Design and implementation of a generalized laboratory data model

<p>Abstract</p> <p>Background</p> <p>Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable.</p> <p>Results</p> <p>We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in <it>ad hoc </it>ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions.</p> <p>Conclusion</p> <p>The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.</p

A model of a generalized chip structure

Three distinct levels can be distinguished in the design of digital systems: architecture, implementation and realization. Description methods are available at each level assuming that at the realization level components such as nands and nors are used. The introduction of programmable components, such as microprocessors and programmable input/output chips, which now form the basis elements at the realization level, forces to reconsider these description methods

Synthesis and control of generalised dynamically substructured systems

The experimental technique for testing engineering systems via the method of dynamic substructuring is receiving significant global interest, for example in the fields of large-scale structural, aerospace, and automotive system testing. Dynamically substructured systems (DSSs) enable full-size, critical components of a complete system to be physically tested in real-time, within a laboratory environment, while the remainder of the system is modelled numerically. The intention is that the combined physical-numerical DSS behaves as if it were the complete (or emulated) system.In an ideal mechanical DSS, for example, perfect synchronization of displacements and forces at the interfaces between the numerical and physical components (or substructures) is required. Hence, a key design feature of successful DSS systems is the high fidelity of the control action. Equally, a DSS controller must be able to cope with non-linear, time-varying, and uncertain parameters within the physical substructure dynamics.The main purpose of this paper is to present a generalized DSS framework, together with associated linear and adaptive control strategies, that are specifically tailored to achieve high synchronization performance. The initial studies of this problem, as described in an earlier paper by Stoten and Hyde, are therefore continued by generalizing both the DSS dynamics and the control strategies to include (a) a number of newly defined modes of operation and (b) multivariable dynamics. In addition, comparative implementation and simulation studies are included, based upon the DSS testing of a mechanical system (a planar quasi-motorcycle rig), which was specifically designed to highlight the main features of this research. The comparative studies show that excellent DSS control can be achieved, especially with the addition of an adaptive component to the controller, despite significant changes to the physical substructure dynamics

GraphBLAST: A High-Performance Linear Algebra-based Graph Framework on the GPU

High-performance implementations of graph algorithms are challenging to implement on new parallel hardware such as GPUs because of three challenges: (1) the difficulty of coming up with graph building blocks, (2) load imbalance on parallel hardware, and (3) graph problems having low arithmetic intensity. To address some of these challenges, GraphBLAS is an innovative, on-going effort by the graph analytics community to propose building blocks based on sparse linear algebra, which will allow graph algorithms to be expressed in a performant, succinct, composable and portable manner. In this paper, we examine the performance challenges of a linear-algebra-based approach to building graph frameworks and describe new design principles for overcoming these bottlenecks. Among the new design principles is exploiting input sparsity, which allows users to write graph algorithms without specifying push and pull direction. Exploiting output sparsity allows users to tell the backend which values of the output in a single vectorized computation they do not want computed. Load-balancing is an important feature for balancing work amongst parallel workers. We describe the important load-balancing features for handling graphs with different characteristics. The design principles described in this paper have been implemented in "GraphBLAST", the first high-performance linear algebra-based graph framework on NVIDIA GPUs that is open-source. The results show that on a single GPU, GraphBLAST has on average at least an order of magnitude speedup over previous GraphBLAS implementations SuiteSparse and GBTL, comparable performance to the fastest GPU hardwired primitives and shared-memory graph frameworks Ligra and Gunrock, and better performance than any other GPU graph framework, while offering a simpler and more concise programming model.Comment: 50 pages, 14 figures, 14 table

Unifying an Introduction to Artificial Intelligence Course through Machine Learning Laboratory Experiences

This paper presents work on a collaborative project funded by the National Science Foundation that incorporates machine learning as a unifying theme to teach fundamental concepts typically covered in the introductory Artificial Intelligence courses. The project involves the development of an adaptable framework for the presentation of core AI topics. This is accomplished through the development, implementation, and testing of a suite of adaptable, hands-on laboratory projects that can be closely integrated into the AI course. Through the design and implementation of learning systems that enhance commonly-deployed applications, our model acknowledges that intelligent systems are best taught through their application to challenging problems. The goals of the project are to (1) enhance the student learning experience in the AI course, (2) increase student interest and motivation to learn AI by providing a framework for the presentation of the major AI topics that emphasizes the strong connection between AI and computer science and engineering, and (3) highlight the bridge that machine learning provides between AI technology and modern software engineering

Designing Software Architectures As a Composition of Specializations of Knowledge Domains

