Per Year

@article{btssocbio-jcm2013,
   apice = {BTSSOCbioJCM2013},
   author = {González-Pérez, Pedro Pablo and Cárdenas-García, Maura and Montagna, Sara},
   eissn = {1792-8850},
   iris = {11585/521588},
   issn = {1792-7625},
   journal = {Journal of Computations \& Modelling},
   keywords = {Signal transduction, Anti-apoptotic signalling pathways, Biochemical Tuple Spaces for Self-Organising Coordination, Tuple space-based computational framework},
   number = 2,
   pages = {35--65},
   publisher = {Scienpress Ltd},
   title = {Understanding the PI3K/AKT Anti-Apoptotic Signalling Pathway: a Tuple Space-Based Computational Framework for Simulating the Signal Transduction},
   volume = 3,
   year = 2013
}

@inproceedings{selforg-sasow2012,
   abstract = {Pervasive context-aware computing networks call for designing algorithms for information propagation and reconfiguration that promote self-adaptation, namely, which can guarantee - at least to a probabilistic extent - certain reliability and robustness properties in spite of unpredicted changes and conditions. The possibility of formally analysing their properties is obviously an essential engineering requirement, calling for general-purpose models and tools. As proposed in recent works, several such algorithms can be modelled by the notion of "computational field": a dynamically evolving spatial data structure mapping every node of the network to a data value. Based on this idea, as a contribution toward formally verifying properties of pervasive computing systems, in this article we propose a specification language to model computational fields, and a framework based on PRISM stochastic model checker explicitly targeted at supporting temporal property verification, exploited for quantitative analysis of systems running on networks composed of hundreds of nodes.},
   apice = {SelforgSasow2012},
   author = {Stevenson, Graeme and Ye, Juan and Dobson, Simon and Viroli, Mirko and Montagna, Sara},
   booktitle = {Self-Adaptive and Self-Organizing Systems Workshops (SASOW)},
   doi = {10.1109/SASOW.2012.39},
   editor = {Pitt, Jeremy},
   isbn = {978-1-4673-5153-9},
   keywords = {bio-inspired, resource discovery, semantic matching},
   month = apr,
   note = {2012 IEEE Sixth International Conference (SASOW 2012), Lyon, France, 10-14~} # sep # {~2012. Proceedings},
   pages = {181--186},
   publisher = {IEEE CS},
   title = {Self-Organising Semantic Resource Discovery for Pervasive Systems},
   year = 2013
}

@inproceedings{sem-matching-sac2013,
   apice = {SemMatchingSAC2013},
   author = {Stevenson, Graeme and Ye, Juan and Dobson, Simon and Pianini, Danilo and Montagna, Sara and Viroli, Mirko},
   booktitle = {SAC},
   editor = {Shin, Sung Y. and Maldonado, José Carlos},
   isbn = {978-1-4503-1656-9},
   location = {Coimbra, Portugal},
   month = mar,
   pages = {1369--1376},
   publisher = {ACM},
   title = {Combining self-organisation, context-awareness and semantic reasoning: the case of resource discovery in opportunistic networks.},
   url = {http://dblp.uni-trier.de/db/conf/sac/sac2013.html#StevensonYDPMV13},
   year = 2013
}

