scientific Publications Search
Birukou, Aliaksandr
Blanzieri, Enrico
Giorgini, Paolo
QA076.7 Programming Languages - Semantics
It is very difficult for beginners to define and find the most relevant literature in a research field. They can search on the web or look at the most important journals and conference proceedings, but it should be much better to receive suggestions directly from experts of the field. Unfortunately, this is not always possible and systems like CiteSeer and GoogleScholar become extremely useful for beginners (and not only). In this paper, we present an agent-based system that facilitates scientific publications search. Users interacting with their personal agents produce a transfer of knowledge about relevant publications from experts to beginners. Each personal agent observes how publications are used and induces behavioral patterns that are used to create more effective recommendations. Feedback exchange allows agents to share their knowledge and virtual communities of cloned experts can be created to support novice users. We present also a set of experimental results obtained using CiteSeer as a source of information, that show the effectiveness of our approach.
2005-10
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/888/1/TechReport_BiblicitAAMAS06.pdf
Birukou, Aliaksandr and Blanzieri, Enrico and Giorgini, Paolo (2005) A Multi-Agent System that Facilitates Scientific Publications Search. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/888/
oai:eprints.biblio.unitn.it:889
2012-02-28T14:18:39Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Toothagent: a Multi-Agent System for Virtual Communities Support
Bryl, Volha
Giorgini, Paolo
Fante, Stefano
QA076.7 Programming Languages - Semantics
People tend to form social networks within geographical areas. This can be explained by the fact that generally geographical localities correspond to common interests (e.g. students located in a university could be interested to buy or sell textbooks adopted for a specific course, to share notes, or just to meet together to play basketball). Cellular phones and more in general mobile devices are currently widely used and represent a big opportunity to support social communities. In this paper, we present a general architecture for multi-agent systems accessible via mobile devices (cellular phones and PDAs), where Bluetooth technology has been adopted to reflect users locality. We illustrate ToothAgent, an implemented prototype of the proposed architecture, and discuss the opportunities offered by the system.
2005-10
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/889/1/TechReport_AAMAS06.pdf
Bryl, Volha and Giorgini, Paolo and Fante, Stefano (2005) Toothagent: a Multi-Agent System for Virtual Communities Support. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/889/
oai:eprints.biblio.unitn.it:890
2012-02-28T14:18:40Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
An Implemented Prototype of Bluetooth-Based Multi-Agent System
Bryl, Volha
Giorgini, Paolo
Fante, Stefano
QA076.7 Programming Languages - Semantics
People tend to form social networks within specific geographical areas. This is motivated by the fact that the geographical locality corresponds generally to common interests and opportunities offered by the people active in the area (e.g., students of a university could be interested to buy or sell text books adopted for a specific course, to share notes, or just to meet together to play basketball). Cellular phones and more in general mobile devices are currently widely used and represent a big opportunity to support social communities. We present an application of multi-agent systems accessible via mobile devices (cellular phones and PDAs), where Bluetooth technology has been adopted to reflect users locality. We illustrate an implemented prototype of the proposed architecture and we discuss the opportunities offered by the system.
2005-10
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/890/1/TechReport_WOA06.pdf
Bryl, Volha and Giorgini, Paolo and Fante, Stefano (2005) An Implemented Prototype of Bluetooth-Based Multi-Agent System. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/890/
oai:eprints.biblio.unitn.it:1132
2012-10-24T11:08:53Z
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Reading between the lines : Using hierarchically structured preferences to capture query semantics
Syed, Hamza Hydri
Andritsos, Periklis
QA076.7 Programming Languages - Semantics
Traditionally, search engines treat the keywords entered by users as a text string, without trying to understand the sense behind the user’s need. Others, employ natural language processing techniques or external dictionaries to find what the users’ needs may be. At the same time there has been some recent work done in trying to understand the user better and model her interests to improve the relevancy of the results retrieved by the search engine. In this paper, we present a new hierarchical modeling of a user’s interests which allows for the placing of a particular preference into context and an intuitive way to order her preferences, such that higher relevancy is achieved in the retrieved results. We discuss an approach that exploits these inherent semantics from the hierarchical structure and re-ranks the retrieved results for the particular information need. We accompany our approach with a set of experimental results, which show the merits of such an approach and open new avenues of research in this area.
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1132/1/TechReport.pdf
Syed, Hamza Hydri and Andritsos, Periklis (2006) Reading between the lines : Using hierarchically structured preferences to capture query semantics. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1132/
oai:eprints.biblio.unitn.it:1155
2012-02-28T14:19:51Z
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Semi-Heuristic Negotiation Protocol for Agent-based Mobile Service Application
Abdel-Naby, Sameh
Giorgini, Paolo
Fante, Stefano
QA076.7 Programming Languages - Semantics
This article has been submitted for publication outside of the Department of Information and Communication Technology (DIT) – University of Trento, and will probably be copyrighted if accepted for publication. It has been issued as a Research Technical Report for early dissemination of its contents. In view of the transfer of copyright to the outside publisher, its distribution outside of DIT prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies of the article. In this paper we present a new negotiation protocol that assists multi-agent systems to differently approach the achievement of complex tasks. In particular, we narrow our research scope to focus on the situation where a multi-agent system is serving lightweight devices through advanced communication methods (e.g., Bluetooth). Like many other schemes, our model provides agents with a monetary system and a mechanism for feedback calculation. We aim at accelerating agent’s interactions while resolving end-user composite tasks. Once its efficiency is proven, our protocol can be integrated in a scenario where multipart mobilebased services are offered to holders of lightweight devices.
2007-02
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1155/1/004.pdf
Abdel-Naby, Sameh and Giorgini, Paolo and Fante, Stefano (2007) Semi-Heuristic Negotiation Protocol for Agent-based Mobile Service Application. UNSPECIFIED. (Submitted)
http://eprints.biblio.unitn.it/1155/
oai:eprints.biblio.unitn.it:1210
2012-02-28T14:20:03Z
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Semantic Cooperation and Knowledge Reuse by Using Autonomous Ontologies
Zhao, Yuting
Wang, Kewen
Topor, Rodney
Pan, Jeff Z.
Giunchiglia, Fausto
QA076.7 Programming Languages - Semantics
Several proposals have been put forward to support distributed agent cooperation in the SemanticWeb, by allowing concepts and roles in one ontology be reused in another ontology. In general, these proposals reduce the autonomy of each ontology by defining the semantics of the ontology to depend on the semantics of the other ontologies. We propose a new framework for managing autonomy in a set of cooperating ontologies (or ontology space). In this framework, each language entity concept/role/individual) in an ontology may have its meaning assigned either locally with respect to the semantics of its own ontology, to preserve the autonomy of the ontology, or globally with respect to the semantics of any neighbouring ontology in which it is defined, thus enabling semantic cooperation between multiple ontologies. In this way, each ontology has a “subjective semantics” based on local interpretation and a “foreign semantics” based on semantic binding to neighbouring ontologies. We study the properties of these two semantics and describe the conditions under which entailment and satisfiability are preserved. We also introduce two reasoning mechanisms under this framework: “cautious reasoning” and “brave reasoning”. Cautious reasoning is done with respect to a local ontology and its neighbours (those ontologies in which its entities are defined); brave reasoning is done with respect to the transitive closure of this relationship. This framework is independent of ontology languages. As a case study, for Description Logic ALCN we present two tableau-based algorithms for performing each form of reasonings and prove their correctness.
2007-05
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1210/1/026.pdf
Zhao, Yuting and Wang, Kewen and Topor, Rodney and Pan, Jeff Z. and Giunchiglia, Fausto (2007) Semantic Cooperation and Knowledge Reuse by Using Autonomous Ontologies. UNSPECIFIED.
http://eprints.biblio.unitn.it/1210/
oai:eprints.biblio.unitn.it:1220
2012-02-28T14:20:08Z
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From Early Requirements Analysis towards Secure Workflows
Frankova, Ganna
Massacci, Fabio
Seguran, Magali
Q360 Information Theory
QA076.7 Programming Languages - Semantics
QA076 Computer software
Requirements engineering is a key step in the software development process that has little counterpart in the development of business processes for web services. Furthermore, the existing design methodologies for web services do not address the issue of developing secure web services, secure business processes and secure workflows. This paper presents a methodology that allows a business process designer to derive the skeleton of the concrete secure business processes from the early requirements analysis. The proposed refinement methodology aims to obtain an appropriate coarse grained secure business process that can be further refined into workflows. We introduce a specification language for secure business processes, which is a dialect of WS-BPEL for the functional parts and abstracts away low level implementation details from WS-Security and WS-Federation specifications. To make the discussion more concrete, we illustrate the proposal with an e-business banking case study.
2007-05
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1220/1/SecureBPEL_FrankovaMassacciSeguran.pdf
Frankova, Ganna and Massacci, Fabio and Seguran, Magali (2007) From Early Requirements Analysis towards Secure Workflows. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1220/
oai:eprints.biblio.unitn.it:1452
2012-02-28T14:21:54Z
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Review on stochastic comparison relations
Schivo, Stefano
QA076.7 Programming Languages - Semantics
The report offers an overview of some stochastic simulation and bisimulation relations based on continuous-time Markov chains and on stochastic (possibly Markovian) process algebras.
2008-02
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1452/1/DISI%2D08%2D34.pdf
Schivo, Stefano (2008) Review on stochastic comparison relations. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1452/
oai:eprints.biblio.unitn.it:1453
2012-02-28T14:21:54Z
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Polyadic Stochastic COWS
Schivo, Stefano
QA076.7 Programming Languages - Semantics
We extend the process algebra COWS by introducing stochastic delays in the language. The resulting language is thus an asynchronous polyadic stochastic calculus.
2008-05
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1453/1/DISI%2D08%2D35.pdf
Schivo, Stefano (2008) Polyadic Stochastic COWS. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1453/
oai:eprints.biblio.unitn.it:1465
2012-02-28T14:21:59Z
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An Open-Domain Dialog Act Taxonomy
Quarteroni, Silvia
Riccardi, Giuseppe
Varges, Sebastian
Bisazza, Arianna
QA076.7 Programming Languages - Semantics
This document defines the taxonomy of dialog acts that are necessary to encode domain-independent dialog moves in the context of a task-oriented, open-domain dialog. Such taxonomy is formulated to satisfy two complementary requirements: on the one hand, domain independence, i.e. the power to cover all the range of possible interactions in any type of conversation (particularly conversation oriented to the performance of tasks). On the other hand, the ability to instantiate a concrete set of tasks as defined by a specific knowledge base (such as an ontology of domain concepts and actions) and within a particular language. For the modeling of dialog acts, inspiration is taken from several well-known dialog annotation schemes, such as DAMSL (Core & Allen, 1997), TRAINS (Traum, 1996) and VERBMOBIL (Alexandersson et al., 1997).
2008-08
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1465/1/techRepADAMACH%2DDAtaxonomy.pdf
Quarteroni, Silvia and Riccardi, Giuseppe and Varges, Sebastian and Bisazza, Arianna (2008) An Open-Domain Dialog Act Taxonomy. UNSPECIFIED. (Submitted)
http://eprints.biblio.unitn.it/1465/
oai:eprints.biblio.unitn.it:1489
2012-02-28T14:22:04Z
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Matching ontologies for emergency evacuation plans
Mion, Luca
Pilati, Ivan
Macii, Davi
Andreatta, Fabio
QA076.7 Programming Languages - Semantics
In case of emergency, the coordination of different services deals with different working methods, different languages, different instruments, different sensors and different data representations. Thus, the coordination of services includes heterogeneity problems that can be managed with the help of ontology matching techniques. In this paper we present a scenario where the requirements for ontology matching arise from emergency evacuation plans, in the specific domain of civil protection applications. We envisage what kind of smart sensor technologies could be used to support critical decisions when heterogeneous sources of information have to be matched.
2008-09
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1489/1/045.pdf
Mion, Luca and Pilati, Ivan and Macii, Davi and Andreatta, Fabio (2008) Matching ontologies for emergency evacuation plans. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1489/
oai:eprints.biblio.unitn.it:1507
2012-02-28T14:22:09Z
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Social tagging: Semantics are actually used
Dutta, Biswanath
Giunchiglia, Fausto
QA076.7 Programming Languages - Semantics
This paper describes the results of a study whose goal is to analyze, evaluate and understand the use of semantics in social networks. As a paradigmatic example, the study concentrates on a fairly large portion of the tags used in del.icio.us (more than 5,000 tags). The results show that semantics are pervasively used. In particular, the large majority (in our experiment, 75%) of the tags are subject related and directly codify the semantics of the resource. Furthermore, the number of tags which are effectively used is only a small proportion of the overall tag set (in our experiment around 30% of the tags covers around 95% of the resources), and these tags tend to remain stable in time, despite the continuous growth of the number of tags and resources being indexed. Finally, it is possible to identify an implicit use of hierarchical relationships (i.e., lightweight ontologies) among the concepts denoted by the terms used.
