Giuseppe Scollo

On discrete models and immunological algorithms for protein structure prediction

Discrete models for protein structure prediction embed the protein amino acid sequence into a discrete spatial structure, usually a lattice, where an optimal tertiary structure is predicted on the basis of simple assumptions relating to the hydrophobic–hydrophilic character of amino acids in the sequence and to relevant interactions for free energy minimization. While the prediction problem is known to be NP complete even in the simple setting of Dill’s model with a 2D-lattice, a variety of bio-inspired algorithms for this problem have been proposed in the literature. Immunological algorithms are inspired by the kind of optimization that immune systems perform when identifying and promoting the replication of the most effective antibodies against given antigens. A quick, state-of-the-art survey of discrete models and immunological algorithms for protein structure prediction is presented in this paper, and the main design and performance features of an immunological algorithm for this problem are illustrated in a tutorial fashion.

Architectural Unit Testing

A formal testing methodology is outlined in this paper, that proves applicable to validation of architectural units in object-oriented models, and its use is illustrated in the context of the design of a robot teleoperation architecture. Automated generation of test cases to validate the functionality of the robot trajectory generation unit showcases the key features of this methodology. A disciplined use of UML state diagrams, to model the units dynamics consistently with its static properties as modeled by class diagrams, enables one to provide such models with Input/Output Labelled Transition Systems (IOLTS) semantics, whence a rich machinery of testing theories and tools based on those theories become readily available. Our case study tells that, besides black-box testing of nal implementation units, white-box analysis of architectural units may greatly benefit from the exibility of parameterized I/O-conformance relations. Test purposes turn out to be a useful methodological link between functional requirements, which they are drawn from, and conformance relations, which they help one to instantiate, thereby delimiting test selection to purposeful tests. Contingent aspects of our methodology include: a mechanical translation of state diagrams in Basic LOTOS, a non-mechanical, use-case driven synthesis of test purposes, expressed in the same language, and the use of the TGV tool for automated test case generation. Other choices in these respects are well possible, without a ecting the characteristic traits of the proposed methodology, that are rather to be found in: 1) the combination of object-oriented architectural modeling with IOLTS semantics; 2) the aim at maximizing the potential for test generation from UML models, in a broad view of testing which applies throughout the development process; 3) the speci c proposal to consider internal actions as testable actions, in view of a better coordination between testing (discovery of faults) and debugging (discovery of internal sources of faults).

A relational view of recurrence and attractors in state transition dynamics

The classical dynamics concepts of recurrence and attractor are analysed in the basic mathematical setting of state transition systems, where both time and space are discrete, and no structure is assumed on the state space besides a binary transition relation. This framework proves useful to the dynamical analysis of computations and biomolecular processes. Here a relational formulation of this framework is presented, where the concepts of attractor and recurrence surface in two variants, respectively relating to the two fundamental modalities. A strong link between recurrence and both existence and extent of attractors, in either variant, is established by a novel characterization theorem.

A temporal ordering specification of some session services

The achievement of widely accepted standards for Open Systems Interconnection (OSI) is closely tied to the ability of producing unambiguous and implementation independent specifications of related protocols and services. LOTOS, the Language fOr Temporal Ordering Specification, is a Formal Description Technique (FDT) whose definition, though not completed, has already reached such a state as to allow trial specifications of rather sophisticated services and protocols. This paper explores the specification in LOTOS of some of the session services whose discussion is underway within various standardization bodies. Conciseness of specification is tried by adopting a few notational variants which are guessed to be useful at various OSI layers. The session services selected for this trial specification comprise the Basic Combined Subset (BCS) enriched with the Expedited Data service.

Some Topics in the Design of the Specification Language Lotos

The definition of Formal Description Techniques is currently being worked out by computer communications standardization bodies in order to produce unambiguous, clear, concise and implementation independent specifications of services and protocols for Open Systems Interconnection (OSI). This paper explores some topics under discussion in the design of one of such techniques, the Language for Temporal Ordering Specification (LOTOS), which has been already used for trial specifications of rather complex protocols and services, though still lacking some essential features like value specification facilities. The language elements rely upon the concepts of synchronized communication events, non deterministic choice between alternative events, value passing, guarding, sequential and parallel composition of processes, process abstraction. Some concepts currently under consideration are argued to be notational variants of the defined language elements; some of them can effectively favour both conciseness and clarity of specification for the intended use of the language. Functional and type abstraction are discussed for what concerns the needed value specification facilities. The addressed topics are illustrated by examples drawn from experience with trial specifications.

Relational state transition dynamics

Abstract Basic concepts of classical dynamics are analysed in the simple mathematical setting of state transition systems, where both time and space are discrete, and no structure is assumed on the state space besides a binary transition relation. This framework proves useful to the dynamical analysis of computations and biomolecular processes. Here a relational formulation of this framework is presented, where the concepts of attractor and recurrence surface in two variants, respectively relating to the two fundamental modalities. A strong link between recurrence and both existence and extent of attractors, in either variant, is established by a novel characterization theorem. Further concepts are easily casted in the relational language, such as product dynamics and projections thereof, which support analysis and reasoning about metabolic P systems. An outline of possible applications and future developments of this work concludes the article.

Strategic planning and service models for the ELViRA project

Building the e-learning policy of a university is a complex process, that involves several stakeholders, requires strategic planning, and relies on a variety of service models and technologies. Requirements on overall system architecture and on eligibility of e-learning technologies follow from strategic planning decisions, and can be expressed as formal constituents of service models. In this work we put forward a few strategic questions that arise in the process of building the e-learning policy of a university where several forms of technology-enhanced learning have been experimented with, some even employing state-of-art methods and devices, but, to date, little attention has been paid to overall co-ordination. The ELViRA project is aimed at promoting adoption of technology-enhanced education methods which would implement strategic decisions on accessibility of educational services, optimality of educational methods, and seamless service integration for undergraduate as well as post-graduate and lifelong education programs. Key strategic questions induce specific traits of service and development models for the ELViRA network architecture, that are argued by way of example.

An Institution Isomorphism for Planar Graph Colouring

Maximal planar graphs with vertex resp. edge colouring are naturally cast as (deceptively similar) institutions. One then tries to embody Tait’s equivalence algorithms into morphisms between them, and is lead to a partial redesign of those institutions. This paper aims at introducing a few pragmatic questions which arise in this case study, which also showcases the use of relational concepts and notations in the design of the subject institutions, and gives an outline of a solution to the problem of designing an isomorphism between them.