@article{montagna-monet2012,
   abstract = {Pervasive service ecosystems are a new paradigm for the design of context-aware systems featuring adaptivity and self-awareness. A theoretical and practical framework has been proposed for addressing these scenarios, taking primary inspirations from natural ecosystems and grounding upon two basic abstractions: ``live semantic annotations'' (LSAs), which are descriptions stored in infrastructure nodes and wrapping data, knowledge, and activities of humans, devices, and services; and ``eco-laws'', acting as system rules evolving the population of LSAs as if they were molecules subject to chemical-like reactions. In this paper, we aim at deepening how self-organisation can be injected in pervasive service ecosystems in terms of spatial structures and algorithms for supporting the design of context-aware applications. To this end, we start from an existing classification of self-organisation patterns, and systematically show how they can be supported in pervasive service ecosystems, and be composed to generate a self-organising emergent behaviour. A paradigmatic crowd steering case study is used to demonstrate the effectiveness of our approach.},
   apice = {SapereMONET2012},
   author = {Montagna, Sara and Viroli, Mirko and Jose Luis Fernandez-Marquez and Giovanna Di Marzo Serugendo and Franco Zambonelli},
   doi = {10.1007/s11036-012-0411-1},
   eissn = {1572-8153},
   issn = {1383-469X},
   journal = {Mobile Networks and Applications},
   keywords = {Pervasive Computing, Self-organisation, Chemical-inspired computing},
   number = 3,
   numpages = 15,
   pages = {398--412},
   publisher = {Springer Netherlands},
   title = {Injecting Self-organisation into Pervasive Service Ecosystems},
   url = {https://link.springer.com/10.1007/s11036-012-0411-1},
   volume = 18,
   year = 2013
}

@article{alchemist-jos2013,
   apice = {AlchemistJos2013},
   author = {Pianini, Danilo and Montagna, Sara and Viroli, Mirko},
   doi = {10.1057/jos.2012.27},
   eissn = {1747-7786},
   issn = {1747-7778},
   journal = {Journal of Simulation},
   keywords = {Stochastic simulation, chemical-oriented computing, pervasive service ecosystems},
   publisher = {Palgrave McMillan},
   title = {Chemical-oriented Simulation of Computational Systems with {ALCHEMIST}},
   url = {https://link.springer.com/10.1057/jos.2012.27},
   year = 2013
}

@article{naco2013,
   apice = {PatternNaco2012},
   author = {Jose Luis Fernandez-Marquez and Giovanna Di Marzo Serugendo and Sara Montagna and Mirko Viroli and Josep Llu\'{\i}s Arcos},
   doi = {10.1007/s11047-012-9324-y},
   journal = {Natural Computing},
   number = 1,
   pages = {43--67},
   title = {Description and composition of bio-inspired design patterns: a complete overview},
   volume = 12,
   year = 2013
}

@inproceedings{sitrecognition-asensis2012,
   address = {SASO 2012, Lyon, France},
   apice = {SitrecognitionSasow2012},
   author = {Stevenson, Graeme and Fernandez-Marquez, Jose Luis and Montagna, Sara and Rosi, Alberto and Ye, Juan and Tchao, Akla and Dobson, Simon and Serugendo, Giovanna Di Marzo and Viroli, Mirko},
   booktitle = {Self-Adaptive and Self-Organizing Systems Workshops (SASOW)},
   doi = {10.1109/SASOW.2012.46},
   editor = {Pitt, Jeremy},
   isbn = {978-1-4673-5153-9},
   month = apr,
   note = {2012 IEEE Sixth International Conference (SASOW 2012), Lyon, France, 10-14~} # sep # {~2012. Proceedings},
   pages = {223--228},
   publisher = {IEEE CS},
   title = {Towards Situated Awareness in Urban Networks: A Bio-Inspired Approach},
   year = 2013
}

@inproceedings{selfcomposition-scw2013,
   address = {AAMAS 2013, Saint Paul, Minnesota, USA},
   apice = {SelfcompositionScw2013},
   author = {Montagna, Sara and Viroli, Mirko},
   booktitle = {6th International Spatial Computing Workshop (SCW 2013)},
   editor = {Giavitto, Jean-Louis and Dulman, Stefan and Spicher, Antoine and Viroli, Mirko},
   month = {6~} # may,
   note = {Proceedings},
   pages = {67--72},
   title = {Composing Gradients for a Context-Aware Navigation of Users in a Smart-City},
   year = 2013
}

