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This paper presents a formal semantics for the Taverna 2 scientific workflow system. Taverna 2 is a successor to Taverna, an open-source workflow system broadly adopted within the e-science community worldwide. The new version improves upon the existing model in two main ways: (i) by adding support for data pipelining, which in turns enables input streams(More)
The conventional model of coalition formation considers every possible subset of agents as a potential coalition. However, in many real-world applications, there are inherent constraints on feasible coalitions: for instance, certain agents may be prohibited from being in the same coalition, or the coalition structure may be required to consist of coalitions(More)
In this paper we propose DFL—a formal, graphical workflow language for dataflows, i.e., workflows where large amounts of complex data are manipulated, and the structure of the manipulated data is reflected in the structure of the workflow. It is a common extension of (1) Petri nets, which are responsible for the organization of the processing tasks, and (2)(More)
A major research challenge in multi-agent systems is the problem of partitioning a set of agents into mutually disjoint coalitions, such that the overall performance of the system is optimized. This problem is difficult because the search space is very large: the number of possible coalition structures increases exponentially with the number of agents.(More)
In this paper we propose a formal, graphical workflow language for dataflows, i.e., workflows where large amounts of complex data are manipulated and the structure of the manipulated data is reflected in the structure of the workflow. It is a common extension of – Petri nets, which are responsible for the organization of the processing tasks, and – Nested(More)
We consider the issue of representing coalitional games in multi-agent systems with externalities (<i>i.e.</i>, in systems where the performance of one coalition may be affected by other co-existing coalitions). In addition to the conventional partition function game representation (<i>PFG</i>), we propose a number of new representations based on a new(More)
Many in silico experiments in bioinformatics can be expressed in the form of workflows where various data-processing steps are connected in a network producing the desired result. Those steps can involve using web-services, invoking software tools, some quick-and-dirty scripts or even manual processing. The process itself is usually data-centered and is(More)
Systems Biology has established numerous approaches for mechanistic modeling of molecular networks in the cell and a legacy of models. The current frontier is the integration of models expressed in different formalisms to address the multi-scale biological system organization challenge. We present MUFINS (MUlti-Formalism Interaction Network Simulator)(More)