2008-10
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1507/1/061.pdf
Dutta, Biswanath and Giunchiglia, Fausto (2008) Social tagging: Semantics are actually used. UNSPECIFIED.
http://eprints.biblio.unitn.it/1507/
oai:eprints.biblio.unitn.it:1623
2012-02-28T14:22:48Z
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ν-types for effects and freshness analysis
Bartoletti, Massimo
Degano, Pierpaolo
Ferrari, Gian Luigi
Zunino, Roberto
QA076.7 Programming Languages - Semantics
We define a type and effect system for a lambda-calculus extended with side effects, in the form of primitives for creating and accessing resources. The analysis correctly over-approximates the sequences of resource accesses performed by a program at run-time. To accurately analyse the binding between the creation of a resource and its accesses, our system exploits a new class of types. Our nu-types have the form nu N.tau |> H, where the names in N are bound both in the type tau and in the effect H, that represents the sequences of resource accesses.
2009-05
Departmental Technical Report
PeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1623/1/nu%2Dtypes%2DTR.pdf
Bartoletti, Massimo and Degano, Pierpaolo and Ferrari, Gian Luigi and Zunino, Roberto (2009) ν-types for effects and freshness analysis. UNSPECIFIED.
http://eprints.biblio.unitn.it/1623/
oai:eprints.biblio.unitn.it:1643
2012-02-28T14:22:54Z
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Semantic Flooding: Semantic Search across Distributed Lightweight Ontologies
Giunchiglia, Fausto
Kharkevich, Uladzimir
Hume, Alethia
QA076.7 Programming Languages - Semantics
Lightweight ontologies are trees where links between nodes codify the fact that a node lower in the hierarchy describes a topic (and contains documents about this topic) which is more specific than the topic of the node one level above. In turn, multiple lightweight ontologies can be connected by semantic links which represent mappings among them and which can be computed, e.g., by ontology matching. In this paper we describe how these two types of links can be used to define a semantic overlay network which can cover any number of peers and which can be flooded to perform a semantic search on documents, i.e., to perform semantic flooding. We have evaluated our approach by simulating a network of 10,000 peers containing classifications which are fragments of the DMoz web directory. The results are promising and show that, in our approach, only a relatively small number of peers needs to be queried in order to achieve high accuracy.
2009-07
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1643/1/036.pdf
Giunchiglia, Fausto and Kharkevich, Uladzimir and Hume, Alethia (2009) Semantic Flooding: Semantic Search across Distributed Lightweight Ontologies. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1643/
oai:eprints.biblio.unitn.it:1650
2012-02-28T14:22:56Z
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The Semantic Web Languages
Giunchiglia, Fausto
Farazi, Feroz
Tanca, Letizia
De Virgilio, Roberto
QA076.7 Programming Languages - Semantics
The Semantic Web is basically an extension of the Web and of the Web-enabling database and Internet technology, and, as a consequence, the Semantic Web methodologies, representation mechanisms and logics strongly rely on those developed in databases. This is the motivation for many attempts to, more or less loosely, merge the two worlds like, for instance, the various proposals to use relational technology for storing web data or the use of ontologies for data integration. This article comes second in this book, after an article on data management, in order to first complete the picture with the description of the languages that can be used to represent information on the Semantic Web, and then highlight a few fundamental differences which make the database and Semantic Web paradigms complementary but somehow difficult to integrate.
2009-07
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1650/1/039.pdf
Giunchiglia, Fausto and Farazi, Feroz and Tanca, Letizia and De Virgilio, Roberto (2009) The Semantic Web Languages. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1650/
oai:eprints.biblio.unitn.it:1651
2012-02-28T14:22:57Z
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On the interdisciplinary foundations of diversity
Maltese, Vincenzo
Giunchiglia, Fausto
Denecke, Kerstin
Lewis, Paul
Wallner, Cornelia
Baldry, Anthony
Madalli, Devika
QA076.7 Programming Languages - Semantics
Designing new-generation diversity-aware tools that face up to the emerging complexity in knowledge is one of the biggest research challenges in recent years. In this paper, we provide key notions about opinion, bias and diversity, and propose an interdisciplinary approach when managing them. Our basic tenet is that diversity should be seen as an asset rather than as a problem to be avoided a priori.
2009-07
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1651/1/040.pdf
Maltese, Vincenzo and Giunchiglia, Fausto and Denecke, Kerstin and Lewis, Paul and Wallner, Cornelia and Baldry, Anthony and Madalli, Devika (2009) On the interdisciplinary foundations of diversity. UNSPECIFIED.
http://eprints.biblio.unitn.it/1651/
oai:eprints.biblio.unitn.it:1653
2012-02-28T14:22:58Z
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Building Heterogeneous Multi-context Systems by Semantic Bindings
Zhao, Yuting
Wang, Kewen
Topor, Rodney
Pan, Jeff Z.
Giunchiglia, Fausto
QA076.7 Programming Languages - Semantics
We propose a framework for heterogeneous multi-context systems, in which a special kind of semantic/implicit bridge rules are introduced. Traditional bridge rules in heterogeneous multi-context systems may make the syntax and the semantics of a context more complex, e.g., in the approach of [3] an agent may have to facing a context composed by a description logic systems and a logic program with default negations. In this paper we hide the bridge rules by semantic binding on foreign knowledge fragment, and track the semantic property of a belief/knowledge in one context by a mirror-image of it in the other context. This framework can manage heterogeneous multi-contexts in a simple way, and it keeps the original reasoning properties of the context so that the original reasoning tools are still useful.
2009-08
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1653/1/043.pdf
Zhao, Yuting and Wang, Kewen and Topor, Rodney and Pan, Jeff Z. and Giunchiglia, Fausto (2009) Building Heterogeneous Multi-context Systems by Semantic Bindings. UNSPECIFIED. (In Press)
http://eprints.biblio.unitn.it/1653/
oai:eprints.biblio.unitn.it:1679
2012-02-28T14:23:07Z
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A Calculus of Contracting Processes
Bartoletti, Massimo
Zunino, Roberto
QA075 Electronic computers. Computer science
QA076.7 Programming Languages - Semantics
We propose a formal theory for contract-based computing. A contract is an agreement stipulated between two or more parties, which specifies the duties and the rights of the parties involved therein. We model contracts as formulae in an intuitionistic logic extended with a "contractual" form of implication. Decidability holds for our logic: this allows us to mechanically infer the rights and the duties deriving from any set of contracts. We embed our logic in a core calculus of contracting processes, which combines features from concurrent constraints and calculi for multiparty sessions, while subsuming several idioms for concurrency. We then show how to exploit our calculus as a tool for modelling services, the interaction of which is driven by contracts.
2009-10
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1679/1/main.pdf
Bartoletti, Massimo and Zunino, Roberto (2009) A Calculus of Contracting Processes. UNSPECIFIED.
http://eprints.biblio.unitn.it/1679/
oai:eprints.biblio.unitn.it:1691
2012-02-28T14:23:08Z
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Causality and Concurrency in Beta-binders
Priami, Corrado
Guierriero, Maria Luisa
QA076.7 Programming Languages - Semantics
Causal relations allow us to understand the causes of single transitions/ events in a computation and, consequently, to acquire information on the whole systems. In this paper a definition of a causal relation and of an enabling relation for Beta-binders is given, together with the description of some important properties of these relations; in particular we show that the concurrency relation is the complement of the union of causal and enabling relations for each possible computation. The application domains which we are mostly interested in are biology and medical sciences, thus the application of the defined relations to a model of the intensively studied ERK/MAPK pathway is described.
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1691/1/TR%2D01%2D2006%2D1.pdf
Priami, Corrado and Guierriero, Maria Luisa (2006) Causality and Concurrency in Beta-binders. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1691/
oai:eprints.biblio.unitn.it:1693
2012-02-28T14:23:09Z
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The pi-calculus with biological transactions
Ciocchetta, Federica
Priami, Corrado
QA076.7 Programming Languages - Semantics
In this work we extend the -calculus with a simple class of trans-actions, suitable to model multi-reactant, multiproduct chemical re-actions. Some examples are reported to validate our extension.
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1693/1/TR%2D02%2D2006.pdf
Ciocchetta, Federica and Priami, Corrado (2006) The pi-calculus with biological transactions. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1693/
oai:eprints.biblio.unitn.it:1694
2012-02-28T14:23:09Z
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Dynamic Epistemic Spatial Logic
Mardare, Radu
Priami, Corrado
QA076.7 Programming Languages - Semantics
We propose a new logic for expressing properties of concurrent and distributed systems, Dynamic Epistemic Spatial Logic, as an extension of Hennessy-Milner logic with spatial and epistemic operators. Aiming to provide a completely axiomatized and decidable logic for concurrency, we devise epistemic operators, indexed by processes, to replace the guarantee operator in the classical spatial logics. The knowledge of a process, considered as epistemic agent, is understood as the information, locally available to our process, about the overall-global system/process in which it is an agent/subprocess. Dynamic Epistemic Spatial Logic supports a semantics based on a fragment of CCS against which the classical spatial logics have been proved to be undecidable. Underpinning on a new congruence relation on processes - the structural bisimulation - we prove the finite model property for our logic, thus concluding on its decidability against the same semantics. A sound complete Hilbert-style axiomatic system is developed, comprehending the behavior of spatial operators in relation with dynamic/temporal and epistemic ones. Eventually we emphasize on the similarities with the classical axioms and rules of knowledge, that present our logic as an authentic dynamic-epistemic logic. This is the preliminary version of a paper that was published in Proceedings of International Conference on Formal Methods for Networked and Distributed Systems (FORTE 2006), LNCS 4229, Springer, 2006. The original publication is available at www.springerlink.com
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1694/1/TR%2D03%2D2006.pdf
Mardare, Radu and Priami, Corrado (2006) Dynamic Epistemic Spatial Logic. UNSPECIFIED.
http://eprints.biblio.unitn.it/1694/
oai:eprints.biblio.unitn.it:1695
2012-02-28T14:23:09Z
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Membrane Systems with Peripheral Proteins: Transport and Evolution
Cavaliere , Matteo
Sedwards, Sean
QA076.7 Programming Languages - Semantics
Transport of substances and communication between compartments are fundamental biological processes, often mediated by the presence of opportune and complementary proteins attached to the surfaces of membranes. Within compartments, substances are acted upon by local biochemical rules. Inspired by this behaviour we present a model based on membrane systems, with objects attached to the sides of the membranes and floating objects that can move between the regions of the system. Moreover, in each region there are evolution rules that rewrite the transported objects, mimicking chemical reactions. We first analyse the system, showing that interesting qualitative properties can be decided (like reachability of configurations) and then present a simulator based on a stochastic version of the introduced model and show how it can be used to simulate relevant quantitative biological processes. This is a preliminary version of a paper that was published in Proceedings of MeCBIC06, Electronic Notes in Theoretical Computer Science, 171:2, 37-53, 2007. The original version can be found at http://www.elsevier.com/wps/find/journaldescription.cws_home/681021/description#description
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1695/1/TR%2D04%2D2006.pdf
Cavaliere , Matteo and Sedwards, Sean (2006) Membrane Systems with Peripheral Proteins: Transport and Evolution. UNSPECIFIED.
