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DecoMetDIA: Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS-Based Untargeted Metabolomics

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ANALYTICAL CHEMISTRY 2019年第18期91卷 11897-11904页

作者： Yin, Yandong Wang, Ruohong Cai, Yuping Wang, Zhuozhong Zhu, Zheng-Jiang Chinese Acad Sci Shanghai Inst Organ Chem Interdisciplinary Res Ctr Biol & Chem Shanghai 200032 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

SWATH-MS-based data-independent acquisition mass spectrometry (DIA-MS) technology has been recently developed for untargeted metabolomics due to its capability to acquire all MS2 spectra with high quantitative accuracy. However, software tools for deconvolving multiplexed MS/MS spectra from SWATH-MS with high efficiency and high quality are still lacking in untargeted metabolomics. Here, we developed a new software tool, namely, DecoMetDIA, to deconvolve multiplexed MS/MS spectra for metabolite identification and support the SWATH-based untargeted metabolomics. In DecoMetDIA, multiple model peaks are selected to model the coeluted and unresolved chromatographic peaks of fragment ions in multiplexed spectra and decompose them into a linear combination of the model peaks. DecoMetDIA enabled us to reconstruct the MS2 spectra of metabolites from a variety of different biological samples with high coverages. We also demonstrated that the deconvolved MS2 spectra from DecoMetDIA were of high accuracy through comparison to the experimental MS2 spectra from data-dependent acquisition (DDA). Finally, about 90% of deconvolved MS2 spectra in various biological samples were successfully annotated using software tools such as MetDNA and Sirius. The results demonstrated that the deconvolved MS2 spectra obtained from DecoMetDIA were accurate and valid for metabolite identification and structural elucidation. The comparison of DecoMetDIA to other deconvolution software such as MS-DIAL demonstrated that it performs very well for small polar metabolites.

关键词： Metabolomics Deconvolution programming tool

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Designing tools that Allows Children in the Early Childhood to Program Robots 4th

Designing Tools that Allows Children in the Early Childhood ...

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4th International Conference on Learning and Collaboration Technologies (LCT) Held as Part of 19th International Conference on Human-Computer Interaction (HCI International)

作者： Ramirez-Benavides, Kryscia Lopez, Gustavo Guerrero, Luis A. Univ Costa Rica San Jose Costa Rica

ISBN: (纸本)9783319585154;9783319585147

This paper describes the design and evaluation process of two mobile programming assistance tools that allow children in the early childhood to develop programs and execute them using robots. The tools are called TITIBOTS and TITIBOTS Colab which incorporates collaboration. The tools have icon-based interfaces and integrate visual programming, robotics, and mobile devices as one tool. The main issues and lessons learned during the design process are described. The methodology used in this project was User-Centered Design (UCD) process. The tools were developed and evaluated applying participatory-design, experience prototyping, and usability testing. The final product are two simple, intuitive, and easy to use tools, for children between 4 and 6 years old. The results were promising: children liked the applications and were willing to continue using it to program robots for solving specific tasks.

关键词： User interfaces and Human computer interaction Interaction design User-Centered Design Early childhood education programming tool programming robots

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Programmer Productivity Analyzer tool 8

Programmer Productivity Analyzer Tool

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8th IEEE International Conference on Computational Intelligence and Computing Research (IEEE ICCIC)

作者： Tejaswini Patil, Srushti Salimath, Suman Naik, Venuprasad Nandi, Ritam Patil, Mahesh S. Bidari, Indira Chickerur, Satyadhyan BVB Coll Engn & Technol Dept Comp Sci & Engn Hubli India KLE Technol Univ Ctr High Performance Comp Hubballi 580031 Karnataka India

ISBN: (纸本)9781509066216

Software companies seek for productive programmer who writes codes that are reusable, maintainable, efficient and documented with coding standards. But companies face challenges in finding and monitoring such programmers due to lack of programmer productivity measuring tools. The available tools are limited to measure parameters like coding standards, bugs and some rule violation. Hence there is need for tools that can measure bad programming constructs, reusability and specific demands of companies in coding to judge a programmer. This paper proposes a novel method and tool to measure programmer productivity based on parameters such as efficient usage of memory and machine cycles. It also assist programmer to improve their productivity. The tool is able to detect 3-4 types and 1-2 types of bad programming constructs in code written by novices and experienced programmers respectively. In future, the tool shall be designed to measure the productivity using other parameters reusability and maintainable.

关键词： Programmer productivity efficient programmer ANTLR bad programming constructs bugs programming tool

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AN APPLICATION INTEGRATED INTO AN LEARNING MANAGEMENT SYSTEM FOR TEACHING AND EVALUATION ENGINEERING DISCIPLINES 16

AN APPLICATION INTEGRATED INTO AN LEARNING MANAGEMENT SYSTEM...

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16th International Multidisciplinary Scientific Geoconference (SGEM 2016)

作者： Runceanu, Adrian Cercel, Constantin Borcosi, Ilie Grofu, Florin Constantin Brancusi Univ Targu Jiu Targu Jiu Romania

ISBN: (纸本)9786197105674

The teaching and evaluation of computer programming is very difficult. The checking of lab topics and making recommendations to all students is a time consuming activity and therefore each teacher had to use tools to automatically check the solutions for problems and exercises proposed. In this article we designed a MOOC (Massive Open Online Course) type application that can be integrated into LMS (Learning Management System) Moodle. This learning environment provides a user interface through which the student interacts by proposing solutions to the proposed problems meanwhile evaluating the results. In recent years the e-learning applications have developed a lot and that is why support platforms for e-learning have evolved proposing new approaches and a range of technical solutions. These solutions have transformed the learning / evaluation in a more efficient activity due the immediately feed-back offered to students. In many universities are using MOOC platforms, approaching increasingly more courses for students. In this article we present a model of application adapted for an introductory teaching course called Computer programming, for students of the technical faculties.

