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The Musite open-source framework for phosphorylation-site prediction

BMC BIOINFORMATICS 2010年第s12期11卷 S9-S9页

作者： Gao, Jianjiong Xu, Dong Univ Missouri Dept Comp Sci CS Bond Life Sci Ctr Columbia MO 65211 USA

Background: With the rapid accumulation of phosphoproteomics data, phosphorylation-site prediction is becoming an increasingly active research area. More than a dozen phosphorylation-site prediction tools have been released in the past decade. However, there is currently no open-source framework specifically designed for phosphorylation-site prediction except Musite. Results: Here we present the Musite open-source framework for building applications to perform machine learning based phosphorylation-site prediction. Musite was implemented with six modules loosely coupled with each other. With its well-designed Java application programming interface (API), Musite can be easily extended to integrate various sources of biological evidence for phosphorylation-site prediction. Conclusions: Released under the GNU GPL open source license, Musite provides an open and extensible framework for phosphorylation-site prediction. The software with its source code is available at http://***.

关键词： Phosphorylation Site application programming interface Machine Learning Problem Feature Extraction Module Phosphorylation Data

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AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures

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BMC BIOINFORMATICS 2013年第1期14卷 1-7页

作者： Earls, John C. Eddy, James A. Funk, Cory C. Ko, Younhee Magis, Andrew T. Price, Nathan D. Inst Syst Biol Seattle WA 98109 USA Univ Washington Dept Comp Sci & Engn Seattle WA 98195 USA Univ Illinois Dept Bioengn Urbana IL 61801 USA Univ Illinois Ctr Biophys & Computat Biol Urbana IL 61801 USA Univ Illinois Dept Comp Sci Urbana IL 61801 USA

Background: Public databases such as the NCBI Gene Expression Omnibus contain extensive and exponentially increasing amounts of high-throughput data that can be applied to molecular phenotype characterization. Collectively, these data can be analyzed for such purposes as disease diagnosis or phenotype classification. One family of algorithms that has proven useful for disease classification is based on relative expression analysis and includes the Top-Scoring Pair (TSP), k-Top-Scoring Pairs (k-TSP), Top-Scoring Triplet (TST) and Differential Rank Conservation (DIRAC) algorithms. These relative expression analysis algorithms hold significant advantages for identifying interpretable molecular signatures for disease classification, and have been implemented previously on a variety of computational platforms with varying degrees of usability. To increase the user-base and maximize the utility of these methods, we developed the program AUREA (Adaptive Unified Relative Expression Analyzer)-a cross-platform tool that has a consistent application programming interface (API), an easy-to-use graphical user interface (GUI), fast running times and automated parameter discovery. Results: Herein, we describe AUREA, an efficient, cohesive, and user-friendly open-source software system that comprises a suite of methods for relative expression analysis. AUREA incorporates existing methods, while extending their capabilities and bringing uniformity to their interfaces. We demonstrate that combining these algorithms and adaptively tuning parameters on the training sets makes these algorithms more consistent in their performance and demonstrate the effectiveness of our adaptive parameter tuner by comparing accuracy across diverse datasets. Conclusions: We have integrated several relative expression analysis algorithms and provided a unified interface for their implementation while making data acquisition, parameter fixing, data merging, and results analysis 'point- and -click' simple.

关键词： Learning Algorithm application programming interface Package Module Matthews Correlation Coefficient Adaptive Module

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Feature-based integration of conceptual and detailed mould design

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INTERNATIONAL JOURNAL OF PRODUCTION RESEARCH 2011年第16期49卷 4833-4855页

作者： Jong, Wen-Ren Wu, Chun-Hsien Lee, Ming-Yen Chung Yuan Christian Univ Dept Mech Engn Chungli 32023 Taiwan Chung Yuan Christian Univ R&D Ctr Mold & Molding Technol Chungli 32023 Taiwan Taiwan Green Point Enterprise Co Taichung Taiwan

The plastic production industry has been growing rapidly in recent years, and injection mould, which is especially widely used in 4C (computer, communication, consumer electronics, and car) products, is the most popular in moulding plastic. The diverse requirements of customers and pressures of just-in-time production are big challenges in the injection mould industry. The advantages, that keep products' quality and increase work efficiency, will decide a company's competitive capabilities. Therefore, this study proposes a feature-based integration of the conceptual and detailed mould design process within the computer-aided design (CAD) tool. It adopts a feature-oriented method and the dedicated application programming interface (API) to implement the features integration function of the conceptual and detailed mould design. Based on intellectualised, customised, and standardised procedures, not only does this prevent probable engineering mistakes and generate consistent web reports, but also transmits the intact feature information from conceptual to detailed mould design, thus shortening detailed mould design processes. In the case studies of this paper, using the feature-based navigating system can result in time savings up to 56% and 59%. The results show significant time savings over traditional mould design processes.