http://eprints.biblio.unitn.it/1695/
oai:eprints.biblio.unitn.it:1696
2012-02-28T14:23:10Z
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Book of abstracts: Scientific Opening of The Microsoft Reasearch Centre for Computational and Systems Biology, Trento, Italy, April 3-5, 2006
Cavaliere, Matteo
Csikasz-Nagy, Attila
Cappello, Igor
Walker, David
Montanari, Ugo
Hillston, Jane
Baralla, Angela
Priami, Corrado
Mura, Ivan
QA076.7 Programming Languages - Semantics
Abstracts of the talks of the Scientific Opening of the Microsoft Research - University of Trento Centre for Computational and Systems Biology held in Trento on April 3-5, 2006
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1696/1/TR%2D05%2D2006.pdf
Cavaliere, Matteo and Csikasz-Nagy, Attila and Cappello, Igor and Walker, David and Montanari, Ugo and Hillston, Jane and Baralla, Angela and Priami, Corrado and Mura, Ivan (2006) Book of abstracts: Scientific Opening of The Microsoft Reasearch Centre for Computational and Systems Biology, Trento, Italy, April 3-5, 2006. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1696/
oai:eprints.biblio.unitn.it:1697
2012-02-28T14:23:10Z
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On the Decidability and Complexity of the Structural Congruence for Beta-binders
Priami, Corrado
Romanel, Alessandro
QA076.7 Programming Languages - Semantics
Beta-binders is a recent process algebra developed for modeling and simulating biological systems. As usual for process calculi, the semantic definition heavily relies on a structural congruence. The treatment of the structural congruence is essential for implementation. The proof of the decidability of this congruence, reported in this paper, is a first step towards implementations. Published in TCS 404(1-2):156-169, c2008 Elsevier, available at http://dx.doi.org/10.1016/j.tcs.2008.04.007
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1697/1/TR%2D06%2D2006.pdf
Priami, Corrado and Romanel, Alessandro (2006) On the Decidability and Complexity of the Structural Congruence for Beta-binders. UNSPECIFIED.
http://eprints.biblio.unitn.it/1697/
oai:eprints.biblio.unitn.it:1698
2012-02-28T14:23:11Z
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7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins
Cavaliere, Matteo
Sedwards, Sean
QA076.7 Programming Languages - Semantics
Membrane systems were introduced as models of computation inspired by the structure and functioning of biological cells. Recently, membrane systems have also been shown to be suitable to model cellular processes. We introduce a new model called Membrane Systems with Peripheral and Integral Proteins. The model has compartments enclosed by membranes, floating objects, objects associated to the internal and external surfaces of the membranes and also objects integral to the membranes. The floating objects can be processed within the compartments and can interact with the objects associated to the membranes. The model can be used to represent cellular processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we model a circadian clock and the G-protein cycle in yeast saccharomyces cerevisiae and present a quantitative analysis using an implemented simulator. This is a preliminary version of a paper that was published in Proceedings of the International Conference on Computational Methods in Systems Biology, CMSB06, Lecture Notes in Bioinformatics, 4210:108-126, 2006. The original publication is available at www.springerlink.com
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1698/1/TR%2D07%2D2006.pdf
Cavaliere, Matteo and Sedwards, Sean (2006) Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins. UNSPECIFIED.
http://eprints.biblio.unitn.it/1698/
oai:eprints.biblio.unitn.it:1699
2012-02-28T14:23:12Z
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7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Artificial Biochemistry
Cardelli, Luca
QA076.7 Programming Languages - Semantics
Chemical and biochemical systems are presented as collectives of interacting stochastic automata: each automaton represents a molecule that undergoes state transitions. This framework constitutes an artificial biochemistry, where automata interact by the equivalent of the law of mass action. We analyze several example systems and networks, both by stochastic simulation and by ordinary differential equations. This is the preliminary version of a paper that was later published in Algorithmic Bioprocesses, A. Condon, D. Harel, J.N. Kok, A. Salomaa, and E. Winfree (Eds.), Springer, 2009, ISBN: 978-3-540-88868-0, available at http://www.springer.com/computer/foundations/book/978-3-540-88868-0
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1699/1/TR%2D08%2D2006.pdf
Cardelli, Luca (2006) Artificial Biochemistry. UNSPECIFIED.
http://eprints.biblio.unitn.it/1699/
oai:eprints.biblio.unitn.it:1700
2012-02-28T14:23:12Z
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7375626A656374733D51:5141:51413736:514137362E37
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Beta-binders with Static Compartments
Guerriero, Maria Luisa
Priami, Corrado
Romanel, Alessandro
QA076.7 Programming Languages - Semantics
We investigate static hierarchies of biological systems through Beta-binders, a recently developed process calculus. We rely on a general interpretation of beta-processes as structured communicating objects. We extend the calculus with the notion of compartment. Objects can either be internal to compartments or reside on compartment borders. Movement in and out of compartments is requested by internal objects and mediated by border objects. We equip the extended calculus with the notion of locality and we define various kinds of relations between actions. Furthermore, we compare our proposal with similar formalisms and we show its application on a biological example. This is the preliminary version of a paper that was published in LNCS 4545:247-261, c2007 Springer-Verlag. The original publication is available at www.springerlink.com
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1700/1/TR%2D09%2D2006.pdf
Guerriero, Maria Luisa and Priami, Corrado and Romanel, Alessandro (2006) Beta-binders with Static Compartments. UNSPECIFIED.
http://eprints.biblio.unitn.it/1700/
oai:eprints.biblio.unitn.it:1701
2012-02-28T14:23:13Z
7374617475733D756E707562
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Beta-binders with Biological Transactions
Ciocchetta, Federica
Priami, Corrado
QA076.7 Programming Languages - Semantics
In this work we propose an extension of Beta-binders with biological transactions, called TBeta-binders, in order to model a sequence of elementary actions atomically. This extension is useful when we need to specify multi-reactant multi-product reactions or when we use a sequence of actions to represent a single biological interaction. Some properties of these transactions are reported. Finally, some simple but explicative examples are described to validate our extension.
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1701/1/TR%2D10%2D2006.pdf
Ciocchetta, Federica and Priami, Corrado (2006) Beta-binders with Biological Transactions. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1701/
oai:eprints.biblio.unitn.it:1702
2012-02-28T14:23:13Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
DNA Splicing: Computing by Observing
Cavaliere, Matteo
Jonoska, Natasha
Leupold, Peter
QA076.7 Programming Languages - Semantics
Motivated by several techniques for observing molecular processes in real-time we introduce a computing device that stresses the role of the observer in biological computations and that is based on the observed behavior of a splicing system. The basic idea is to introduce a marked DNA strand into a test tube with other DNA strands and restriction enzymes. Under the action of these enzymes the DNA starts to splice. An external observer monitors and registers the evolution of the marked DNA strand. The input marked DNA strand is then “accepted” if its observed evolution follows a certain expected pattern. We prove that using simple observers (finite automata), applied on finite splicing systems (finite set of rules, i.e., enzymes and finite set of axioms, i.e., initial strands), the class of recursively enumerable languages can be recognized. This is the preliminary version of a paper that was published in Natural Computing, 8,1, 2009. The original publication is available at http://www.springerlink.com
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1702/1/TR%2D11%2D2006.pdf
Cavaliere, Matteo and Jonoska, Natasha and Leupold, Peter (2006) DNA Splicing: Computing by Observing. UNSPECIFIED.
http://eprints.biblio.unitn.it/1702/
oai:eprints.biblio.unitn.it:1703
2012-02-28T14:23:13Z
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7375626A656374733D51:5141:51413736:514137362E37
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Decision Problems in Membrane Systems with Peripheral Proteins, Transport and Evolution
Cavaliere, Matteo
Sedwards, Sean
QA076.7 Programming Languages - Semantics
Transport of substances and communication between compartments are fundamental biological processes, often mediated by the presence of complementary proteins attached to the surfaces of membranes. Within compartments, substances are acted upon by local biochemical rules. Inspired by this behaviour we present a model based on Membrane Systems, with objects attached to the sides of the membranes and floating objects that can be moved between the regions of the system. Moreover, in each region there are evolution rules that rewrite the transported objects, mimicking chemical reactions. We investigate qualitative properties, like configuration reachability, in relation to the use of cooperative or non-cooperative evolution and transport rules and in the contexts of free- and maximal-parallel evolution. This is a preliminary version of a paper that was published in Theoretical Computer Science, 404, pp. 40–51, 2008. The original publication is available at http://www.elsevier.com/locate/tcs
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1703/1/TR%2D12%2D2006.pdf
Cavaliere, Matteo and Sedwards, Sean (2006) Decision Problems in Membrane Systems with Peripheral Proteins, Transport and Evolution. UNSPECIFIED.
http://eprints.biblio.unitn.it/1703/
oai:eprints.biblio.unitn.it:1704
2012-02-28T14:23:14Z
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Process Calculi Abstractions for Biology
Guerriero, Maria Luisa
Prandi, Davide
Priami, Corrado
Quaglia, Paola
QA076.7 Programming Languages - Semantics
Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-0
2006
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1704/1/TR%2D13%2D2006.pdf
Guerriero, Maria Luisa and Prandi, Davide and Priami, Corrado and Quaglia, Paola (2006) Process Calculi Abstractions for Biology. UNSPECIFIED.
http://eprints.biblio.unitn.it/1704/
oai:eprints.biblio.unitn.it:1705
2012-02-28T14:23:14Z
7374617475733D707562
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Emergence and Maintanence of Functional Modules in Signaling Pathways
Soyer, Orkun
QA076.7 Programming Languages - Semantics
While detection and analysis of functional modules in biological systems have received great attention in recent years, we still lack a complete understanding of how such modules emerge. One theory is that systems must encounter a varying selection (i.e. environment) in order for modularity to emerge. Here, we provide an alternative and simpler explanation using a realistic model of biological signaling pathways and simulating their evolution. These evolutionary simulations start with a homogenous population of a minimal pathway containing two effectors coupled to two signals via a single receptor. This population is allowed to evolve under a constant selection pressure for mediating two separate responses. Results of these evolutionary simulations show that under such a selective pressure, mutational processes easily lead to the emergence of pathways with two separate sub-pathways (i.e. modules) each mediating a distinct response only to one of the signals. Such functional modules are maintained as long as mutations leading to creation of new interactions among existing proteins in the pathway are rare. While supporting a neutralistic view for the emergence of modularity in biological systems, these findings highlight the relevant rate of different mutational processes and the distribution of functional pathways in the topology space as key factors for its maintenance. This is the preliminary version of a paper that was published in BMC Evolutionary Biology. The original publication is available at http://www.biomedcentral.com/bmcevolbiol/
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1705/1/TR%2D01%2D2007.pdf
Soyer, Orkun (2007) Emergence and Maintanence of Functional Modules in Signaling Pathways. UNSPECIFIED.
http://eprints.biblio.unitn.it/1705/
oai:eprints.biblio.unitn.it:1706
2012-02-28T14:23:14Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Dynamic-Epistemic reasoning on distributed systems
Mardare, Radu
QA076.7 Programming Languages - Semantics
We propose a new logic designed for modelling and reasoning about information flow and information exchange between spatially located (but potentially mobile), interconnected agents witnessing a distributed computation. This is a major problem in the field of distributed systems, covering many different issues, with potential applications from Computer Science and Economy to Chemistry and Systems Biology. Underpinning on the dual algebraical-coalgebraical characteristics of process calculi, we design a decidable and completely axiomatizad logic that combines the processalgebraical/ equational and the modal/coequational features and is developed for process-algebraical semantics. The construction is done by mixing operators from dynamic and epistemic logics with operators from spatial logics for distributed and mobile systems. This is the preliminary version of a paper that will appear in Proceedings of the second Conference on Algebra and Coalgebra in Computer Science (CALCO2007), LNCS 4624, Springer, 2007. The original publication is available at www.springerlink.com
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1706/1/TR%2D02%2D2007.pdf
Mardare, Radu (2007) Dynamic-Epistemic reasoning on distributed systems. UNSPECIFIED.
