1,721,123 research outputs found
On the Characterization and Software Implementation of General Protein Lattice Models
Full text linkAbstract models of proteins have been widely used as a practical means to computationally investigate general properties of the system. In lattice models any sterically feasible conformation is represented as a self-avoiding walk on a lattice, and residue types are limited in number. So far, only two- or three-dimensional lattices have been used. The inspection of the neighborhood of alpha carbons in the core of real proteins reveals that also lattices with higher coordination numbers, possibly in higher dimensional spaces, can be adopted. In this paper, a new general parametric lattice model for simplified protein conformations is proposed and investigated. It is shown how the supporting software can be consistently designed to let algorithms that operate on protein structures be implemented in a lattice-agnostic way. The necessary theoretical foundations are developed and organically presented, pinpointing the role of the concept of main directions in lattice- agnostic model handling. Subsequently, the model features across dimensions and lattice types are explored in tests performed on benchmark protein sequences, using a Python implementation. Simulations give insights on the use of square and triangular lattices in a range of dimensions. The trend of potential minimum for sequences of different lengths, varying the lattice dimension, is uncovered. Moreover, an extensive quantitative characterization of the usage of the so- called ‘‘move types’’ is reported for the first time. The proposed general framework for the development of lattice models is simple yet complete, and an object-oriented architecture can be proficiently employed for the supporting software, by designing ad-hoc classes. The proposed framework represents a new general viewpoint that potentially subsumes a number of solutions previously studied. The adoption of the described model pushes to look at protein structure issues from a more general and essential perspective, making computational investigations over simplified models more straightforward as well
Management and Storage of In-situ Oceanographic Data: An ECM-based Approach
No full textManagement of scientific data poses a number of challenging problems involving both procedures and tools, and the field of operational oceanography makes no exception. During oceanographic cruises, significant amounts of heterogeneous data are collected by means of a wide variety of measuring devices, and the sequences of registered values mostly come as plain text files. Each instrument has its own data format. Raw data parsed from the acquisition files undergo some preliminary processing phases and, at the end, in the form of refined data, they can be considered ready to be kept as actual descriptions of the observed phenomena. This paper, based on experiences carried out in an oceanographic research center, describes problems and possible architectural solutions in managing heterogeneous oceanographic data from collection up to proper repositories. It is shown how a careful employment of ECM (Enterprise Content Manage- ment) systems may be beneficial in this setting, with no need to adopt complex ad-hoc solutions, difficult to be maintained by non-overspecialized personnel. A data model to support the storage of refined data in structured repositories is developed as well. It is well-known that database technology is not pervasive yet in the scientific community, as it is in other areas. The proper concerted use of ECM, DBMS, and possibly scientific workflow frameworks may represent the means to enable an effective adoption and a fruitful exploitation of the existing database technology also in the field of operational oceanography
Extension of Web Server Systems for E-Commerce: Incremental Crowding vs. Functional Doubling-Up
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Performance-steered design of software architectures for embedded multicore systems
No full textMany software applications demanding a considerable computing power are moving towards the field of embedded systems (and, in particular, hand-held devices). A possible way to increase the computing power of this kind of platform, so that both cost and power consumption are kept low, is the employment of multiple CPU cores on the same chipset. Consequently, it is essential to design applications that meet performance requirements leveraging the underlying parallel platform. As embedded applications are usually built using different components (whose source code is often not available) from different companies, the designer can mostly only operate at the architectural level. So far, methodologies for designing software architectures have mainly addressed general-purpose systems, often relying on hardware platforms with a high degree of parallelism. In this paper, we present our experience in architectural design of parallel embedded applications; as a result, we propose a possible methodology for the application design at the architectural level, targeted to embedded systems built upon multicore chipsets with a low degree of parallelism. It makes use of performance predictions, obtained by simulations. Such a methodology can be employed both for retargeting existing sequential applications to parallel processing platforms and for designing complete applications from scratch. We show the application of the proposed methodology to an embedded digital cartographic system. Starting with a software description using UML diagrams, candidate software architectures (utilizing different parallel solutions) are first defined and then evaluated, to end with the selection of the one yielding the highest performance gain
Timestamps for Programs Using Messages and Shared Variables
No full textAlgorithms for vector timestamps have been developed to determine the “happened before” relations between events of an execution of a message passing program. Many message passing programs contain variables shared by multiple processes (including threads). Such programs need to have vector timestamps for send, receive, read and write events. We define two “happened-before” relations, called strong happened-before (SHB) and weak happened-before (WHB), between events of an execution involving send, receive, read and write statements. We then present two timestamp assignment algorithms, one for SHB and the other for WHB, and show how to use such timestamps to determine the SHB or WHB relation between any two events of an execution involving send, receive, read and write statements. For a program containing n processes, the size of a vector timestamp for SHB or WHB is n, regardless of the number of shared variables in the program. Finally, we show how to apply WHB timestamps to perform race analysis for programs using messages and shared variable
Behavior investigation of concurrent Java programs: an approach based on source-code instrumentation
No full textJava makes easier the coding phase of concurrent applications and provides friendly mechanisms for the information exchange among threads and different processes. The nature of communication and synchronization mechanisms and the actual parallelism of a distributed environment introduce potential sources of non-deterministic behavior in concurrent applications. In order to investigate on undesired effects related to non-deterministic behaviors, tracing and replay capabilities can be added to the programming environment. Such capabilities are useful for testing, debugging, monitoring, performance evaluation and program profiling purposes. This paper presents a solution for providing tracing and replay capabilities to a number of Java concurrent applications. Such a solution addresses portability and it is based on the automatic instrumentation of the original source code. Some transformation schemes have been applied to some classes in the standard Java packages in order to make easier and more efficient the automatic instrumentation task. It is shown how the object-oriented structure of Java can be exploited in a deep and efficient way both in the instrumentation and in the tracing and replay phases. (C) 2001 Elsevier Science B.V. All rights reserved
Track on Embedded Systems: New Perspectives for Hardware, System Software, and Applications
No full textInstrumentation of Concurrent Java Applications for Program Behavior Investigation
No full textJava makes easier the coding phase of concurrent applications and provides friendly mechanisms for the information exchange among threads and different processes. The nature of communication and synchronization mechanisms and the actual parallelism of a distributed environment introduce potential sources of non-deterministic behavior in concurrent applications. In order to investigate on undesired effects related to non-deterministic behaviors, tracing and replay capabilities can be added to the programming environment. Such capabilities are useful for testing, debugging, monitoring and performance evaluation purposes. This paper presents a solution for providing tracing and replay capabilities to Java concurrent applications. Such a solution addresses portability and it is based on the automatic instrumentation of the original source code. Some transformation schemes have been applied to some classes in the standard Java packages in order to make easier and more efficient the automatic instrumentation task. It is shown how the object-oriented structure of Java can be exploited in a deep and efficient way both in the instrumentation and in the tracing and replay phases
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