@inproceedings{montagna-sac12,
   abstract = {The development of multicellular organisms, from the early forms of zygote, involves a range of phenomena that control cell growth and differentiation, making the overall process of morphogenesis highly complex. A well studied example of such a huge phenomenon is given by Drosophila Melanogaster morphogenesis that has been object of several models, whose main goal was to investigate the mechanisms involved in the spatial and temporal evolution of the patterning process. They have been identified in gene regulatory network, morphogen diffusion, synthesis and degradation. In this paper we present a model of Drosophila development that considers also nuclear division and movements as basic morphogenetic mechanisms. The model is run on top of a prototype simulator which is based on a variation of an existing SSA (Stochastic Simulation Algorithm), tailored to the specific features of embryo development, including dynamicity of compartment network topology.},
   address = {Riva del Garda (Trento), Italy},
   apice = {BioSac2012},
   author = {Montagna, Sara and Pianini, Danilo and Viroli, Mirko},
   booktitle = {Proceedings of the 27th Annual ACM Symposium on Applied Computing (SAC 2012)},
   editor = {Dongwan Shin and Chih-Cheng Hung and Jiman Hong},
   isbn = {978-1-4503-0857-1},
   month = {26-30 March},
   numpages = 7,
   pages = {1406--1412},
   publisher = {ACM},
   title = {A Model for Drosophila Melanogaster Development from a Single Cell to Stripe Pattern Formation},
   venue = {SAC},
   year = 2012
}

@inproceedings{anticipativegradient-saso12,
   apice = {AnticipativegradientSaso2012},
   author = {Montagna, Sara and Pianini, Danilo and Viroli, Mirko},
   booktitle = {Proceedings of 6th IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO 2012)},
   doi = {10.1109/SASO.2012.25},
   isbn = {978-1-4673-3126-5},
   isbn13 = {978-0-7695-4851-7},
   keywords = {Anticipative adaptation, Pervasive service ecosystem, Gradient pattern},
   location = {Lyon, France},
   month = sep,
   pages = {169--174},
   publisher = {IEEE Computer Society},
   title = {Gradient-based Self-organisation Patterns of Anticipative Adaptation},
   venue = {SASO},
   year = 2012
}

@inproceedings{sapereecolaws-sac2012,
   address = {Riva del Garda, TN, Italy},
   apice = {SapereEcoLawsSac2012},
   author = {Viroli, Mirko and Pianini, Danilo and Montagna, Sara and Stevenson, Graeme},
   booktitle = {27th Annual ACM Symposium on Applied Computing (SAC 2012)},
   doi = {10.1145/2245276.2245336},
   editor = {Ossowski, Sascha and Lecca, Paola and Hung, Chih-Cheng and Hong, Jiman},
   isbn = {978-1-4503-0857-1},
   month = {26--30~} # mar,
   publisher = {ACM},
   title = {Pervasive Ecosystems: a Coordination Model based on Semantic Chemistry},
   url = {https://dl.acm.org/doi/10.1145/2245276.2245336},
   year = 2012
}

@inproceedings{semmatch-asensis2012,
   address = {SASO 2012, Lyon, France},
   apice = {SemmatchAsensis2012},
   author = {Stevenson, Graeme and Viroli, Mirko and Ye, Juan and Montagna, Sara and Dobson, Simon},
   booktitle = {1st International Workshop on Adaptive Service Ecosystems: Natural and Socially Inspired Solutions (ASENSIS 2012)},
   editor = {Fernandez-Marquez, Jos\'e Luis and Montagna, Sara and Omicini, Andrea and Zambonelli, Franco},
   month = {10~} # sep,
   note = {Pre-proceedings},
   pages = {47--52},
   title = {Self-organising Semantic Resource Discovery for Pervasive Systems},
   year = 2012
}

@incollection{montagna-morphoeng,
   apice = {MorphoEngBook13},
   author = {Montagna, Sara and Viroli, Mirko},
   booktitle = {Morphogenetic Engineering},
   doi = {10.1007/978-3-642-33902-8_15},
   editor = {Doursat, Ren\'e and Sayama, Hiroki and Michel, Olivier},
   isbn = {978-3-642-33901-1},
   language = {English},
   pages = {383--405},
   publisher = {Springer Berlin Heidelberg},
   series = {Understanding Complex Systems},
   title = {A Computational Framework for Multilevel Morphologies},
   url = {https://doi.org/10.1007/978-3-642-33902-8_15},
   year = 2012
}