http://eprints.biblio.unitn.it/1706/
oai:eprints.biblio.unitn.it:1707
2012-02-28T14:23:15Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
The Beta Workbench
Romanel, Alessandro
Priami, Corrado
Dematte', Lorenzo
QA076.7 Programming Languages - Semantics
This paper presents a system to model and simulate biological processes. It is based on process calculi theory and incorporates a language, a compiler, the execution environment and some graphical interface components. The language is based on Beta-binders, a recently introduced process algebra bio-inspired and developed to be suitable for the biological applicative domain. The runtime environment is based on a stochastic abstract machine that extends and improve the classical Gillespie’s approach. The quantitative aspects included in the stochastic information associated with the language allow to simulate and plot quantitative parameters of the system under investigation. We define the syntax, semantics and implementation of the language comparing our design choices with the most common features of process calculi applied to biology. A relevant part of this work is the description of design patterns for the most common biological features in molecular interactions. This is an important aspect in exploiting the expressive power of the language and in providing a preliminary guide to the use of the compositional properties of process calculi.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1707/1/TR%2D03%2D2007.pdf
Romanel, Alessandro and Priami, Corrado and Dematte', Lorenzo (2007) The Beta Workbench. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1707/
oai:eprints.biblio.unitn.it:1708
2012-02-28T14:23:15Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Simulating reaction-diffusion with state-dependent diffusion coefficients
Lecca, Paola
Dematte', Lorenzo
Priami, Corrado
QA076.7 Programming Languages - Semantics
The present models and simulation algorithms of intracellular kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even for small prokaryotic cells. In this work we first present a mathematical description of the diffusion induced by concentration gradient. In our model the diffusion coefficients and mechanical quantities as frictional forces are dependent on the local values of solutes concentration. We then present an algorithm implementing our model and simulating a reaction-diffusion system. The algorithm is an efficient modification of the well known Gillespie algorithm, adapted for systems that are both reactive and diffusive.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1708/1/TR%2D04%2D2007.pdf
Lecca, Paola and Dematte', Lorenzo and Priami, Corrado (2007) Simulating reaction-diffusion with state-dependent diffusion coefficients. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1708/
oai:eprints.biblio.unitn.it:1709
2012-02-28T14:23:16Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Effective Index: a formal measure of drug effects
Dematte', Lorenzo
Prandi, Davide
Priami, Corrado
Romanel, Alessandro
QA076.7 Programming Languages - Semantics
This paper proposes the Effective Index, a formal tool to support decision processes in drug discovery. The Effective Index is based on concurrency theory and process calculi to describe incrementally complex biological systems and on Markov process theory to handle quantitative information. A running case study concerning the pathways and the drugs related to hypertension exploits the approach.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1709/1/TR%2D05%2D2007.pdf
Dematte', Lorenzo and Prandi, Davide and Priami, Corrado and Romanel, Alessandro (2007) Effective Index: a formal measure of drug effects. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1709/
oai:eprints.biblio.unitn.it:1710
2012-02-28T14:23:16Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Simulating a faulty mechanism of protein folding in the pathogenesis of familial Parkinson's disease
Lecca, Paola
QA076.7 Programming Languages - Semantics
A growing body of evidence suggests that the accumulation of misfolded proteins in brain tissues is a crucial event in the Parkinson's disease neurodegeneration. Pathogenic mutations may directly induce abnormal protein conformations or compromise the ability of the cellular machinery to detect and degrade misfolded proteins. Although the recent explosion in the rate of discovery of genetic defects linked to Parkinson's disease (PD) have provided tangible clues to the neurobiology of the disorder, they have provided neither direct explanation for the disease process or its key biochemical mechanism. The aim of the work is to provide quantitative models for in silico experiments, that can help the researchers either to elucidate important and still elusive aspects of the Parkinson's disease or to design new wet-experiments. Here we present three stochastic models of a faulty mechanism of protein re-folding and degradation of misfolded proteins. Our models are specified in biochemical stochastic pi-calculus and are based on what is currently known about the genetic mutations causing PD. The expressive capabilities of this formalism in the description of parallel and competive nature of biochemical interactions make it particularly suitable for modeling the intricate mechanism of proteins folding, re-folding and eventually degradation. Furthermore, the simulation results point out those kinetic quantitative parameters, whose variations lead to significant changes in the capability of the system to react to the accumulation of dangerous proteins. This is the preliminary version of a paper that was published in Online Journal of Bioinformatics 9 (1):30-43, 2008. The original version of the publication is available at http://www.cpb.ouhsc.edu/ojvr/bioinfo.htm#20072.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1710/1/TR%2D06%2D2007.pdf
Lecca, Paola (2007) Simulating a faulty mechanism of protein folding in the pathogenesis of familial Parkinson's disease. UNSPECIFIED.
http://eprints.biblio.unitn.it/1710/
oai:eprints.biblio.unitn.it:1711
2012-02-28T14:23:16Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Molecular mechanism of energy metabolism in astrocytes: a parametric model from FDG PET images
Lecca, Paola
Lecca, Michela
QA076.7 Programming Languages - Semantics
The signals detected during physiological activation of the brain with F-deoxyglucose DG PET reflect predominantly uptake of this tracer into astrocytes. This notion provides a cellular and molecular basis for the FDG PET technique. Although in recent years the functional brain imaging has experienced enormous advances, the cellular and, in particular, the molecular mechanisms generating the signals detected by these techniques are not completely known. In this paper, we present a computational model that attempts to disentangle the intricate nature of the molecular interactions governing the brain energy metabolism. The model describes the glutamate-stimulated glucose uptake and use into astrocytes. It consists of a set of ordinary dif- ferential equations, each of which specifying the time-behavior of the main molecular species involved in the astrocytic glucose use (i. e. glutamate, glucose, Na+, beta-threohydroxyaspartate) and the dynam- ical rates of glutamate, glucose and Na+ uptake. The kinetic rates constants of the model have been identified on a set of dynamic PET images. As far as we know, a mathematical and computational model of the brain energy metabolism at the molecular level has been never proposed. The relevance of such a model to the PET functional brain imaging consists in providing an in silico framework, in which to experiment the molecular glucose dynamics and elucidate their still elusive aspects. This is the preliminary version of a paper that was published in Advances in Brain, Vision, and Artificial Intelligence, Lecture Notes in Computer Science, Springer. The original version of the publication is available at http://www.springerlink.com/content/28543x414441760p/
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1711/1/TR%2D07%2D2007.pdf
Lecca, Paola and Lecca, Michela (2007) Molecular mechanism of energy metabolism in astrocytes: a parametric model from FDG PET images. UNSPECIFIED.
http://eprints.biblio.unitn.it/1711/
oai:eprints.biblio.unitn.it:1712
2012-02-28T14:23:17Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Stochastic pi-calculus modelling of multisite phosphorylation based signaling: in silico analysis of the Pho4 transcription factor and the PHO pathway in Saccharomyces cerevisiae
Segata, Nicola
Blanzieri, Enrico
Priami, Corrado
QA076.7 Programming Languages - Semantics
Multisite phosphorylation is known to be an important and dynamic mechanism for regulating the activity of transcription factors. Here we propose a stochastic pi-calculus modelling approach able to handle the complexity of post-translational modifications and to overcome the limitations of the ordinary differential equations based methods. The model can be applied without a priori assumptions to every (multisite) phosphorylation regulation for which some basic rates are known or can be indirectly set with experimental data. We apply it to the multisite phosphorylation of the Pho4 transcription factor that plays a crucial role in the phosphate starvation signalling in Saccharomyces cerevisiae using available in vitro experiments for the model tuning and validation. The innovative modelling of the sub-path with the stochastic pi-calculus allows quantitative analyses of the kinetic characteristics of the Pho4 phosphorylation, the different phosphorylation dynamics for each site (possibly combined) and the variation of the kinase activity as the reaction goes to completion. One of the performed predictions indicates that the Pho80-Pho85 kinase activity on the Pho4 substrate is nearly distributive and not semi-processive as previously found analysing only the phosphoform concentrations in vitro. This result is obtained because the model can consider and quantify the binding events without phosphorylations that cannot be experimentally measured. Thanks to the compositionality property of process algebras, we also developed the whole PHO pathway model that gives new suggestions and confirmations about its general behaviour. The potentialities of process calculi based in silico simulations for biological systems are highlighted and discussed.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1712/1/TR%2D08%2D2007.pdf
Segata, Nicola and Blanzieri, Enrico and Priami, Corrado (2007) Stochastic pi-calculus modelling of multisite phosphorylation based signaling: in silico analysis of the Pho4 transcription factor and the PHO pathway in Saccharomyces cerevisiae. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1712/
oai:eprints.biblio.unitn.it:1713
2012-02-28T14:23:17Z
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Asynchronous Spiking Neural P Systems
Cavaliere, Matteo
Egecioglu, Omer
Ibarra, Oscar H.
Woodworth, Sara
Ionescu, Mihai
Păun, Gheorghe
QA076.7 Programming Languages - Semantics
We consider here spiking neural P systems with a non-synchronized (i.e., asynchronous) use of rules: in any step, a neuron can apply or not apply its rules which are enabled by the number of spikes it contains (further spikes can come, thus changing the rules enabled in the next step). Because the time between two firings of the output neuron is now irrelevant, the result of a computation is the number of spikes sent out by the system, not the distance between certain spikes leaving the system. The additional non-determinism introduced in the functioning of the system by the non-synchronization is proved not to decrease the computing power in the case of using extended rules (several spikes can be produced by a rule). That is, we obtain again the equivalence with Turing machines (interpreted as generators of sets of (vectors of) numbers). However, this problem remains open for the case of restricted spiking neural P systems, whose rules can only produce one spike. On the other hand we prove that asynchronous systems, with extended rules, and where each neuron is either bounded or unbounded, are not computationally complete. For these systems, the configuration reachability, membership (in terms of generated vectors), emptiness, infiniteness, and disjointness problems are shown to be decidable. However, containment and equivalence are undecidable. This is the preliminary version of a paper that was published in Theoretical Computer Science, 410, Issues 24-25, 2009, pages 2352-2364. The original publication is available at http://www.elsevier.com
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1713/1/TR%2D09%2D2007.pdf
Cavaliere, Matteo and Egecioglu, Omer and Ibarra, Oscar H. and Woodworth, Sara and Ionescu, Mihai and Păun, Gheorghe (2007) Asynchronous Spiking Neural P Systems. UNSPECIFIED.
http://eprints.biblio.unitn.it/1713/
oai:eprints.biblio.unitn.it:1714
2012-02-28T14:23:18Z
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7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Computational Thinking in Biology
Priami, Corrado
QA076.7 Programming Languages - Semantics
The paper presents a new approach based on process calculi to systems modeling suitable for biological systems. The main characteristic of process calculi is a linguistic description level to dene incrementally and compositionally executable models. The formalism is suitable to be exploited on the same systems at dierent levels of abstractions connected through well dened formal rules. The abstraction principle that represents biological entities as interacting computational units is the basis of the computational thinking that can help biology to unravel the functions of the cell machinery. We discuss then the perspectives that process calculi can open to life sciences and the impact that this can in turn produce on computer science. This is the preliminary version of a paper that was published in Transactions on Computational Systems Biology. The original publication is available at http://www.springerlink.com/content/p2246002t2568021/
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1714/1/TR%2D10%2D2007.pdf
Priami, Corrado (2007) Computational Thinking in Biology. UNSPECIFIED.
http://eprints.biblio.unitn.it/1714/
oai:eprints.biblio.unitn.it:1715
2015-02-03T09:00:04Z
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74797065733D746563687265706F7274
Colonies of Synchronizing Agents
Cavaliere, Matteo
Mardare, Radu
Sedwards, Sean
QA076.7 Programming Languages - Semantics
We propose a modelling framework and computational paradigm called Colonies of Synchronizing Agents (CSAs) inspired by the intracellular and intercellular mechanisms present in biological tissue. The proposed model is based on a multiset of agents present in a common environment. Each agent has a local state, stored in the form of a multiset of atomic objects, which is updated by global multiset rewriting rules either asynchronously or in synchrony with another agent. We first define the model, then study its computational power, considering trade-offs between internal rewriting (i.e., intracellular mechanism) and synchronization among the agents (i.e., intercellular mechanisms). We also investigate dynamic properties of CSAs, including behavioral robustness (ability to generate a core behavior despite agents or rule failure) and safety of synchronization (ability for an agent to synchronize with another agent, whenever needed). This is the preliminary version of a paper that was published in Proceedings of International Workshop Automata for Cellular and Molecular Computing, Computer and Automation Research Institute of the Hungarian Academy of Sciences, 2007.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1715/1/TR%2D11%2D2007.pdf
Cavaliere, Matteo and Mardare, Radu and Sedwards, Sean (2007) Colonies of Synchronizing Agents. UNSPECIFIED.
http://eprints.biblio.unitn.it/1715/
oai:eprints.biblio.unitn.it:1716
2012-02-28T14:23:19Z
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An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra
Guerriero, Maria Luisa
Heath, John
Priami, Corrado
QA076.7 Programming Languages - Semantics
The aim of this work is twofold. First, we propose an high level textual modelling language, which is meant to be biologically intuitive and hence easily usable by life scientists in modelling intra-cellular systems. Secondly, we provide an automatic translation of the proposed language into Beta-binders, a bio-inspired process calculus, which allows life scientists to formally analyse and simulate their models. We use the Gp130 signalling pathway as a case study. This is the preliminary version of a paper that was published in Proceedings of CMSB07, LNBI 4695, 136-151, 2007. The original publication is available at http://www.springerlink.com/content/vt23126776012835/
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1716/1/TR%2D12%2D2007.pdf
Guerriero, Maria Luisa and Heath, John and Priami, Corrado (2007) An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra. UNSPECIFIED.
