Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database.

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.)

C to O-O Translation: Beyond the Easy Stuff

Can we reuse some of the huge code-base developed in C to take advantage of modern programming language features such as type safety, object-orientation, and contracts? This paper presents a source-to-source translation of C code into Eiffel, a modern object-oriented programming language, and the supporting tool C2Eif. The translation is completely automatic and supports the entire C language (ANSI, as well as many GNU C Compiler extensions, through CIL) as used in practice, including its usage of native system libraries and inlined assembly code. Our experiments show that C2Eif can handle C applications and libraries of significant size (such as vim and libgsl), as well as challenging benchmarks such as the GCC torture tests. The produced Eiffel code is functionally equivalent to the original C code, and takes advantage of some of Eiffel's object-oriented features to produce safe and easy-to-debug translations

Cautious Adaptation of Defiant Components

Systems-of-systems are formed by the composition of independently created software components. These components are designed to satisfy their individual requirements, rather than the global requirements of the systems-of-systems. We refer to components that cannot be adapted to meet both individual and global requirements as defiant components. In this paper, we propose a cautious adaptation approach which supports changing the behaviour of such defiant components under exceptional conditions to satisfy global requirements, while continuing to guarantee the satisfaction of the components’ individual requirements. The approach represents both normal and exceptional conditions as scenarios; models the behaviour of exceptional conditions as wrappers implemented using an aspect-oriented technique; and deals with both single and multiple instances of defiant components with different precedence order at runtime. We evaluated an implementation of the approach using drones and boats for an organ delivery application conceived by our industrial partners, in which we assess how the proposed approach helps achieve the system-of-systems’ global requirements while accommodating increased complexity of hybrid aspects such as multiplicity, precedence ordering, openness, and heterogeneity

Re(presenting) habit

Department Head: Gary Wayne Voss.2010 Spring.Includes bibliographical references (pages 46-47).In my work, I cultivate intimate encounters that invite people to contemplate the larger narratives in which we participate. I (re)present objects in order to create microcosms of these narratives. Over the last three years, my interest in stories revealed by artifacts of daily living, particularly those used in significant routines, led to my investigation of the lingering evidence of habitual consumption: receipts, wrappers, and disposable containers. When recontextualized, these ephemera remain potently descriptive of the activities for which they were originally purposed. The things we live among, what we strive to possess, the detritus we try to eliminate—these all shape our notions regarding beauty, position, status, and belonging. Through staged scenarios that incorporate carefully rendered illusions of trash, sometimes incorporating the material presence of these leftovers themselves, In Memoriam construes habitual consumption to be an act of petition, a process of recollection, and an expression of devotion

Programmability and Performance of Parallel ECS-based Simulation of Multi-Agent Exploration Models

While the traditional objective of parallel/distributed simulation techniques has been mainly in improving performance and making very large models tractable, more recent research trends targeted complementary aspects, such as the “ease of programming”. Along this line, a recent proposal called Event and Cross State (ECS) synchronization, stands as a solution allowing to break the traditional programming rules proper of Parallel Discrete Event Simulation (PDES) systems, where the application code processing a specific event is only allowed to access the state (namely the memory image) of the target simulation object. In fact with ECS, the programmer is allowed to write ANSI-C event-handlers capable of accessing (in either read or write mode) the state of whichever simulation object included in the simulation model. Correct concurrent execution of events, e.g., on top of multi-core machines, is guaranteed by ECS with no intervention by the programmer, who is in practice exposed to a sequential-style programming model where events are processed one at a time, and have the ability to access the current memory image of the whole simulation model, namely the collection of the states of any involved object. This can strongly simplify the development of specific models, e.g., by avoiding the need for passing state information across concurrent objects in the form of events. In this article we investigate on both programmability and performance aspects related to developing/supporting a multi-agent exploration model on top of the ROOT-Sim PDES platform, which supports ECS