This paper summarizes our experimental research and software development activities in designing robust, adaptable and reusable software architectures. Several years ago, based on our previous experiences in object-oriented software development, we made the following assumption: ‘A software architecture should be a composition of specializations of knowledge domains’. To verify this assumption we carried out three pilot projects. In addition to the application of some popular domain analysis techniques such as use cases, we identified the invariant compositional structures of the software architectures and the related knowledge domains. Knowledge domains define the boundaries of the adaptability and reusability capabilities of software systems. Next, knowledge domains were mapped to object-oriented concepts. We experienced that some aspects of knowledge could not be directly modeled in terms of object-oriented concepts. In this paper we describe our approach, the pilot projects, the experienced problems and the adopted solutions for realizing the software architectures. We conclude the paper with the lessons that we learned from this experience

Application Of Nonlinear Models For A Well-defined Description Of The Dynamics Of Rotors In Magnetic Bearings

A research report has been submitted. It deals with implementing a method for a mathematical description of the nonlinear dynamics of rotors in magnetic bearings of different types (passive and active). The method is based on Lagrange-Maxwell differential equations in a form similar to that of Routh equations in mechanics. The mathematical models account for such nonlinearities as the nonlinear dependencies of magnetic forces on gaps in passive and active magnetic bearings and on currents in the windings of electromagnets; nonlinearities related to the inductances in coils; the geometric link between the electromagnets in one AMB and the link between all AMBs in one rotor, which results in relatedness of processes in orthogonal directions, and other factors. The suggested approach made it possible to detect and investigate different phenomena in nonlinear rotor dynamics. The method adequacy has been confirmed experimentally on a laboratory setup, which is a prototype of a complete combined magnetic-electromagnetic suspension in small-size rotor machinery. Different variants of linearizing the equations of motion have been considered. They provide for both linearization of restoring magnetic or electromagnetic forces in passive and active magnetic bearings, and exclusion of nonlinear motion equation terms. Calculation results for several linearization variants have been obtained. An appraisal of results identified the drawbacks of linearized mathematical models and allowed drawing a conclusion on the necessity of applying nonlinear models for a well-defined description of the dynamics of rotor systems with magnetic bearings

Enabling High-Dimensional Hierarchical Uncertainty Quantification by ANOVA and Tensor-Train Decomposition

Hierarchical uncertainty quantification can reduce the computational cost of stochastic circuit simulation by employing spectral methods at different levels. This paper presents an efficient framework to simulate hierarchically some challenging stochastic circuits/systems that include high-dimensional subsystems. Due to the high parameter dimensionality, it is challenging to both extract surrogate models at the low level of the design hierarchy and to handle them in the high-level simulation. In this paper, we develop an efficient ANOVA-based stochastic circuit/MEMS simulator to extract efficiently the surrogate models at the low level. In order to avoid the curse of dimensionality, we employ tensor-train decomposition at the high level to construct the basis functions and Gauss quadrature points. As a demonstration, we verify our algorithm on a stochastic oscillator with four MEMS capacitors and 184 random parameters. This challenging example is simulated efficiently by our simulator at the cost of only 10 minutes in MATLAB on a regular personal computer.Comment: 14 pages (IEEE double column), 11 figure, accepted by IEEE Trans CAD of Integrated Circuits and System

A Process Algebra Software Engineering Environment

In previous work we described how the process algebra based language PSF can be used in software engineering, using the ToolBus, a coordination architecture also based on process algebra, as implementation model. In this article we summarize that work and describe the software development process more formally by presenting the tools we use in this process in a CASE setting, leading to the PSF-ToolBus software engineering environment. We generalize the refine step in this environment towards a process algebra based software engineering workbench of which several instances can be combined to form an environment

Crossing the death valley to transfer environmental decision support systems to the water market

Environmental decision support systems (EDSSs) are attractive tools to cope with the complexity of environmental global challenges. Several thoughtful reviews have analyzed EDSSs to identify the key challenges and best practices for their development. One of the major criticisms is that a wide and generalized use of deployed EDSSs has not been observed. The paper briefly describes and compares four case studies of EDSSs applied to the water domain, where the key aspects involved in the initial conception and the use and transfer evolution that determine the final success or failure of these tools (i.e., market uptake) are identified. Those aspects that contribute to bridging the gap between the EDSS science and the EDSS market are highlighted in the manuscript. Experience suggests that the construction of a successful EDSS should focus significant efforts on crossing the death-valley toward a general use implementation by society (the market) rather than on development.The authors would like to thank the Catalan Water Agency (Agència Catalana de l’Aigua), Besòs River Basin Regional Administration (Consorci per la Defensa de la Conca del Riu Besòs), SISLtech, and Spanish Ministry of Science and Innovation for providing funding (CTM2012-38314-C02-01 and CTM2015-66892-R). LEQUIA, KEMLG, and ICRA were recognized as consolidated research groups by the Catalan Government under the codes 2014-SGR-1168, 2013-SGR-1304 and 2014-SGR-291.Peer ReviewedPostprint (published version