@incollection{biocore-bionetics2011,
   affiliation = {University of Geneva, Switzerland},
   apice = {BiocoreBionetics2011},
   author = {Fernandez-Marquez, Jose Luis and Serugendo, Giovanna Di Marzo and Montagna, Sara},
   booktitle = {Bio-Inspired Models of Networks, Information, and Computing Systems},
   editor = {Hart, Emma and Timmis, Jon and Mitchell, Paul and Nakamo, Takadash and Dabiri, Foad and Akan, Ozgur and Bellavista, Paolo and Cao, Jiannong and Dressler, Falko and Ferrari, Domenico and Gerla, Mario and Kobayashi, Hisashi and Palazzo, Sergio and Sahni, Sartaj and Shen, Xuemin (Sherman) and Stan, Mircea and Xiaohua, Jia and Zomaya, Albert and Coulson, Geoffrey},
   isbn = {978-3-642-32711-7},
   keywords = {Computer Science},
   note = {10.1007/978-3-642-32711-7_5},
   pages = {59--72},
   publisher = {Springer Berlin Heidelberg},
   series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering},
   title = {BIO-CORE: Bio-inspired Self-organising Mechanisms Core},
   url = {https://doi.org/10.1007/978-3-642-32711-7_5},
   volume = 103,
   year = 2012
}

@proceedings{preproceedings-asensis2012,
   address = {SASO 2012, Lyon, France},
   apice = {PreproceedingsAsensis2012},
   booktitle = {1st International Workshop on Adaptive Service Ecosystems: Natural and Socially Inspired Solutions (ASENSIS 2012)},
   editor = {Fernandez-Marquez, José Luis and Montagna, Sara and Omicini, Andrea and Zambonelli, Franco},
   iris = {11585/126918},
   month = {10~} # sep,
   note = {Pre-proceedings},
   title = {1st International Workshop on Adaptive Service Ecosystems: Natural and Socially Inspired Solutions (ASENSIS 2012)},
   year = 2012
}

@inproceedings{selfcomp-woa2012,
   abstract = {Pervasive service ecosystems are emerging as a new paradigm for understanding and designing future pervasive computing systems featuring high degrees of scale, openness, adaptivity and toleration of long-term evolution. A key issue in this context is making certain patterns of behaviour emerge without any supervision or design-time intention, and a primary example is the fully-spontaneous composition of services, possibly at multiple levels. We argue that this can be successfully achieved only by a comprehensive approach exploiting together the main ingredients proposed so far in literature: (i) existence of intel- ligent components finding proper (semantic) matches of service descriptions, (ii) use of distributed evolutionary techniques to dynamically select appropriate ways of composing services, and (iii) approaches in which rating quality of composition is solely based on their successful exploitation. This proposal is presented through an example of spontaneous composition in crowd steering services.},
   apice = {SelfCompWOA2012},
   author = {Montagna, Sara and Viroli, Mirko and Pianini, Danilo and Jose Luis Fernandez-Marquez},
   booktitle = {Proceedings of the 13th Workshop on Objects and Agents},
   editor = {Flavio De Paoli and Giuseppe Vizzari},
   issn = {1613-0073},
   month = {12 September},
   publisher = {CEUR-WS},
   title = {Towards a comprehensive approach to spontaneous self-composition in pervasive ecosystems},
   urlpdf = {http://ceur-ws.org/Vol-892/paper1.pdf},
   venue = {WOA},
   year = 2012
}

@article{nettab-embnetjournal2012,
   apice = {CardenasBTSSOCmodel},
   author = {Cárdenas-García, Maura and González-Pérez, Pedro Pablo and Montagna, Sara},
   doi = {10.14806/ej.18.B.563},
   journal = {EMBnet.journal},
   number = {B},
   title = {Simulation of caspases apoptotic signalling pathway in a tuple space-based bioinformatics infrastructure},
   url = {https://journal.embnet.org/index.php/embnetjournal/article/view/563},
   volume = 18,
   year = 2012
}