http://eprints.biblio.unitn.it/1716/
oai:eprints.biblio.unitn.it:1717
2012-02-28T14:23:19Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A formal and integrated framework to simulate evolution of biological pathways
Dematte', Lorenzo
Priami, Corrado
Romanel, Alessandro
Soyer, Orkun
QA076.7 Programming Languages - Semantics
We present a formal approach to the study of evolution of biological pathways. The basic idea is to use the Beta Workbench to model and simulate pathway in connection with evolutionary algorithms to implement mutations. A fitness function is used to select individuals at any generation. The feasibility of the approach is demonstrated on the MAPK pathway. This is the preliminary version of a paper that was published in Theoretical Computer Science. The original publication is available at http://www.elsevier.com/wps/find/journaldescription.cws_home/505625/description#description
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1717/1/TR%2D13%2D2007.pdf
Dematte', Lorenzo and Priami, Corrado and Romanel, Alessandro and Soyer, Orkun (2007) A formal and integrated framework to simulate evolution of biological pathways. UNSPECIFIED.
http://eprints.biblio.unitn.it/1717/
oai:eprints.biblio.unitn.it:1718
2012-02-28T14:23:20Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Towards the integration of computational systems biology and high-throughput data: a way to support differential analysis of microarray gene expression data
Segata, Nicola
Blanzieri, Enrico
Priami, Corrado
QA076.7 Programming Languages - Semantics
The paradigmatic shift occurred in biology that led first to high-throughput experimental techniques and later to computational systems biology must be applied also to the analysis paradigm of the relation between local models and data to obtain an effective prediction framework. In this work we show that the new relation between systems biology models and high-throughput data permits new integrations on the systemic scale like the use of in silico predictions to support the mining of gene expression datasets. We introduce a unifying notational framework in which we propose two applications concerning the use of system level models to support the differential analysis of microarray expression data. The approach is tested with a specific microarray experiment on the phosphate system in Saccharomyces cerevisiae and a computational model of the PHO pathway that supports the systems biology concepts. This is the preliminary version of a paper that was published in Journal of Integrative Bioinformatics, 5(1):87-103, 2008. The original publication is available at http://journal.imbio.de/
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1718/1/TR%2D14%2D2007.pdf
Segata, Nicola and Blanzieri, Enrico and Priami, Corrado (2007) Towards the integration of computational systems biology and high-throughput data: a way to support differential analysis of microarray gene expression data. UNSPECIFIED.
http://eprints.biblio.unitn.it/1718/
oai:eprints.biblio.unitn.it:1719
2012-02-28T14:23:21Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Chemotaxis mediated by non-adaptive dynamics
Goldstein, Richard A.
Soyer, Orkun
QA076.7 Programming Languages - Semantics
Chemotaxis is the ability of bacteria to locate high attractant sources in the environment. The extensive knowledge gained from the pathway in the model organism Escherichia coli shows that adaptation to stimuli is a hallmark underlying chemotaxis. Studies on certain mutant strains and other bacterial species, however, indicate that some form of chemotaxis could also be achieved without adaptation. It is not clear how efficient such chemotaxis is, how it could be mediated, and how widespread it is among different bacterial species. In order to explore alternative pathway structures and dynamics that can underlie chemotaxis, we employ an evolutionary approach. This approach starts with a population of bacteria that move in a virtual environment based on the dynamics of simple pathways they harbour. As mutations lead to changes in pathway structure and dynamics, bacteria with better ability to localize with high attractant sources gain a selective advantage. We find that chemotaxis via non-adaptive dynamics evolves consistently under different model assumptions and environments. These dynamics directly couple tumbling probability of the cell to increasing attractant levels. Further analyses of evolved pathway structures show that this alternative behaviour can be mediated with as few as two components. The non-adaptive mechanisms mediating chemotaxis provide an explanation for experimental observations made in mutant strains of E. coli and in wild type Rhodobacter sphaeroides and that could not be explained with existing knowledge. These mechanisms could allow a straightforward link between cell metabolism and chemotaxis. Furthermore, they could have acted as the origin of the conventional chemotaxis involving adaptation. This is the preliminary version of a paper that was published in PLoS Computational Biology. The original publication is available at http://www.ploscompbiol.org/home.action
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1719/1/TR%2D15%2D2007.pdf
Goldstein, Richard A. and Soyer, Orkun (2007) Chemotaxis mediated by non-adaptive dynamics. UNSPECIFIED.
http://eprints.biblio.unitn.it/1719/
oai:eprints.biblio.unitn.it:1720
2012-02-28T14:23:21Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
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A Process Algebraical Approach to Modelling Compartmentalized Biological Systems
Ihekwaba, Adaoha
Mardare, Radu
QA076.7 Programming Languages - Semantics
This paper introduces Protein Calculus, a special modeling language designed for encoding and calculating the behaviors of compartmentilized biological systems. The formalism combines, in a unified framework, two successful computational paradigms - process algebras and membrane systems. The goal of Protein Calculus is to provide a formal tool for transforming collected information from in vivo experiments into coded definition of the different types of proteins, complexes of proteins, and membrane-organized systems of such entities. Using this encoded information as input, our calculus computes, in silico, the possible behaviors of a living system. This is the preliminary version of a paper that was published in Proceedings of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2: 642-646, 2007 (http://scitation.aip.org/dbt/dbt.jsp?KEY=APCPCS&Volume=963&Issue=2).
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1720/1/TR%2D16%2D2007.pdf
Ihekwaba, Adaoha and Mardare, Radu (2007) A Process Algebraical Approach to Modelling Compartmentalized Biological Systems. UNSPECIFIED.
http://eprints.biblio.unitn.it/1720/
oai:eprints.biblio.unitn.it:1721
2012-02-28T14:23:21Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A Parallel Beta-binders Simulator
Leye, Stefan
Priami, Corrado
Uhrmacher, Adelinde
QA076.7 Programming Languages - Semantics
Beta-binders is a comparatively new modeling formalism introduced for systems biology. To execute Beta-binders models, suitable simulators are required which translate the operational semantics of Beta-binders into a sound and efficent execution. Efficiency can be reached by parallel and distributed simulation and by a proper representation of models to ensure a fast manipulation. Both possibilities are considered in the implementation of the described hierarchical Beta-binders simulator. The description includes a tree structure which reflects p-calculus and Beta-binders processes and the algorithm of the simulator which enables a distributed and optimistic, parallel execution.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1721/1/TR%2D17%2D2007.pdf
Leye, Stefan and Priami, Corrado and Uhrmacher, Adelinde (2007) A Parallel Beta-binders Simulator. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1721/
oai:eprints.biblio.unitn.it:1722
2012-02-28T14:23:22Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Rate sensitivity analysis of a Beta binders model of lymphocyte recruitment control mechanism
Lecca, Paola
Ooi, Wen Fong
Priami, Corrado
QA076.7 Programming Languages - Semantics
The interaction between lymphocyte in the circulation and endothelial cells lining the blood vessels is a crucial control point in the mechanism of chemotactic detection of inflammation sites. This interaction is mediated by a multisptep process, termed lymphocyte recruit ment, involving lymphocyte rolling along the endothelium, activation of lymphocyte integrins, adhesion to endothelial ligands and lymphocyte crossing the endothelium. The events of the lymphocyte extravasation, called diapedesis is crucial in the pathogenesis of autoimmune neurological diseases, like multiple sclerosis. Recent wet-labs studies provided the data and the observations proving that chemokines modulate the control of the lymphocyte-endothelial cell recognition and regulate the arrest of lymphocyte. In this paper we present a model of lymphocyte recruitment expressed in the formalism of beta-binders and we explore its sensitivity in response to changes of the rates of interaction between chemokines and their receptors. The study is motivated by the intention to individuate those ligand/receptor interactions and their kinetic parameters that are significantly influential in determining the firm arrest of the lymphocyte. We focuses the analysis on the rate coefficients of the chemokines interations. By tuning these parameters we estimate the sensitivity of the model to the rapidity of the lymphocyte adhesion, that recent in vivo observations suggest to be an important factor determining the final result of the rolling process.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1722/1/TR%2D18%2D2007.pdf
Lecca, Paola and Ooi, Wen Fong and Priami, Corrado (2007) Rate sensitivity analysis of a Beta binders model of lymphocyte recruitment control mechanism. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1722/
oai:eprints.biblio.unitn.it:1723
2012-02-28T14:23:24Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Simplifying the Stochastic Petri Nets Formalism for Representing Biological Phenomena
Mura, Ivan
QA076.7 Programming Languages - Semantics
This paper proposes a simplification of the stochastic Petri nets graphical notation with the purpose of defining a more compact and clearer graphical way of building formal models of biological phenomena. Three biological examples are first presented, then modeled with the classical SPN modeling formalism, and their key modeling patterns distilled to identify the main features that need to be represented in a stochastic model. The key features are then the object of the original part of the paper, in which a simplified and more concise, although formal, graphical notation, is proposed, and applied to the selected examples. The paper demonstrates the effectiveness of the simplified notation in producing more compact and understandable models of biological phenomena, still retaining the nice properties of Stochastic Petri Nets, i.e., their flexible abstraction level and formal semantics.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1723/1/TR%2D19%2D2007.pdf
Mura, Ivan (2007) Simplifying the Stochastic Petri Nets Formalism for Representing Biological Phenomena. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1723/
oai:eprints.biblio.unitn.it:1724
2012-02-28T14:23:24Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A new model for kinetic parameter estimation in biochemical reactions.
Lecca, Paola
Sanguinetti, Guido
Palmisano, Alida
Priami, Corrado
QA076.7 Programming Languages - Semantics
We present a novel method for estimating rate coefficients from noisy observations of concentration levels at discrete time points. This is traditionally done by computing the least-squares estimator. However, estimation of the error function generally requires solving the reaction rate equations, which can become computationally unfeasible. Here we present an alternative approach based on a probabilistic, generative model of the variations in reactant concentration. Our method returns the rate coefficients, the level of noise and an error range on the estimates of rate constants. Its probabilistic formulation is key to a principled handling of the noise inherent in biological data, and it allows a number of further extensions.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1724/1/TR%2D20%2D2007.pdf
Lecca, Paola and Sanguinetti, Guido and Palmisano, Alida and Priami, Corrado (2007) A new model for kinetic parameter estimation in biochemical reactions. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1724/
oai:eprints.biblio.unitn.it:1725
2012-02-28T14:23:24Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Solving a system of Master Equations for parallel chemical interactions
Fronza, Ilenia
Lecca, Paola
QA076.7 Programming Languages - Semantics
The stochastic kinetics of a well-stirred mixture of molecular species interacting through different biochemical reactions can modelled by the chemical master equation. Till now the scientific computing community has focussed mostly on the development of numerical techniques to approximate the solution of the chemical master equation many realizations of the associated Markov jump process. Consequeltly, the domain of exact algorithms for directly solving a chemiacl master equation is still an open research area. In this work we present a method to solve analytically a chemical master equation to describe a reversible molecular reaction and we propose a method to solve a system of such equations. In this method molecular populations are considered as time-dependent, integer-valued random variables. Moreover, we developed mathematical procedures for solving a system of chemical master equations referred to a set of parallel and interdependent biochemical interactions. The causal dependence between reactions is modeled on the time scale in the following way: a reaction starts when its antecessor has produced a sufficient quantity of reactants.