关键词： feature-based web-based application programming interface conceptual mould design

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RAN-Map: a system for automatically producing API layers from RDF schemas

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JOURNAL OF AMBIENT INTELLIGENCE AND HUMANIZED COMPUTING 2017年第2期8卷 291-299页

作者： Toti, Daniele Rinelli, Marco Roma Tre Univ Dept Sci Rome RM Italy RAN Innovat Srl Rome Italy

This work describes a system for the automatic generation of full-fledged API layers from RDF schemas, providing the whole set of Object-Oriented functionalities to retrieve, store, edit and delete the corresponding data in a semantic Triplestore. The layers the system is capable of producing range from an underlying domain model, resulting from the classes, data properties and object properties of the input schema, to the related lower-level data source and access components, up to higher-level facades and web service interfaces, all of which are immediately operational and can be used out-of-the-box for development purposes either as stand-alone components or integrated into external applications. A user-friendly graphical interface allows for an easy configuration and customization of the generation process to suit specific development needs. Once configured, the execution of the generation process takes place almost instantaneously, bringing about a full set of API components in a matter of seconds and thus dramatically saving design and development time and effort. Experimentation of the system has been carried out within the context of a EU-funded research project featuring a large semantic schema, a significant portion of which represented a Learning Model specifically engineered to be used for a plethora of e-learning solutions;nevertheless, the system is generic enough to be employed for a variety of applications relying upon semantic schemas and data.

关键词： Semantic framework Abstraction layer application programming interface Object-oriented paradigm Mapping Middleware Software Software engineering Triplestore Ontology RDF SPARQL

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Computational Solutions to Lambert's Problem on Modern Graphics Processing Units

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JOURNAL OF GUIDANCE CONTROL AND DYNAMICS 2015年第7期38卷 1306-U15页

作者： Wagner, Sam Wie, Bong Kaplinger, Brian Iowa State Univ Dept Aerosp Engn Asteroid Deflect Res Center Ames IA 50010 USA Florida Inst Technol Dept Mech & Aerosp Engn Melbourne FL 32901 USA

The Battin, Gooding, and Sun algorithms are able to converge for nearly 100% of all orbit combinations. Both the Gooding and Sun algorithms have approximately the same performance, whereas the Battin algorithm is consistently slower. The performance for each Lambert algorithm, when run on the graphics processing unit (GPU), has been compared. Each Lambert solution algorithm is able to compute tens of millions of solutions per second, with Sun's method having the best performance at nearly 32 million solutions per second. This represents an increase in performance of two orders of magnitude when using GPUs over standard CPU algorithms. Although even the grid search CPU run times are not high when compared with common high-performance computing algorithms, mission optimization algorithms often require run times ranging from hours to multiple days. By offloading computations for solutions to Lambert's problem to GPU(s) and sufficiently parallelizing optimization algorithms, performance increases of up to two orders of magnitude can be realized when compared with standard CPU algorithms. This will allow mission designers to quickly compute complex trajectories when evaluating potential mission architectures.

关键词： Lambert Algorithm Graphics Processing Unit Algorithm Performance application programming interface Orbit Determination Highly Elliptical Orbit High Performance Computing Optimization Algorithm Search Algorithm Mars Missions

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Verification of Unstructured Grid Adaptation Components

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AIAA JOURNAL 2020年第9期58卷 3947-3962页