@inproceedings{pianini-woa2011,
   address = {Rende, Italy},
   apice = {PianiniWoa2011},
   author = {Pianini, Danilo and Viroli, Mirko and Montagna, Sara},
   booktitle = {WOA 2011 -- XII Workshop Nazionale ``Dagli Oggetti agli Agenti''},
   editor = {Fortino, Giancarlo and Garro, Alfredo and Palopoli, Luigi and Russo, Wilma and Spezzano, Giandomenico},
   issn = {1613-0073},
   month = {4-6~} # jul,
   pages = {150--157},
   publisher = {Sun SITE Central Europe, RWTH Aachen University},
   series = {CEUR Workshop Proceedings},
   title = {A Simulation Framework for Pervasive Services Ecosystems},
   url = {https://ceur-ws.org/Vol-741/ID15_PianiniViroliMontagna.pdf},
   volume = 741,
   year = 2011
}

@inproceedings{selforg-bads11,
   address = {Karlsruhe, Germany},
   apice = {SelforgpatternBads2011},
   author = {Fernandez-Marquez, Jose Luis and Arcos, Josep Lluis and Di Marzo Serugendo, Giovanna and Viroli, Mirko and Montagna, Sara},
   booktitle = {3rd Workshop on Bio-Inspired and Self-* Algorithms for Distributed Systems},
   month = {14~} # jun,
   publisher = {ACM},
   title = {Description and Composition of Bio-Inspired Design Patterns: the Gradient Case},
   year = 2011
}

@article{spatial-taas11,
   abstract = {To support and engineer the spatial coordination of distributed pervasive services, we propose a chemical-inspired model, which extends tuple spaces with the ability of evolving tuples mimicking chemical systems, that is, in terms of reaction and diffusion rules that apply to tuples modulo semantic match. The suitability of this model is studied by considering a self-adaptive display infrastructure providing people nearby with several visualization services (advertisements, news, personal and social content). The key result of this article is that general-purpose chemical reactions inspired by population dynamics can be used in pervasive applications to enact spatial computing patterns of competition and gradient-based interaction.},
   address = {New York, NY, USA},
   apice = {SpatialTaas11},
   author = {Viroli, Mirko and Casadei, Matteo and Montagna, Sara and Franco Zambonelli},
   doi = {10.1145/1968513.1968517},
   issn = {1556-4665},
   journal = {ACM Transactions on Autonomous and Adaptive Systems},
   keywords = {Chemical-inspired computation, tuple spaces},
   month = {June},
   number = 2,
   numpages = 24,
   pages = {14:1--14:24},
   publisher = {ACM},
   title = {Spatial Coordination of Pervasive Services through Chemical-inspired Tuple Spaces},
   url = {https://doi.acm.org/10.1145/1968513.1968517},
   urlpdf = {http://portal.acm.org/ft_gateway.cfm?id=1968517&ftid=991523&dwn=1&CFID=31487229&CFTOKEN=42827646},
   venue = {TAAS},
   volume = 6,
   year = 2011
}

@phdthesis{montagna-phdthesis11,
   address = {Bologna, Italy},
   apice = {MontagnaPhDThesis11},
   author = {Montagna, Sara},
   institution = {Alma Mater Studiorum--Università di Bologna},
   keywords = {Morphogenesis, Developmental Biology, Self-Organisation, Computational Biology, Multi-level Models, Formal Methods, Agent-based Model, Stochastic Simulation, Meta-heuristic, Parameter Optimisation},
   month = mar,
   school = {Dottorato in Ingegneria Elettronica, Informatica e delle Telecomunicazioni},
   title = {Multi-level models and infrastructures for simulating biological system development},
   year = 2011
}