Asynchronous Validations using Programming Contracts in Java

Design by Contract is a software development methodology based on the idea of having contracts between two software components. Programming contracts are invariants specified as pre-conditions and post-conditions. The client component must ensure that all the pre-conditions are satisfied before calling the server component. The server component must guarantee the post-conditions are met before the call returns to the client component. Current work in Design by Contract in Java focuses on writing shorthand contracts using annotations that are processed serially. Modern software systems require a lot of business rules validations on complicated domain objects. Often, such validations are in the form of a chain of independent tasks that need to be validated one after another. These tasks are computation-intensive and often involve numerous database calls and API calls over the web. This paper presents a validation rule engine framework, Rule4j to facilitate writing such business rules with the help of programming contracts in Java. The contracts are organized in a hierarchy similar to the Racket programming language. The programmer can specify the business rules in the form of a series of higher-order contracts that form a chain. These chains of contracts are validated concurrently and asynchronously to present a final validation result to the programmer. A sample scenario of trade execution is used to demonstrate the performance gain and maintainability of the framework. The experiments conducted show that validations executed using Rule4J run four times faster than the traditional approach. A clear separation of business logic and business validations for the trade execution scenario was achieved using Rule4J

The Vadalog System: Datalog-based Reasoning for Knowledge Graphs

Over the past years, there has been a resurgence of Datalog-based systems in the database community as well as in industry. In this context, it has been recognized that to handle the complex knowl\-edge-based scenarios encountered today, such as reasoning over large knowledge graphs, Datalog has to be extended with features such as existential quantification. Yet, Datalog-based reasoning in the presence of existential quantification is in general undecidable. Many efforts have been made to define decidable fragments. Warded Datalog+/- is a very promising one, as it captures PTIME complexity while allowing ontological reasoning. Yet so far, no implementation of Warded Datalog+/- was available. In this paper we present the Vadalog system, a Datalog-based system for performing complex logic reasoning tasks, such as those required in advanced knowledge graphs. The Vadalog system is Oxford's contribution to the VADA research programme, a joint effort of the universities of Oxford, Manchester and Edinburgh and around 20 industrial partners. As the main contribution of this paper, we illustrate the first implementation of Warded Datalog+/-, a high-performance Datalog+/- system utilizing an aggressive termination control strategy. We also provide a comprehensive experimental evaluation.Comment: Extended version of VLDB paper <https://doi.org/10.14778/3213880.3213888

Why not empower knowledge workers and lifelong learners to develop their own environments?

In industrial and educational practice, learning environments are designed and implemented by experts from many different fields, reaching from traditional software development and product management to pedagogy and didactics. Workplace and lifelong learning, however, implicate that learners are more self-motivated, capable, and self-confident in achieving their goals and, consequently, tempt to consider that certain development tasks can be shifted to end-users in order to facilitate a more flexible, open, and responsive learning environment. With respect to streams like end-user development and opportunistic design, this paper elaborates a methodology for user-driven environment design for action-based activities. Based on a former research approach named 'Mash-Up Personal Learning Environments'(MUPPLE) we demonstrate how workplace and lifelong learners can be empowered to develop their own environment for collaborating in learner networks and which prerequisites and support facilities are necessary for this methodology

Immersive Composition for Sensory Rehabilitation: 3D Visualisation, Surround Sound, and Synthesised Music to Provoke Catharsis and Healing

There is a wide range of sensory therapies using sound, music and visual stimuli. Some focus on soothing or distracting stimuli such as natural sounds or classical music as analgesic, while other approaches emphasize the active performance of producing music as therapy. This paper proposes an immersive multi-sensory Exposure Therapy for people suffering from anxiety disorders, based on a rich, detailed surround-soundscape. This soundscape is composed to include the users’ own idiosyncratic anxiety triggers as a form of habituation, and to provoke psychological catharsis, as a non-verbal, visceral and enveloping exposure. To accurately pinpoint the most effective sounds and to optimally compose the soundscape we will monitor the participants’ physiological responses such as electroencephalography, respiration, electromyography, and heart rate during exposure. We hypothesize that such physiologically optimized sensory landscapes will aid the development of future immersive therapies for various psychological conditions, Sound is a major trigger of anxiety, and auditory hypersensitivity is an extremely problematic symptom. Exposure to stress-inducing sounds can free anxiety sufferers from entrenched avoidance behaviors, teaching physiological coping strategies and encouraging resolution of the psychological issues agitated by the sound