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1725/1/TR%2D21%2D2007.pdf
Fronza, Ilenia and Lecca, Paola (2007) Solving a system of Master Equations for parallel chemical interactions. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1725/
oai:eprints.biblio.unitn.it:1726
2012-02-28T14:23:25Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
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Stochastic Modeling of Budding Yeast Cell Cycle
Mura, Ivan
Csikasz-Nagy, Attila
QA076.7 Programming Languages - Semantics
This report presents the definition, solution and validation of a stochastic model of the budding yeast cell cycle, based on Stochastic Petri Nets. A well-established deterministic model, based on ODEs, is considered as the basis for the stochastic modeling. A specific class of Stochastic Petri Nets is selected for building a stochastic version of the deterministic model, with applying the same abstractions of biological phenomena as the ones adopted in the deterministic model. We describe in the report the procedure followed in defining the SPN model from the deterministic one, a procedure that can be largely automated. The validation of the SPN model is conducted with respect to both the results provided by the deterministic one and the results available from wet-lab experiments. A very good match is obtained for the budding yeast wild type and for a variety of mutants that have been experimentally constructed in wet-labs. The results of the two models were compared against experimental data. We show that the stochasticity allows predicting characteristics that cannot be determined with the deterministic model. Moreover, we also show that the stochastic model can fine-tune the results of the deterministic model, enriching the breadth and the quality of the model. This is the preliminary version of a paper that was published in Journal of Theoretical Biology. The original publication is available at http://www.elsevier.com/wps/find/journaldescription.cws_home/622904/description\#description
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1726/1/TR%2D22%2D2007.pdf
Mura, Ivan and Csikasz-Nagy, Attila (2007) Stochastic Modeling of Budding Yeast Cell Cycle. UNSPECIFIED.
http://eprints.biblio.unitn.it/1726/
oai:eprints.biblio.unitn.it:1727
2012-02-28T14:23:25Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A Logical Characterization of Robustness, Mutants and Species in Colonies of Agents
Mardare, Radu
Cavaliere, Matteo
Sedwards, Sean
QA076.7 Programming Languages - Semantics
We study a modeling framework and computational paradigm called Colonies of Syn- chronizing Agents (CSAs), which abstracts intracellular and intercellular mechanisms of biological tissues. The model is based on a multiset of agents (cells) in a com- mon environment. Each agent has a local contents, stored in the form of a multiset of atomic objects, updated by multiset rewriting rules which may act on individual agents (intracellular action) or synchronize the contents of pairs of agents (intercellu-lar action). In this paper we investigate dynamic properties of CSAs, by means of temporal logic, and we give a logical characterization of some notions inspired by evolutionary biology such as robustness, mutants and species. We reveal the relation that exists between the concept of robustness for CSAs and the bisimulation relation on colonies. We also present some decidability results for particular cases of robustness. Preprint of an article submitted for consideration in International Journal of Foundations of Computer Science ©2008 copyright World Scientific Publishing Company [http://www.worldscinet.com/ijfcs/ijfcs.shtml]
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1727/1/TR%2D23%2D2007.pdf
Mardare, Radu and Cavaliere, Matteo and Sedwards, Sean (2007) A Logical Characterization of Robustness, Mutants and Species in Colonies of Agents. UNSPECIFIED.
http://eprints.biblio.unitn.it/1727/
oai:eprints.biblio.unitn.it:1728
2012-02-28T14:23:25Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
An integration of miRNA target predictions for the characterization of human miRNAs
Fronza, Ilenia
Quattrone, Alessandro
Re, Angela
QA076.7 Programming Languages - Semantics
Master Thesis Second Level International Master in Computational and Systems Biology
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1728/1/TR%2D24%2D2007.pdf
Fronza, Ilenia and Quattrone, Alessandro and Re, Angela (2007) An integration of miRNA target predictions for the characterization of human miRNAs. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1728/
oai:eprints.biblio.unitn.it:1729
2012-02-28T14:23:26Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
A BetaWB model for the NFkB pathway
Larcher, Roberto
Ihekwaba, Adaoha
Priami, Corrado
QA076.7 Programming Languages - Semantics
Master Thesis Second Level International Master in Computational and Systems Biology
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1729/1/TR%2D25%2D2007.pdf
Larcher, Roberto and Ihekwaba, Adaoha and Priami, Corrado (2007) A BetaWB model for the NFkB pathway. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1729/
oai:eprints.biblio.unitn.it:1730
2012-02-28T14:23:27Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Experiments on the Reliability of Stochastic Spiking Neural P Systems
Cavaliere, Matteo
Mura, Ivan
QA076.7 Programming Languages - Semantics
In the area of membrane computing, time-freeness has been defined as the ability for a timed membrane system to produce always the same result, independently of the execution times associated to the rules. In this paper, we use a similar idea in the framework of spiking neural P systems, a model inspired by the structure and the functioning of neural cells. In particular, we introduce stochastic spiking neural P systems where the time of firing for an enabled spiking rule is probabilistically chosen and we investigate when, and how, these probabilities can influence the ability of the systems to simulate, in a reliable way, universal machines, such as register machines. This is the preliminary version of a paper that was published in Natural Computing, 7, 4, 2008. The original publication is available at http://www.springerlink.com
2007
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1730/1/TR%2D26%2D2007.pdf
Cavaliere, Matteo and Mura, Ivan (2007) Experiments on the Reliability of Stochastic Spiking Neural P Systems. UNSPECIFIED.
http://eprints.biblio.unitn.it/1730/
oai:eprints.biblio.unitn.it:1731
2012-02-28T14:23:27Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Modeling and parameter estimation of the SOS response network in E.coli
Baralla, Angela
Cavaliere, Matteo
de la Fuente, Alberto
QA076.7 Programming Languages - Semantics
The SOS response is an inducible DNA repair system that allows bacteria to survive in presence of an increased level of DNA damage. More than 40 genes are induced in response to DNA damage as part of the SOS regulon in Escherichia coli. Two main proteins play a key role in the regulation of this response: a repressor LexA that prevents the expression of these genes and an inducer RecA that induces the LexA cleavage reaction and the subsequent expression of the response genes. Most of these response genes are responsible for error-free DNA-damage repair and for the regulation of cell division. In this thesis we have investigated a network of nine genes including the principal mediators of the SOS response: lexA, recA, ssB, recF, dinI and umuDC and three sigma factor genes: rpoD, rpoH and rpoS.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1731/1/TR%2D01%2D2008.pdf
Baralla, Angela and Cavaliere, Matteo and de la Fuente, Alberto (2008) Modeling and parameter estimation of the SOS response network in E.coli. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1731/
oai:eprints.biblio.unitn.it:1732
2012-02-28T14:23:27Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
On the Computational Power of BlenX
Romanel, Alessandro
Priami, Corrado
QA076.7 Programming Languages - Semantics
We present some decidability and undecidability results for subsets of the BlenX Language, a process-calculi-based programming language developed for modelling biological processes. We show that for a core subset of the language (which considers only communications primitives) termination is decidable. Moreover, we prove that by adding either global priorities or events to this core language, we obtain Turing equivalent languages. The proof is through encodings of Random Access Machines (RAMs), a well known Turing equivalent formalism, into our subsets of BlenX. All the encodings are shown to be correct.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1732/1/TR%2D02%2D2008.pdf
Romanel, Alessandro and Priami, Corrado (2008) On the Computational Power of BlenX. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1732/
oai:eprints.biblio.unitn.it:1733
2012-02-28T14:23:28Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Rule based modeling of gene regulation and biosynthesis of tryptophan in E. coli
Passini, Valerio
Lhoussaine, Cedric
Nebut, Mirabelle
Kuttler, Celine
QA076.7 Programming Languages - Semantics
The genetic regulation of the Trp operon in the bacterium E. coli relies on a sophisticated control mechanism. It tightly couples the advance of transcribing RNA polymerase to the efficiency of the contemporaneous translation of the nascent transcript by a ribosome. The concurrent control of this process involves interdependencies between multiple molecular actors. Within process algebra based modeling languages focused on pairwise interaction, its representation required sophisticated coding tricks. In this work, we abstract the mechanism of transcriptional attenuation within a novel rule base modeling language. It allows non-trivial concurrent control by representing molecules as parametrized terms.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1733/1/TR%2D03%2D2008.pdf
Passini, Valerio and Lhoussaine, Cedric and Nebut, Mirabelle and Kuttler, Celine (2008) Rule based modeling of gene regulation and biosynthesis of tryptophan in E. coli. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1733/
oai:eprints.biblio.unitn.it:1734
2012-02-28T14:23:28Z
7374617475733D756E707562
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Automated generation of narrative language programs from NCI-Nature's Pathway Interaction Database
Polo, Filippo
Priami, Corrado
QA076.7 Programming Languages - Semantics
Second Level International Master in Computational and Systems Biology-Master Thesis
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1734/1/TR%2D04%2D2008.pdf
Polo, Filippo and Priami, Corrado (2008) Automated generation of narrative language programs from NCI-Nature's Pathway Interaction Database. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1734/
oai:eprints.biblio.unitn.it:1736
2012-02-28T14:23:29Z
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7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Query-based Verification of Biochemical Oscillations through Probabilistic Model Checking
Ballarini, Paolo
Mura, Ivan
Mardare, Radu
QA076.7 Programming Languages - Semantics
Automated verification of stochastic models has been proved to be an effective technique for the analysis of a large class of stochastically behaving systems. In this paper we show how stochastic modelchecking can be effectively applied to the analysis of biological systems. We consider a few models of biological systems taken from the literature, and we consider both their encodings as ordinary differential equations and Markovian models. We show that stochastic model-checking verification of biological systems can complement both deterministic and stochastic simulation techniques when dealing with dynamical properties of oscillators. We demonstrate how stochastic model-checking can provide exact quantitative characterization of properties of systems exhibiting oscillatory behavior, providing insights that cannot be obtained with differential equations models and that would require a large number of runs with stochastic simulation approaches. This is the preliminary version of a paper that was published in the Proceedings of the International Workshop From Biology To Concurrency and back (FBTC 2008), satellite workshop of ICALP 2008, July 12, 2008, Reykjavik, Iceland, ENTCS 194(3). The original publication is available at DOI:10.1016/j.entcs.2009.02.002
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1736/1/TR%2D05%2D2008.pdf
Ballarini, Paolo and Mura, Ivan and Mardare, Radu (2008) Query-based Verification of Biochemical Oscillations through Probabilistic Model Checking. UNSPECIFIED.
http://eprints.biblio.unitn.it/1736/
oai:eprints.biblio.unitn.it:1737
2012-02-28T14:23:29Z
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Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes
Sedwards, Sean
Mazza, Tommaso
QA076.7 Programming Languages - Semantics
Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. It is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, however few explicitly model the topology of the membranes themselves. Discrete stochastic simulation of molecular kinetics potentially oers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described by simple mass action chemistry. Moreover, modelling every individual molecular interac- tion in the cell is probably unnecessary and currently impractical. Simulation is a form of computer aided analysis, relying on human inter- pretation to derive meaning. To improve eciency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version [Sean Sedwards and Tommaso Mazza, Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes, Bioinformatics, 15 October 2007; 23: 2800 - 2802] is available online at: http://bioinformatics.oxfordjournals.org/ [doi:10.1093/bioinformatics/btm416].
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1737/1/TR%2D06%2D2008.pdf
Sedwards, Sean and Mazza, Tommaso (2008) Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes. UNSPECIFIED.
http://eprints.biblio.unitn.it/1737/
oai:eprints.biblio.unitn.it:1738
2012-02-28T14:23:29Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Independent Component Analysis for the Aggregation of Stochastic Simulation Output
Forlin, Michele
Mura, Ivan
QA076.7 Programming Languages - Semantics
Computational models and simulation algorithms are commonly applied tools in biological sciences. Among those, discrete stochastic models and stochastic simulation proved to be able to effectively capture the effects of intrinsic noise at molecular level, improving over deterministic approaches when system dynamics is driven by a limited amount of molecules. A challenging task that is offered to researchers is then the analysis and ultimately the inference of knowledge from a set of multiple, noisy, simulated trajectories. We propose in this paper a method, based on Independent Component Analysis (ICA), to automatically analyze multiple output traces of stochastic simulation runs. ICA is a statistical technique for revealing hidden factors that underlie sets of signals. Its applications span from digital image processing, to audio signal reconstruction and economic indicators analysis. Here we propose the application of ICA to identify and describe the noise in time-dependent evolution of biochemical species and to extract aggregate knowledge on simulated biological systems. We present the results obtained with the application of the proposed methodology on the well-known MAPK cascade system, which demonstrate the ability of the proposed methodology to decompose and identify the noisy components of the evolution. Quantitative descriptions of the noise component can be further analytically characterized by a simple first order autoregressive model.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1738/1/TR%2D07%2D2008.pdf
Forlin, Michele and Mura, Ivan (2008) Independent Component Analysis for the Aggregation of Stochastic Simulation Output. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1738/
oai:eprints.biblio.unitn.it:1739
2012-02-28T14:23:30Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
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Study on an Optimistic Reaction-Diusion Simulator based on Gillespie SSA
Dematte', Lorenzo
Mazza, Tommaso
QA076.7 Programming Languages - Semantics
The parallel simulation of biochemical reactions is a very interesting problem: biochemical systems are inherently parallel, yet the majority of the algorithms to simulate them, including the well-known and widespread Gillespie SSA, are strictly sequential. Here we investigate, in a general way, how to characterize the simulation of biochemical systems in terms of Discrete Event Simulation. We dissect their inherent parallelism in order both to exploit the work done in this area and to speed-up their simulation. We study the peculiar characteristics of discrete biological simulations in order to select the parallelization technique which provides the greater benefits, as well as to touch its limits. We then focus on reaction-diffusion systems: we design and implement an efficient parallel algorithm for simulating such systems that include both reactions between entities and movements throughout the space. This is the preliminary version of a paper that was published in Proceedings of the sixth international conference on Computational Methods in Systems Biology (CMSB2008), LNBI 5307, pp. 191 – 210. The original publication is available at http://www.springerlink.com/content/w341771l12012560/
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1739/1/TR%2D08%2D2008.pdf
Dematte', Lorenzo and Mazza, Tommaso (2008) Study on an Optimistic Reaction-Diusion Simulator based on Gillespie SSA. UNSPECIFIED.