@inproceedings{pianini-mass2011,
   abstract = {This paper grounds on the SAPERE project (Self-Aware PERvasive Service Ecosystems), which aims at proposing a multi-agent framework for pervasive computing, based on the idea of making each agent (service, device, human) manifest its existence in the ecosystem by a ~~Live Semantic Annotation~~ (LSA), and of coordinating agent activities by a small and fixed set of so-called ~~eco-laws~~ - sort of chemical-like reactions over patterns of LSAs. System dynamics in SAPERE is complex because of opennes and due to the self-* requirements imposed by the pervasive computing setting: a simulation framework is hence needed for what-if analysis prior to deployment. In this paper we present a prototype simulator we are developing. Due to the role of chemical-like dynamics, this is based on a variation of an existing SSA (Stochastic Simulation Algorithm), suitable tailored to the specific features of SAPERE, including dynamicity of network topology, pattern-based application of eco-laws, and temporal triggers. The simulator is tested on a crowd steering scenario where the navigation of groups is guided towards the preferential destination by showing the direction on public or private screens.},
   address = {Szczecin, Poland},
   apice = {PianiniMASS11},
   author = {Pianini, Danilo and Montagna, Sara and Viroli, Mirko},
   booktitle = {Proceedings of the Federated Conference on Computer Science and Information Systems (FedCSIS 2011)},
   editor = {Maria Ganzha and Leszek Maciaszek and Marcin Paprzycki},
   isbn = {978-83-60810-22-4},
   month = {18-21 September},
   numpages = 8,
   pages = {667--674},
   publisher = {IEEE Computer Society Press},
   title = {A Chemical Inspired Simulation Framework for Pervasive Services Ecosystems},
   url = {https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6078316},
   venue = {MASS},
   year = 2011
}

@incollection{montagna-serene2011,
   address = {Geneva, Switzerland},
   apice = {Montagna-Serene2011},
   author = {Montagna, Sara and Viroli, Mirko and Risoldi, Matteo and Pianini, Danilo and Di Marzo Serugendo, Giovanna},
   booktitle = {3rd International Workshop on Software Engineering for Resilient Systems},
   doi = {10.1007/978-3-642-24124-6_12},
   keywords = {pervasive computing, software ecosystems, self-adaptation, self-organisation},
   month = {29--30~} # sep,
   pages = {115--129},
   publisher = {Springer},
   series = {Lecture Notes in Computer Science},
   title = {Self-organising Pervasive Ecosystems: A Crowd Evacuation Example},
   url = {https://link.springer.com/10.1007/978-3-642-24124-6_12},
   volume = 6968,
   year = 2011
}

@article{montagna2010115,
   apice = {BionetCs2bio10},
   author = {Montagna, Sara and Viroli, Mirko},
   doi = {10.1016/j.entcs.2010.12.009},
   issn = {1571-0661},
   journal = {Electronic Notes in Theoretical Computer Science},
   keywords = {Formal methods, Multi-level model, Developmental biology},
   month = dec,
   note = {Proceedings of the 1st International Workshop on Interactions between Computer Science and Biology (CS2Bio'10)},
   pages = {115--129},
   publisher = {Elsevier Science B.V.},
   title = {A Framework for Modelling and Simulating Networks of Cells},
   volume = 268,
   year = 2010
}

@incollection{biosimulation-massimulationbook09,
   apice = {BiosimulationMabsbook09},
   author = {d'Inverno, Mark and Howells, Paul and Montagna, Sara and Roeder, Ingo and Saunders, Rob},
   booktitle = {Multi-Agent Systems: Simulation and Applications},
   chapter = 13,
   editor = {Uhrmacher, Adelinde M. and Weyns, Danny},
   isbn = {978-1-4200-7023-1},
   isbn10 = {1-4200-7023-1},
   keywords = {Multi-Agent Based Simulation, Computational Biology, Stem cells, Multi-level model},
   month = jun,
   pages = {389--418},
   publisher = {CRC Press},
   series = {Computational Analysis, Synthesis, and Design of Dynamic Systems},
   title = {Agent-based Modelling of Stem Cells},
   url = {https://crcpress.com/product/isbn/9781420070231},
   year = 2009
}