作者： Galbraith, Marshall C. Caplan, Philip C. Carson, Hugh A. Park, Michael A. Balan, Aravind Anderson, W. Kyle Michal, Todd Krakos, Joshua A. Kamenetskiy, Dmitry S. Loseille, Adrien Alauzet, Frederic Frazza, Loic Barral, Nicolas MIT Dept Aeronaut & Astronaut Cambridge MA 02139 USA NASA Langley Res Ctr Computat AeroSci Branch Hampton VA 23681 USA NASA Langley Res Ctr Hampton VA 23681 USA NASA Computat AeroSci Branch Hampton VA 23681 USA Boeing Res & Technol St Louis MO 63042 USA Boeing Res & Technol Seattle WA 98275 USA Natl Inst Res Comp Sci & Automat Paris Saclay GAMMA3 Team Alan Turing Bldg F-91120 Palaiseau France Sorbonne Univ GAMMA3 Team Pierre & Marie Curie Campus4 Pl Jussieu F-75252 Paris 05 France Imperial Coll London Dept Earth Sci & Engn South Kensington Campus London SW7 2AZ England

Unstructured grid techniques have the potential of minimizing discretization errors for production analysis workflows where the control of errors is critical to obtaining reliable simulation results. Recent progress has matured a number of independent implementations of flow solvers, error estimation methods, and anisotropic grid adaptation mechanics. Here, the interoperability of several separately developed unstructured grid adaptation tools is verified using analytic functions and the Code Comparison Principle. Three analytic functions with different smoothness properties are adapted to show the impact of smoothness on implementation differences. A scalar advection-diffusion problem with an analytic solution that models a boundary layer is adapted to test individual grid adaptation components. While optimal asymptotic error convergence rates are achieved with many grid adaptation tool combinations for the scalar problems, the scalar problems also illustrate known differences in grid adaptation component implementations and a previously unknown interaction between components. Laminar flow over a delta wing is verified with multiple, independent grid adaptation procedures to show consistent convergence to fine-grid forces and pitching moment. These verification efforts form the nucleus of a benchmark to verify the integration of unstructured grad adaptation components and support production analysis workflows.

关键词： Unstructured Grid Boundary Layer Freestream Conditions Delta Wing Advection External Flows Courant Friedrichs Lewy Galerkin Finite Element Method Reynolds Averaged Navier Stokes application programming interface

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Serverless Computing for Society 5.0

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IT PROFESSIONAL 2024年第5期26卷 79-84页

作者： Corradi, Antonio Sabbioni, Andrea Univ Bologna Comp Engn I-40136 Bologna Italy Univ Bologna Comp Sci & Engn I-40136 Bologna Italy

The advancement and increasing availability of novel technologies are widely recognized as crucial in building both a more resilient society and a sustainable economy. These technology factors are paving the way to a Society 5.0, where all domains, spanning from economic to technical areas, are encouraged to collaborate in the creation of a more dynamic, reliable, and valuable novel ecosystem. However, the enormous fragmentation in standards and protocols, even worsened by the geographical dispersion of these sources, hinders the integration of typically heterogeneous information data and applications produced by different partners. To solve this problem, new cloud computing models have emerged by proposing abstract interfaces and rapid prototyping of services, to specifically address the intrinsic dynamicity of these environments. In this work, we propose leveraging and evolving serverless cloud computing as support for Society 5.0 service integrations by providing a fast development environment that hides most of the complexities of infrastructure management.

关键词： Protocols Soft Sensors Ecosystems Serverless Computing Rapid Prototyping Security Reliability Sustainable Development Standards Resilience Serverless Computing Cloud Computing Internet Of Things Human Computer Interaction Economic Sustainability Smart City Integration Of Services Society Support Cloud Providers Resilient Societies Novel Ecosystems Start Up Modularity Interoperability application programming interface Triggering Event Specific Implementation Infrastructure Support Cold Start Execution Environment Microservices Execution Of Functions HTTP Requests Business Logic Heterogeneous Data Sources Adaptive Layer Management Layer

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Software Framework for Prototyping Embedded Integrated Vehicle Health Management applications

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JOURNAL OF AEROSPACE INFORMATION SYSTEMS 2014年第2期11卷 82-96页

作者： Sreenuch, T. Tsourdos, A. Jennions, I. K. Cranfield Univ Integrated Vehicle Hlth Management Ctr Cranfield MK43 0AL Beds England Cranfield Univ Dept Engn Phys Cranfield MK43 0AL Beds England