http://eprints.biblio.unitn.it/1739/
oai:eprints.biblio.unitn.it:1740
2012-02-28T14:23:30Z
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The BlenX Language: A Tutorial
Dematte', Lorenzo
Priami, Corrado
Romanel, Alessandro
QA076.7 Programming Languages - Semantics
This paper presents a new programming language, BlenX. BlenX is inspired to the process calculus Beta-binders and it is intended for modelling any system whose basic step of computation is an interaction between sub-components. The original development was thought for biological systems. Therefore this tutorial exemplifies BlenX features on biology-related systems. This is the preliminary version of a paper that was published in LNCS 5016:313-365, c2008 Springer-Verlag. The original publication is available at www.springerlink.com
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1740/1/TR%2D09%2D2008.pdf
Dematte', Lorenzo and Priami, Corrado and Romanel, Alessandro (2008) The BlenX Language: A Tutorial. UNSPECIFIED.
http://eprints.biblio.unitn.it/1740/
oai:eprints.biblio.unitn.it:1741
2012-02-28T14:23:31Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
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From Solvable to Executable Models of Biological Systems
Palmisano, Alida
Priami, Corrado
QA076.7 Programming Languages - Semantics
Classical modeling approaches for biology are mainly grounded in mathematics, and specifically on ordinary differential equations (ODE). Process calculi-based conceptual and computational tools are an alternative and emergent approach. Here we focus our analysis on BlenX (a beta-binders inspired programming language) showing how it is possible to easily re-use ODE models within this framework. An example will show then the advantages of moving into a stochastic approach. This is the preliminary version of a paper that was published in Proceedings of Pacific Symposium on Biocomputing (PSB 2009), January, 2009. The original publication is available at http://psb.stanford.edu/psb-online/proceedings/psb09/
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1741/1/TR%2D10%2D2008.pdf
Palmisano, Alida and Priami, Corrado (2008) From Solvable to Executable Models of Biological Systems. UNSPECIFIED.
http://eprints.biblio.unitn.it/1741/
oai:eprints.biblio.unitn.it:1742
2012-02-28T14:23:31Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
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Simulation of non-Markovian Processes in BlenX
Prandi, Davide
Priami, Corrado
Romanel, Alessandro
QA076.7 Programming Languages - Semantics
BlenX is a programming language explicitly designed for modeling biological processes inspired by Beta-binders. The actual framework assumes biochemical interactions being exponentially distributed, i.e., an underlying Markov process is associated with BlenX programs. In this paper we relax this condition by providing formal tools for managing non-Markovian processes within BlenX.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1742/1/TR%2D11%2D2008.pdf
Prandi, Davide and Priami, Corrado and Romanel, Alessandro (2008) Simulation of non-Markovian Processes in BlenX. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1742/
oai:eprints.biblio.unitn.it:1743
2012-02-28T14:23:31Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
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Exactness and Approximation of the Stochastic Simulation Algorithm
Mura, Ivan
QA076.7 Programming Languages - Semantics
This short note intends to clarify about the applicability of the Stochastic Simulation Algorithm proposed by Gillespie for the analysis of systems of coupled biochemical reactions. The derivation of Gillespie’s results is revisited to pinpoint those steps at which, depending on the validity of the assumptions adopted about the system to be studied, approximations may be introduced. We discuss about the ways the inaccuracies entailed by the approximations may propagate and affect simulation results.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1743/1/TR%2D12%2D2008.pdf
Mura, Ivan (2008) Exactness and Approximation of the Stochastic Simulation Algorithm. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1743/
oai:eprints.biblio.unitn.it:1744
2012-02-28T14:23:32Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Calibration of biochemical network models
Lecca, Paola
Palmisano, Alida
Priami, Corrado
Sanguinetti, Guido
QA076.7 Programming Languages - Semantics
The estimation of parameter values (model calibration) is the bottleneck of the computational analysis of biological systems. Modeling approaches are central in systems biology, as they provide a rational framework to guide systematic strategies for key issues in medicine as well as the pharmaceutical and biotechnological industries. Inter- and intra-cellular processes require dynamic models, that contain the rate constants of the biochemical reactions. These kinetic parameters are often not accessible directly through experiments. Therefore methods that estimate rate constants with the maximum precision and accuracy are needed. We present here a new method for estimating rate coefficients from noisy observations of concentration levels at discrete time points. This is traditionally done by computing the least-squares estimator. However, estimation of the error function generally requires solving the reaction rate equations, which can become computationally unfeasible. We propose an alternative approach based on a probabilistic, generative model of the variations in reactant concentration. Our method returns the rate coefficients, the level of noise and an error range on the estimates of rate constants. Its probabilistic formulation is key to a principled handling of the noise inherent in biological data, and it allows for a number of further extensions. The mathematical procedure presented here has been implemented in a software tool, named KInfer.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1744/1/TR%2D13%2D2008.pdf
Lecca, Paola and Palmisano, Alida and Priami, Corrado and Sanguinetti, Guido (2008) Calibration of biochemical network models. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1744/
oai:eprints.biblio.unitn.it:1745
2012-02-28T14:23:33Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
An Efficient and Exact Stochastic Simulation Method to Analyze Rare Events in Biochemical Systems
Kuwahara, Hiroyuki
Mura, Ivan
QA076.7 Programming Languages - Semantics
In robust biological systems, wide deviations from highly controlled normal behavior may be rare, yet they may result in catastrophic complications. While in silico analysis has gained an appreciation as a tool to offer insights into systems-level properties of biological systems, analysis of such rare events provides a particularly challenging computational problem. This paper proposes an efficient stochastic simulation method to analyze rare events in biochemical systems. Our new approach can substantially increase the frequency of the rare events of interest by appropriately manipulating the underlying probability measure of the system, allowing high-precision results to be obtained with substantially fewer simulation runs than the conventional direct Monte Carlo simulation. Here, we show the algorithm of our new ap- proach, and we apply it to the analysis of rare deviant transitions of two systems, resulting in several orders of magnitude speedup in generating high-precision estimates compared with the conventional Monte Carlo simulation. This is the preliminary version of a paper that was published in Journal of Chemical Physics. The original publication is available at http://jcp.aip.org/jcp/top.jsp
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1745/1/TR%2D14%2D2008.pdf
Kuwahara, Hiroyuki and Mura, Ivan (2008) An Efficient and Exact Stochastic Simulation Method to Analyze Rare Events in Biochemical Systems. UNSPECIFIED.
http://eprints.biblio.unitn.it/1745/
oai:eprints.biblio.unitn.it:1746
2012-02-28T14:23:33Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins
Mazza, Tommaso
Cavaliere, Matteo
QA076.7 Programming Languages - Semantics
Membrane systems with peripheral proteins are essentially standard membrane systems with the possibility of having multisets of objects (proteins) embedded in the membranes and with the presence of rules that control the transport and the change of configurations of these proteins. The model intends to abstract the activities of the receptors embedded in the cellular membranes. In this paper we use an extension of this paradigm to model and simulate some of the mechanisms underlying cell cycle and breast tumor growth. In particular we have defined a membrane system that abstracts the G2/M cell cycle phase transition and extends the corresponding Reactome model. The model has been then simulated by using the software Cyto-Sim and we have monitored the interplay between activators and inhibitors of the cell cycle. This is the preliminary version of a paper that was published in Electronic Notes in Theoretical Computer Science 227(4) January 2009, pages 127-141. The original publication is available at http://dx.doi.org/10.1016/j.entcs.2008.12.108
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1746/1/TR%2D15%2D2008.pdf
Mazza, Tommaso and Cavaliere, Matteo (2008) Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins. UNSPECIFIED.
http://eprints.biblio.unitn.it/1746/
oai:eprints.biblio.unitn.it:1747
2015-02-02T11:48:15Z
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Modeling and simulating bio-molecule diffusion in non-homogeneous solutions. Diffusive spatial effects on chaperone-assisted protein folding: a case study
Lecca, Paola
Dematte', Lorenzo
Priami, Corrado
QA076.7 Programming Languages - Semantics
In this report we present a new stochastic algorithm to simulate reaction-diffusion systems and its application to the simulation of spatial effects on the chaperone-assisted protein folding in cytoplasm. This is the preliminary version of a paper that was published in Proceedings of World Academy of Science, Engineering and Technology Vol. 44 Int. Conference on Bioinformatics and Biomedicine, Venice, Italy 2008. The original publication is available at http://www.waset.org/journals/waset/v44.php
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1747/1/TR%2D16%2D2008.pdf
Lecca, Paola and Dematte', Lorenzo and Priami, Corrado (2008) Modeling and simulating bio-molecule diffusion in non-homogeneous solutions. Diffusive spatial effects on chaperone-assisted protein folding: a case study. UNSPECIFIED.
http://eprints.biblio.unitn.it/1747/
oai:eprints.biblio.unitn.it:1748
2012-02-28T14:23:34Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Inferring rate coefficents of biochemical reactions from noisy data with KInfer
Lecca, Paola
Palmisano, Alida
Priami, Corrado
QA076.7 Programming Languages - Semantics
Dynamical models of inter- and intra-cellular processes contain the rate constants of the biochemical reactions. These kinetic parameters are often not accessible directly through experiments, but they can be inferred from time-resolved data. Time resolved data, that is, measurements of reactant concentration at series of time points, are usually affected by different types of error, whose source can be both experimental and biological. The noise in the input data makes the estimation of the model parameters a very difficult task, as if the inference method is not sufficiently robust to the noise, the resulting estimates are not reliable. Therefore "noise-robust" methods that estimate rate constants with the maximum precision and accuracy are needed. In this report we present the probabilistic generative model of parameter inference implemented by the software prototype KInfer and we show the ability of this tool of estimating the rate coefficients of models of biochemical network with a good accuracy even from very noisy input data.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1748/1/TR%2D17%2D2008.pdf
Lecca, Paola and Palmisano, Alida and Priami, Corrado (2008) Inferring rate coefficents of biochemical reactions from noisy data with KInfer. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1748/
oai:eprints.biblio.unitn.it:1749
2012-02-28T14:23:35Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
From BlenX to chemical reactions via SBML
Larcher, Roberto
Priami, Corrado
QA076.7 Programming Languages - Semantics
Recently process calculi have been used to model biological systems. We use the process calculi-based language BlenX to develop executable models starting from the composition of the description of the molecules involved in the system. BlenX programs can be run through a stochastic run-time that makes the molecules interact together, mimicking different kinds of reactions. The goal of the paper is to extract from BlenX programs a description of the same system based on chemical reactions that can be executed through chemical-based stochastic simulators. We present an algorithm that extracts the list of these reactions from the model definition given in BlenX. The translation is done without run- ning the system, but just analysing the model. The boxes in the BlenX models, used to represent molecules, often perform immediate actions (i.e. reactions with infinite rate) to change their internal state, some of which can be removed by the algorithm to optimize the model. The outcome of the algorithm is an SBML file that can be easily im- ported in SBML-supporting simulators that in some cases may run faster then executing BlenX programs due to model reduction and optimization. Furthermore, exporting our models in SBML allow us to share the models we develop in BlenX with the scientific community.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1749/1/TR%2D18%2D2008.pdf
Larcher, Roberto and Priami, Corrado (2008) From BlenX to chemical reactions via SBML. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1749/
oai:eprints.biblio.unitn.it:1750
2012-02-28T14:23:35Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
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Notes on stochastic simulation of chemical kinetics with cycle-leaping
Lecca, Paola
Teso, Stefano
QA076.7 Programming Languages - Semantics
In this report we review the Riedel-Bruck stochastic simulation algorithm, which makes use of a cycle-leaping strategy to improve the simulation performance. We implemented the algorithmi and tested our implementation on some stochastic models, such as the Lotka-Volterra model of predation, the Brusselator model, and the Michaelis-Menten model of enzymatic catalysis. We discuss the advantages and the disadvantages of this algorithm from the viewpoint of its use in a systemic approach to modeling and simulation of biochemical and biological processes.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1750/1/TR%2D19%2D2008.pdf
Lecca, Paola and Teso, Stefano (2008) Notes on stochastic simulation of chemical kinetics with cycle-leaping. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1750/
oai:eprints.biblio.unitn.it:1751
2012-02-28T14:23:36Z
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Algorithmic Systems Biology: An Opportunity for Computer Science
Priami, Corrado
QA076.7 Programming Languages - Semantics
The convergence between computer science and biology occurred in successive waves involving deeper and deeper concepts of computing. The current status makes computer science a suitable candidate to become a philosophical foundation for systems biology with the same importance as mathematics, chemistry and physics. However, this great opportunity is not a free lunch. New development and a strong integration of different fields of computing are needed to cope with the challenges of systems biology: a complex and expanding applicative domain that can open completely new avenues of research in computing and eventually help it become a natural, quantitative science. © ACM, 2008. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Communications of the ACM, {52(5):80-88 (May 2009)} doi:10.1145/1506409.1506427, http://cacm.acm.org/magazines/2009/5/24650-algorithmic-systems-biology/abstract
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1751/1/TR%2D20%2D2008.pdf
Priami, Corrado (2008) Algorithmic Systems Biology: An Opportunity for Computer Science. UNSPECIFIED.
