The representation of protein complexes in the Protein Ontology

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/

The failure tolerance of mechatronic software systems to random and targeted attacks

This paper describes a complex networks approach to study the failure tolerance of mechatronic software systems under various types of hardware and/or software failures. We produce synthetic system architectures based on evidence of modular and hierarchical modular product architectures and known motifs for the interconnection of physical components to software. The system architectures are then subject to various forms of attack. The attacks simulate failure of critical hardware or software. Four types of attack are investigated: degree centrality, betweenness centrality, closeness centrality and random attack. Failure tolerance of the system is measured by a 'robustness coefficient', a topological 'size' metric of the connectedness of the attacked network. We find that the betweenness centrality attack results in the most significant reduction in the robustness coefficient, confirming betweenness centrality, rather than the number of connections (i.e. degree), as the most conservative metric of component importance. A counter-intuitive finding is that "designed" system architectures, including a bus, ring, and star architecture, are not significantly more failure-tolerant than interconnections with no prescribed architecture, that is, a random architecture. Our research provides a data-driven approach to engineer the architecture of mechatronic software systems for failure tolerance.Comment: Proceedings of the 2013 ASME International Design Engineering Technical Conferences & Computers and Information in Engineering Conference IDETC/CIE 2013 August 4-7, 2013, Portland, Oregon, USA (In Print

A collaborative platform for integrating and optimising Computational Fluid Dynamics analysis requests

A Virtual Integration Platform (VIP) is described which provides support for the integration of Computer-Aided Design (CAD) and Computational Fluid Dynamics (CFD) analysis tools into an environment that supports the use of these tools in a distributed collaborative manner. The VIP has evolved through previous EU research conducted within the VRShips-ROPAX 2000 (VRShips) project and the current version discussed here was developed predominantly within the VIRTUE project but also within the SAFEDOR project. The VIP is described with respect to the support it provides to designers and analysts in coordinating and optimising CFD analysis requests. Two case studies are provided that illustrate the application of the VIP within HSVA: the use of a panel code for the evaluation of geometry variations in order to improve propeller efficiency; and, the use of a dedicated maritime RANS code (FreSCo) to improve the wake distribution for the VIRTUE tanker. A discussion is included detailing the background, application and results from the use of the VIP within these two case studies as well as how the platform was of benefit during the development and a consideration of how it can benefit HSVA in the future

Generalized Method Of Designing Unmanned Remotely Operated Complexes Based On The System Approach

Self-propelled underwater systems belong to the effective means of marine robotics. The advantages of their use include the ability to perform underwater work in real time with high quality and without risk to the life of a human operator. At present, the design of such complexes is not formalized and is carried out separately for each of the components – a remotely operated vehicle, a tether-cable and cable winch, a cargo device and a control and energy device. As a result, the time spent on design increases and its quality decreases. The system approach to the design of remotely operated complexes ensures that the features of the interaction of the components of the complex are taken into account when performing its main operating modes. In this paper, the system interaction between the components of the complex is proposed to take into account in the form of decomposition of “underwater tasks (mission) – underwater technology of its implementation – underwater work on the selected technology – task for the executive mechanism of the complex” operations. With this approach, an information base is formed for the formation of a list of mechanisms of the complex, the technical appearance of its components is being formed, which is important for the early design stages. Operative, creative and engineering phases of the design of the complex are proposed. For each phase, a set of works has been formulated that cover all the components of the complex and use the author's existence equations for these components as a tool for system analysis of technical solutions.The perspective of the scientific task of the creative phase to create accurate information models of the functioning of the components of the complex and models to support the adoption of design decisions based on a systematic approach is shown.The obtained results form the theoretical basis for finding effective technical solutions in the early stages of designing remotely operated complexes and for automating the design with the assistance of modern applied computer research and design packages

Characterizing urban landscapes using fuzzy sets

Characterizing urban landscapes is important given the present and future projections of global population that favor urban growth. The definition of “urban” on a thematic map has proven to be problematic since urban areas are heterogeneous in terms of land use and land cover. Further, certain urban classes are inherently imprecise due to the difficulty in integrating various social and environmental inputs into a precise definition. Social components often include demographic patterns, transportation, building type and density while ecological components include soils, elevation, hydrology, climate, vegetation and tree cover. In this paper, we adopt a coupled human and natural system (CHANS) integrated scientific framework for characterizing urban landscapes. We implement the framework by adopting a fuzzy sets concept of “urban characterization” since fuzzy sets relate to classes of object with imprecise boundaries in which membership is a matter of degree. For dynamic mapping applications, user-defined classification schemes involving rules combining different social and ecological inputs can lead to a degree of quantification in class labeling varying from “highly urban” to “least urban”. A socio-economic perspective of urban may include threshold values for population and road network density while a more ecological perspective of urban may utilize the ratio of natural versus built area and percent forest cover. Threshold values are defined to derive the fuzzy rules of membership, in each case, and various combinations of rules offer a greater flexibility to characterize the many facets of the urban landscape. We illustrate the flexibility and utility of this fuzzy inference approach called the Fuzzy Urban Index for the Boston Metro region with five inputs and eighteen rules. The resulting classification map shows levels of fuzzy membership ranging from highly urban to least urban or rural in the Boston study region. We validate our approach using two experts assessing accuracy of the resulting fuzzy urban map. We discuss how our approach can be applied in other urban contexts with newly emerging descriptors of urban sustainability, urban ecology and urban metabolism.This research was partially supported by "Boston University Initiative on Cities Early Stage Urban Research Awards 2015-16" (Gopal & Phillips) and the Frederick S. Pardee Center for the Study of the Longer-Range Future at Boston University. We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. (Boston University Initiative on Cities Early Stage Urban Research Awards; Frederick S. Pardee Center for the Study of the Longer-Range Future at Boston University)https://doi.org/10.1016/j.compenvurbsys.2016.02.002Published versio

RTD based logic circuits using generalized threshold gates

Many logic circuit applications of Resonant Tunneling Diodes are based on the MOnostable-BIstable Logic Element (MOBILE). Threshold logic is a computational model widely used in the design of MOBILE circuits, i.e. these circuits are built from threshold gates (TGs). The MOBILE realization of generalized threshold gates is being investigated. Multi-Threshold Threshold Gates (MTTGs) have been proposed which further increase the functionality of the original TGs. Recently, we have proposed a novel MOBILE circuit topology obtained by fundamental properties of threshold functions. This paper describes the design of n-bit adders using these novel MOBILE circuit topologies. A comparison with designs based on TGs and MTTGs is carried out showing advantages in terms of speed and power delay product and device counts.España, Gobierno TEC2007-67245Junta de Andalucía EXC/2007/TIC-296

Building safe software

Murphy is a set of techniques and tools under investigation for their potential in enhancing the safety of software. This paper describes some of the work which has been done and some which is planned

Creating Quality Integrated and Interdisciplinary Arts Programs

The report offers some reflection on arts integration while examining a diverse group of partnerships and a set of new important tools to aid efforts in improving arts teaching and learning across the classroom