Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

Towards formal models and languages for verifiable Multi-Robot Systems

Incorrect operations of a Multi-Robot System (MRS) may not only lead to unsatisfactory results, but can also cause economic losses and threats to safety. These threats may not always be apparent, since they may arise as unforeseen consequences of the interactions between elements of the system. This call for tools and techniques that can help in providing guarantees about MRSs behaviour. We think that, whenever possible, these guarantees should be backed up by formal proofs to complement traditional approaches based on testing and simulation. We believe that tailored linguistic support to specify MRSs is a major step towards this goal. In particular, reducing the gap between typical features of an MRS and the level of abstraction of the linguistic primitives would simplify both the specification of these systems and the verification of their properties. In this work, we review different agent-oriented languages and their features; we then consider a selection of case studies of interest and implement them useing the surveyed languages. We also evaluate and compare effectiveness of the proposed solution, considering, in particular, easiness of expressing non-trivial behaviour.Comment: Changed formattin

An architecture and methodology for the design and development of Technical Information Systems

In order to meet demands in the context of Technical Information Systems (TIS) pertaining to reliability, extensibility, maintainability, etc., we have developed an architectural framework with accompanying methodological guidelines for designing such systems. With the framework, we aim at complex multiapplication information systems using a repository to share data among applications. The framework proposes to keep a strict separation between Man-Machine-Interface and Model data, and provides design and implementation support to do this effectively.\ud The framework and methodological guidelines have been developed in the context of the ESPRIT project IMPRESS. The project also provided for ldquotesting groundsrdquo in the form of a TIS for the Spanish Electricity company Iberdrola.\ud This work has been conducted within the ESPRIT project IMPRESS (Integrated, Multi-Paradigm, Reliable and Extensible Storage System), ESPRIT No. 635

Huddl: the Hydrographic Universal Data Description Language

Since many of the attempts to introduce a universal hydrographic data format have failed or have been only partially successful, a different approach is proposed. Our solution is the Hydrographic Universal Data Description Language (HUDDL), a descriptive XML-based language that permits the creation of a standardized description of (past, present, and future) data formats, and allows for applications like HUDDLER, a compiler that automatically creates drivers for data access and manipulation. HUDDL also represents a powerful solution for archiving data along with their structural description, as well as for cataloguing existing format specifications and their version control. HUDDL is intended to be an open, community-led initiative to simplify the issues involved in hydrographic data access

Multi-touch 3D Exploratory Analysis of Ocean Flow Models

Modern ocean flow simulations are generating increasingly complex, multi-layer 3D ocean flow models. However, most researchers are still using traditional 2D visualizations to visualize these models one slice at a time. Properly designed 3D visualization tools can be highly effective for revealing the complex, dynamic flow patterns and structures present in these models. However, the transition from visualizing ocean flow patterns in 2D to 3D presents many challenges, including occlusion and depth ambiguity. Further complications arise from the interaction methods required to navigate, explore, and interact with these 3D datasets. We present a system that employs a combination of stereoscopic rendering, to best reveal and illustrate 3D structures and patterns, and multi-touch interaction, to allow for natural and efficient navigation and manipulation within the 3D environment. Exploratory visual analysis is facilitated through the use of a highly-interactive toolset which leverages a smart particle system. Multi-touch gestures allow users to quickly position dye emitting tools within the 3D model. Finally, we illustrate the potential applications of our system through examples of real world significance

Supporting user-oriented analysis for multi-view domain-specific visual languages

This is the post-print version of the final paper published in Information and Software Technology. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2008 Elsevier B.V.The integration of usable and flexible analysis support in modelling environments is a key success factor in Model-Driven Development. In this paradigm, models are the core asset from which code is automatically generated, and thus ensuring model correctness is a fundamental quality control activity. For this purpose, a common approach is to transform the system models into formal semantic domains for verification. However, if the analysis results are not shown in a proper way to the end-user (e.g. in terms of the original language) they may become useless. In this paper we present a novel DSVL called BaVeL that facilitates the flexible annotation of verification results obtained in semantic domains to different formats, including the context of the original language. BaVeL is used in combination with a consistency framework, providing support for all steps in a verification process: acquisition of additional input data, transformation of the system models into semantic domains, verification, and flexible annotation of analysis results. The approach has been validated analytically by the cognitive dimensions framework, and empirically by its implementation and application to several DSVLs. Here we present a case study of a notation in the area of Digital Libraries, where the analysis is performed by transformations into Petri nets and a process algebra.Spanish Ministry of Education and Science and MODUWEB

Designing Improved Sediment Transport Visualizations

Monitoring, or more commonly, modeling of sediment transport in the coastal environment is a critical task with relevance to coastline stability, beach erosion, tracking environmental contaminants, and safety of navigation. Increased intensity and regularity of storms such as Superstorm Sandy heighten the importance of our understanding of sediment transport processes. A weakness of current modeling capabilities is the ability to easily visualize the result in an intuitive manner. Many of the available visualization software packages display only a single variable at once, usually as a two-dimensional, plan-view cross-section. With such limited display capabilities, sophisticated 3D models are undermined in both the interpretation of results and dissemination of information to the public. Here we explore a subset of existing modeling capabilities (specifically, modeling scour around man-made structures) and visualization solutions, examine their shortcomings and present a design for a 4D visualization for sediment transport studies that is based on perceptually-focused data visualization research and recent and ongoing developments in multivariate displays. Vector and scalar fields are co-displayed, yet kept independently identifiable utilizing human perception\u27s separation of color, texture, and motion. Bathymetry, sediment grain-size distribution, and forcing hydrodynamics are a subset of the variables investigated for simultaneous representation. Direct interaction with field data is tested to support rapid validation of sediment transport model results. Our goal is a tight integration of both simulated data and real world observations to support analysis and simulation of the impact of major sediment transport events such as hurricanes. We unite modeled results and field observations within a geodatabase designed as an application schema of the Arc Marine Data Model. Our real-world focus is on the Redbird Artificial Reef Site, roughly 18 nautical miles offshor- Delaware Bay, Delaware, where repeated surveys have identified active scour and bedform migration in 27 m water depth amongst the more than 900 deliberately sunken subway cars and vessels. Coincidently collected high-resolution multibeam bathymetry, backscatter, and side-scan sonar data from surface and autonomous underwater vehicle (AUV) systems along with complementary sub-bottom, grab sample, bottom imagery, and wave and current (via ADCP) datasets provide the basis for analysis. This site is particularly attractive due to overlap with the Delaware Bay Operational Forecast System (DBOFS), a model that provides historical and forecast oceanographic data that can be tested in hindcast against significant changes observed at the site during Superstorm Sandy and in predicting future changes through small-scale modeling around the individual reef objects

Atomic: an open-source software platform for multi-level corpus annotation

This paper presents Atomic, an open-source platform-independent desktop application for multi-level corpus annotation. Atomic aims at providing the linguistic community with a user-friendly annotation tool and sustainable platform through its focus on extensibility, a generic data model, and compatibility with existing linguistic formats. It is implemented on top of the Eclipse Rich Client Platform, a pluggable Java-based framework for creating client applications. Atomic - as a set of plug-ins for this framework - integrates with the platform and allows other researchers to develop and integrate further extensions to the software as needed. The generic graph-based meta model Salt serves as Atomic’s domain model and allows for unlimited annotation levels and types. Salt is also used as an intermediate model in the Pepper framework for conversion of linguistic data, which is fully integrated into Atomic, making the latter compatible with a wide range of linguistic formats. Atomic provides tools for both less experienced and expert annotators: graphical, mouse-driven editors and a command-line data manipulation language for rapid annotation