@proceedings{montagnaroli-aixia09,
   abstract = {In this paper we address the problem of tuning parameters of a biological model, in particular a simulator of stochastic processes. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. We tackle the problem with a metaheuristic algorithm for continuous variables, Particle swarm optimisation, and show the effectiveness of the method in a prominent case-study, namely the mitogen-activated protein kinase cascade.},
   apice = {BiometaheuristicAIxIA09},
   author = {Montagna, Sara and Roli, Andrea},
   booktitle = {AI*IA 2009: Emergent Perspectives in Artificial Intelligence – XIth International Conference of the Italian Association for Artificial Intelligence Reggio Emilia, Italy, December 9-12, 2009 Proceedings},
   doi = {10.1007/978-3-642-10291-2},
   editor = {Roberto Serra and Rita Cucchiara},
   isbn = {978-3-642-10290-5},
   numpages = 10,
   pages = {466--475},
   publisher = {Springer Berlin / Heidelberg},
   series = {Lecture Notes in Computer Science},
   title = {Parameter tuning of a stochastic biological simulator by metaheuristics},
   volume = 5883,
   year = 2009
}

@inproceedings{bioframework-cec09,
   abstract = {A state-of-the-art problem in Computational Systems Biology is to provide suitable tools to model and predict the behaviour of multicellular systems (tissues, embryos) where biological interactions occur both inside and between cells (or compartments in general). Starting from existing computational models and languages such as stochastic pi-calculus, Petri Nets, mobile ambients, and membrane computing, we developed a new computational framework based on {{{(i)}} a compositional model for biological compartments, and (ii) an enhanced model of chemical rules addressing also biomechanical actions such as substances diffusion across membranes or compartments splitting. We tested the framework using a case study based on spatial pattern formation in embryogenesis, where the interplay between cells' internal dynamics and cell-to-cell interactions seems to have a central role.}},
   address = {Trondheim, Norway},
   apice = {BioframeworkCec09},
   author = {Montagna, Sara and Viroli, Mirko},
   booktitle = {2009 IEEE Congress on Evolutionary Computation (CEC 2009)},
   isbn = {978-1-4244-2959-2},
   month = {18-21 May},
   numpages = 8,
   pages = {2233--2240},
   publisher = {IEEE Computer Society Press},
   title = {A computational framework for modelling multicellular biochemistry},
   year = 2009
}

@inproceedings{abmhsc-masbio08,
   address = {Cittadella dei Musei, Cagliari, Italy},
   apice = {AbmhscMasbio08},
   author = {Montagna, Sara and Omicini, Andrea and Alberti, Marco},
   booktitle = {Intelligenza Artificiale e Scienze della Vita},
   editor = {Armano, Giuliano and Schaerf, Marco and Semeraro, Giovanni},
   iris = {11585/62600},
   lens = {158-373-444-685-517},
   month = sep,
   note = {10\textsuperscript{o} Convegno Associazione Italiana per l'Intelligenza Artificiale (AI*IA 2008), Workshop ``Multi-agent Systems \& Bioinformatics'' (MAS\&BIO 2008). Proceedings},
   openalex = {W3147533462},
   pages = {201--214},
   title = {Lineage Commitment of Hematopoietic Stem Cells: An Agent-based Model},
   year = 2008
}

@inproceedings{sysbio-fosbe07,
   address = {Stuttgart, Germany},
   apice = {SysbioFosbe07},
   author = {Montagna, Sara and Omicini, Andrea and Ricci, Alessandro and d'Inverno, Mark},
   booktitle = {2nd Conference ``Foundations of Systems Biology in Engineering'' (FOSBE 2007)},
   editor = {Allgöwer, Frank and Reuss, Matthias},
   isbn = {978-3-8167-7436-5},
   month = {9--12~} # sep,
   pages = {243--248},
   publisher = {Fraunhofer IBR Verlag},
   title = {Modelling Hematopoietic Stem Cell Behaviour: An Approach Based on Multi-Agent Systems},
   year = 2007
}