http://eprints.biblio.unitn.it/1751/
oai:eprints.biblio.unitn.it:1752
2012-02-28T14:23:36Z
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Towards a Complete Axiomatization for Spatial Logic
Mardare, Radu
Policriti, Alberto
QA076.7 Programming Languages - Semantics
The process-based Spatial Logics are multi-modal logics developed for semantics on Process Algebras and designed to specify concurrent properties of dynamic systems. On the syntactic level, they combine modal operators similar to operators of Hennessy-Milner logic, dynamic logic, arrow logic, relevant logic, or linear logic. This combination generates expressive logics, sometimes undecidable, for which a wide range of applications have been proposed. In the literature, there exist some sound proof systems for spatial logics, but the problem of completeness against process-algebraic semantics is still open. The main goal of this paper is to identify a sound-complete axiomatization for such a logic. We focus on a particular spatial logic that combines the basic spatial operators with dynamic and classical operators. The semantics is based on a fragment of CCS calculus that embodies the core features of concurrent behaviors. We prove the logic decidable both for satisfiability/validity and mode-checking, and we propose a sound-complete Hilbert-style axiomatic system for it. This is the preliminary version of a paper that was published in Proc. of the International Symposium on Mathematical Foundations of Computer Science, MFCS 2008
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1752/1/TR%2D21%2D2008.pdf
Mardare, Radu and Policriti, Alberto (2008) Towards a Complete Axiomatization for Spatial Logic. UNSPECIFIED.
http://eprints.biblio.unitn.it/1752/
oai:eprints.biblio.unitn.it:1753
2012-02-28T14:23:36Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
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Decision problems for Spatial Logics revisited
Mardare, Radu
Policriti, Alberto
QA076.7 Programming Languages - Semantics
Spatial Logics are modal logics developed for process-algebraic semantics. They have been proposed for specifying concurrent properties of dynamic systems and have been proved useful in a wide range of applications. Their expresivity often comes with the price of undecidability, however, even against finite fragments of process calculi. This paper investigates the decidability of satisfiability, validity, and model checking for various Spatial Logics against semantics based on a fragment of CCS that embodies the core features of concurrent behaviors. We prove some decidability and undecidability prop- erties for (combinations of) basic modal operators of spatial logics that entail some of the already known results in the field and provide a taxonomy for this class of problems.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1753/1/TR%2D22%2D2008.pdf
Mardare, Radu and Policriti, Alberto (2008) Decision problems for Spatial Logics revisited. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1753/
oai:eprints.biblio.unitn.it:1754
2012-02-28T14:23:37Z
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74797065733D746563687265706F7274
An analysis of irreversible transitions in a model of the buddying yeast cell cycle
Ballarini, Paolo
Csikasz-Nagy, Attila
Mazza, Tommaso
Palmisano, Alida
QA076.7 Programming Languages - Semantics
Cells life follows a cycling behaviour which starts at cell birth and leads to cell division through a number of distinct phases. The transitions through the various cell cycle phases are controlled by a complex network of signalling pathways. Many cell cycle transitions are irreversible: once they are started they must reach completion. In this study we investigate the existence of conditions which lead to cases when irreversibility may be broken. Specifically, we characterise the elements of the cell cycle signalling network that are responsible for the irreversibility and we determine conditions for which the irreversible transitions may become reversible. We illustrate our results through a formal approach in which stochastic simulation analysis and model checking verification are combined. Through probabilistic model checking we provide a quantitative measure for the probability of irreversibility in the ``Start" transition of the cell cycle. This is the preliminary version of a paper that was published in Proceedings of the third International Workshop on Practical Applications of Stochastic Modelling (PASM 2008), ENTCS 232, pp. 39-53, 2009. (DOI:10.1016/j.entcs.2009.02.049)
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1754/1/TR%2D23%2D2008.pdf
Ballarini, Paolo and Csikasz-Nagy, Attila and Mazza, Tommaso and Palmisano, Alida (2008) An analysis of irreversible transitions in a model of the buddying yeast cell cycle. UNSPECIFIED.
http://eprints.biblio.unitn.it/1754/
oai:eprints.biblio.unitn.it:1755
2012-02-28T14:23:37Z
7374617475733D707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Narrative-based Computational Modelling of the Gp130/JAK/STAT Signalling Pathway
Dudka, Anna
Guerriero, Maria Luisa
Heath, John
Priami, Corrado
Underhill-Day, Nicholas
QA076.7 Programming Languages - Semantics
Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by “in silico” experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format. We introduce this approach by presenting a computational model of the gp130/JAK/STAT signalling pathway derived from a biological narrative and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then “experiment” on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. This is the preliminary version of a paper that was published in BMC Systems Biology, 3:40, 2009. The original publication is available at http://www.biomedcentral.com/1752-0509/3/40
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1755/1/TR%2D24%2D2008.pdf
Dudka, Anna and Guerriero, Maria Luisa and Heath, John and Priami, Corrado and Underhill-Day, Nicholas (2008) Narrative-based Computational Modelling of the Gp130/JAK/STAT Signalling Pathway. UNSPECIFIED.
http://eprints.biblio.unitn.it/1755/
oai:eprints.biblio.unitn.it:1756
2012-02-28T14:23:38Z
7374617475733D756E707562
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
Graph Transformations and Game Theory: A Generative Mechanism for Network Formation
Cavaliere, Matteo
Csikasz-Nagy, Attila
Jordan, Ferenc
QA076.7 Programming Languages - Semantics
Many systems can be described in terms of networks with characteristic structural properties. To better understand the formation and the dynamics of complex networks one can develop generative models. We propose here a generative model (named dynamic spatial game) that combines graph transformations and game theory. The idea is that a complex network is obtained by a sequence of node-based transformations determined by the interactions of nodes present in the network. We model the node-based transformations by using graph grammars and the interactions between the nodes by using game theory. We illustrate dynamic spatial games on a couple of examples: the role of cooperation in tissue formation and tumor development and the emergence of patterns during the formation of ecological networks.
2008
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1756/1/TR%2D25%2D2008.pdf
Cavaliere, Matteo and Csikasz-Nagy, Attila and Jordan, Ferenc (2008) Graph Transformations and Game Theory: A Generative Mechanism for Network Formation. UNSPECIFIED. (Unpublished)
http://eprints.biblio.unitn.it/1756/
oai:eprints.biblio.unitn.it:1790
2012-10-24T11:12:16Z
7374617475733D756E707562
7375626A656374733D4B:4B31
7375626A656374733D51:5141:51413736:514137362E37
74797065733D7072657072696E74
Copyright law, Contract law, Rights Expression Languages and Value-Centered Design Approach
Moscon, Valentina
K Law (General)
QA076.7 Programming Languages - Semantics
Technological instrument constitutes a mean for pursuing the human goals . Technique is an human intelligence’s product: scientific and technological development has characterized the culture evolution. Nowadays, however, the technical means are so much increasing that man is loosing control over them. There are many ways interpret the relationship between technology and society: some scholars assume technology is an independent and autonomous force ; other describe it as a factor that defines how we relate to the world we live in. The “neutralists”, on the other hand, believe technology is nothing but a tool and has no bearing on our behavioural freedom as such. The technique could be used for different goals: for the freedom but also for the oppression, for the centralisation of power, as for decentralization. The technique seeks to conceal its power declaring its diversity from political power because of its neutrality and objectivity. In the digital environment, the development of Digital Rights Management (DRM) systems, demonstrates (not only in the copyright area) the power of technology to supplement and even supplant legal regulation. Much as physical barriers and spatial relations constrain behaviour in actual space, technical standards constrain behaviour in cyberspace. In the physical world, people cannot walk through solid walls or occupy two spaces simultaneously. Similarly, there are certain activities that simply cannot be performed on a particular computer system, because the system is not built to accommodate the behaviour – the system may be programmed to deny access without a password, prevent logging on simultaneously from two terminals, or prohibit alteration of a file that is designed “read only”. In cyberspace , however, how Lessig (and other scholars) argued, the prevailing instrument of regulation is not the rule of law, but what he calls architecture: the commands that are embedded in the communication protocols of the Internet and the software application. Human behaviour is steered by this invisible hand. Technical standards, which are within the control of the designer, conferring on him the power to “govern” behaviour with regard to that system, become a “law”. In other words, the information “code” is becoming, de facto, a regulation built in architecture: the code structures the users freedom and behaviour as a given: no alternatives are visible and no choice can be made. In the information environment, each step in the advancement of technology and particularly in the communication technology, enable maximum access and individual expression, but maximum control over individual behaviour, as well. The implications and mutual relations between technique and law are incontestable and the tie is even stronger in the digital technologies environment : the law evolves with and adapts to the technical development. At the same time the technique reveals new forms of regulation. One can distinguish several interactions between information technology and law, in summary it would be said: 1. Code could partly complements law. We can think, for instance, of the speed limits enforced though law and supported by constructed bumps in the road. 2. Law regulate code. The laws regulating technological measures that are used to protect copyrighted works may serve as an example of that relationship (See Dir. 2001/29 EU and DMCA in U.S.). 3. Code development influences law itself. Because technological standards control user behaviour, they may directly supplant competing legal rule sets (DRM, for instance) . In legal terms, the latter perspective seems to be the most risky because it opens the doors to company self-regulation threating fundamental rights
2009
Preprint
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1790/1/RELs_and_valuecenterddesign_approach.doc.pdf
Moscon, Valentina (2009) Copyright law, Contract law, Rights Expression Languages and Value-Centered Design Approach. [Preprint] (Unpublished)
http://eprints.biblio.unitn.it/1790/
oai:eprints.biblio.unitn.it:1817
2012-02-28T14:24:01Z
7374617475733D7375626D6974746564
7375626A656374733D51:5141:51413736
7375626A656374733D51:5141:51413736:514137362E37
74797065733D746563687265706F7274
ResEval: An Open and Resource-oriented Research Impact Evaluation tool
Muhammad, Imran
Marchese, Maurizio
Ragone, Azzurra
Birukou, Aliaksandr
Casati, Fabio
Jara Laconich, Juan Jose
QA076.7 Programming Languages - Semantics
QA076 Computer software
In this paper we present the concepts and the architecture of an open and resource-oriented tool for evaluating research impact of individual researchers and groups. The advantages of the tool are that it relies on several sources for computing metrics, freely available on the Internet, and provide an easy way for defining and computing custom metrics for individuals and research groups.
2010-02
Departmental Technical Report
NonPeerReviewed
application/pdf
http://eprints.biblio.unitn.it/1817/1/ResEval_An_open_and_resource_oriented_impact_evaluation_tool.pdf
Muhammad, Imran and Marchese, Maurizio and Ragone, Azzurra and Birukou, Aliaksandr and Casati, Fabio and Jara Laconich, Juan Jose (2010) ResEval: An Open and Resource-oriented Research Impact Evaluation tool. UNSPECIFIED. (Submitted)
http://eprints.biblio.unitn.it/1817/
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