Integrated vehicle health management is a major component in a new, future fleet-management paradigm where a conscious effort is made to shift aircraft maintenance from a schedule-based approach to a more proactive and predictive approach (that is, condition-based maintenance). Its goal is to maximize fleet operational availability while minimizing the logistics footprint through monitoring of the deterioration of equipment conditions. A comprehensive integrated vehicle health-management system will be executed in an environment that includes different sensor technologies, multiple information systems, and different data models. Integrated vehicle healthmanagement implementers have to therefore deal with an integration problem that involves different specialized algorithms and embedded hardware platforms. Integrated vehicle health management applications will have common execution logic, and many will share the same data-processing algorithms;hence, development productivity and the quality of integrated vehicle health management applications can be increased through reusable software building blocks and algorithm libraries or, in particular, by using a software development framework. This paper presents an approach to distributed integrated vehicle health management systems that offers reusable software architecture for a class of integrated vehicle health management applications. The focus of this paper deals with an open software framework for development of integrated vehicle health management applications stemming from the open system architecture for a condition-based maintenance specification, which is an architecture-promoting interoperability and a component framework that enables reuse, data-process partitioning, configuration, and rapid prototyping. The framework is developed using Java and Internet communications engines' distributed middleware, and its application is demonstrated through a gearbox health-monitoring system, where the integrated vehicle he

关键词： Data Processing application programming interface Unified Modeling Language Middleware Technology Central Processing Unit Rapid Prototyping Sensor Technology Aircraft Maintenance Information System Metadata

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Implementation and Benchmarking of Two-Dimensional Vortex Interactions on a Graphics Processing Unit

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JOURNAL OF AEROSPACE INFORMATION SYSTEMS 2014年第6期11卷 372-385页

作者： Chabalko, Christopher C. Balachandran, Balakumar Univ Maryland College Pk MD 20742 USA

A parallel single-instruction multiple data implementation of a two-level nested loop, which uses shared memory, is implemented via general-purpose computing on a graphics processing unit. The general-purpose computing on a graphics processing unit implementation is compared to MATLAB (R), C, and other implementations of the same algorithm, which are primarily executed on the central processing unit. The general-purpose computing on a graphics processing unit implementation is determined to be decisively faster (80 times) than the fastest single threaded implementation. A linear algebra implementation is determined to consume excessive memory without a corresponding increase in computational performance. Although the speedup is hardware dependent, the general-purpose computing on a graphics processing unit algorithm exploits cache memory in a manner that is severely constrained on conventional multicore central processing units. For this reason, the nested loop described here is a natural fit for the single-instruction multiple data shared memory architecture. Details of the implementation are provided. The algorithm is applied to the simulation of vortex dynamics. In particular, it is applied to simulate the rollup of a vortex filament and carry out an unsteady simulation of a thin plate in ground effect. The cases presented here would be intractable to compute without the acceleration offered by the general-purpose computing on a graphics processing unit.

关键词： Vortex Filaments Graphics Processing Unit application programming interface Central Processing Unit General Purpose Computing Biot Savart Law Smoothed Particle Hydrodynamics Convection Discrete Element Method Vorticity

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Orymold: ontology based gene expression data integration and analysis tool applied to rice

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BMC BIOINFORMATICS 2009年第1期10卷 1-12页

作者： Mercade, Jaume Espinosa, Antonio Adsuara, Jose-Enrique Adrados, Rosa Segura, Jordi Maes, Tamara Oryzon Genom Barcelona 08028 Spain

Background: Integration and exploration of data obtained from genome wide monitoring technologies has become a major challenge for many bioinformaticists and biologists due to its heterogeneity and high dimensionality. A widely accepted approach to solve these issues has been the creation and use of controlled vocabularies (ontologies). Ontologies allow for the formalization of domain knowledge, which in turn enables generalization in the creation of querying interfaces as well as in the integration of heterogeneous data, providing both human and machine readable interfaces. Results: We designed and implemented a software tool that allows investigators to create their own semantic model of an organism and to use it to dynamically integrate expression data obtained from DNA microarrays and other probe based technologies. The software provides tools to use the semantic model to postulate and validate of hypotheses on the spatial and temporal expression and function of genes. In order to illustrate the software's use and features, we used it to build a semantic model of rice (Oryza sativa) and integrated experimental data into it. Conclusion: In this paper we describe the development and features of a flexible software application for dynamic gene expression data annotation, integration, and exploration called Orymold. Orymold is freely available for non-commercial users from http://***/media/***

关键词： application programming interface Semantic Model Complex Query Insertion Time Joint Photographic Expert Group

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