关键词： programming tool e-learning Learning Management System Moodie Massive Open Online Course

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ProSe: A programming tool for Rapid Prototyping of Sensor Networks

ProSe: A Programming Tool for Rapid Prototyping of Sensor Ne...

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1st International ICST Conference on Sensor Systems and Software (S-CUBE 2009)

作者： Arumugam, Mahesh Kulkarni, Sandeep S. Cisco Syst Inc San Jose CA 95134 USA Michigan State Univ E Lansing MI 48823 USA

ISBN: (纸本)9783642115271

We focus on application of abstract network protocols towards prototyping sensor networks. Such abstract programs exist for several applications, e.g., routing, tracking, dissemination, etc. These programs are often specified in terms of event-driven actions where the program responds to actions in the environment or previous actions taken by the program. Hence, they are easy to specify, verify and manipulate. However, they cannot be applied directly in sensor networks as the computation model in sensor networks (write all with collision) differs from that (read/write or shared memory) used in abstract programs. Towards this end, we propose ProSe, a programming tool that enables the designers to (1) specify protocols in simple, abstract models, (2) reuse existing fault-tolerant/self-stabilizing protocols from the literature, and (3) automatically generate and deploy code. ProSe hides the deficiencies of existing programming platforms that require the designers to explicitly deal with buffer management, stack management, and flow control. As a result, we expect that ProSe will enable rapid prototyping and quick deployment of protocols.

关键词： programming tool Network Protocols Sensor Networks

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Improvement of P-CUBE: Algorithm Education tool for Visually Impaired Persons

Improvement of P-CUBE: Algorithm Education Tool for Visually...

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Robotic Intelligence In Informationally Structured Space (RiiSS)

作者： Kakehashi, Shun Motoyoshi, Tatsuo Koyanagi, Ken'ichi Oshima, Toru Masuta, Hiroyuki Kawakami, Hiroshi Toyama Prefectural Univ Dept Intelligent Syst Design Engn Kurokawa 5180 Imizu Toyama Japan Kyoto Univ Unit Design Sakyo Ku Kyoto Kyoto Japan

ISBN: (纸本)9781479944644

As a method of teaching fundamental programming concepts to visually impaired persons and novice programmers, we developed the P-CUBE algorithm education tool, with which users are able to control a mobile robot simply by positioning wooden blocks on a mat. The fundamental programming concepts taught by P-CUBE consist of three elements: sequences, branches and loops. The P-CUBE system consists of a mobile robot, a program mat, programming blocks, and a personal computer (PC). The programming blocks utilize radio frequency identification (RFID) tags alone, and thus require no precision equipment such as microcomputers. Furthermore, since P-CUBE is designed to be operated via tactile information, it can be utilized by visually impaired persons. In this paper, we report on the P-CUBE system configuration and a programming workshop held for visuarlly impaired persons. We then propose P-CUBE device improvements formulated through subjective assessments obtained from workshop participants.

关键词： Algorithm education Block interface Tangible interface programming tool

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PROVIZ: An Integrated Visualization and Programming Framework for WSNs

PROVIZ: An Integrated Visualization and Pro...

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38th Annual IEEE Conference on Local Computer Networks (LCN)

作者： Chandrasekar, Ramalingam K. Uluagac, A. Selcuk Beyah, Raheem Georgia Inst Technol Sch Elect & Comp Engn Commun Assurance & Performance Grp Atlanta GA 30332 USA

ISBN: (纸本)9781479905409

Wireless Sensor Networks (WSNs) are rapidly gaining popularity in various critical domains like health care, critical infrastructure, and climate monitoring, where application builders have diversified development needs. Independent of the functionalities provided by the WSN applications, many of the developers use visualization, simulation, and programming tools. However, these tools are designed as separate stand-alone applications, which force developers to use multiple tools. This situation often poses confusion and hampers an efficient development experience. To avoid the complexity of using multiple tools, we have designed a new extensible, multi-platform, scalable, and open-source framework called PROVIZ, which is an integrated visualization and programming framework. In this paper, we explain the various features of PROVIZ's visualization and programming framework and discuss how PROVIZ can be used as a visual debugging tool to aid in providing a software fix.

关键词： Wireless Sensor Networks PROVIZ Visualization and Monitoring tool programming tool Simulation tool

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RA: ResearchAssistant for the computational sciences 07

RA: ResearchAssistant for the computational sciences

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Proceedings of the 2007 workshop on Experimental computer science

作者： Daniel Ramage Adam J. Oliner Stanford University Stanford CA

ISBN: (纸本)9781595937513

Computational experiments often discard large amounts of valuable data, such as invocation parameters and the lineage of output. Our goal is to identify, manage, capture, and organize this information. These data can be used to make the scientific process simpler and more efficient, and to increase the value of the research by making it more rigorous and reproducible. Research Assistant (RA) is an open source Java programming tool that helps to plug this information leak. RA ensures that all console output is valid XML; saves invocation parameters, the random seed, and code version information; automatically checkpoints intermediate results; creates runnable experiment packages; and keeps meticulous notes. This paper presents the design and implementation of RA, and shows how RA easily scales to make complex experiments repeatable.

关键词： reproducible research programming tool Reproducibility Java XML

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Feasibility study on CFD code acceleration using FPGA

Feasibility study on CFD code acceleration using FPGA

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10th World Multi-Conference on Systemics, Cybernetics and Informatics/12th International Conference on Information Systems Analysis and Synthesis

作者： Fujita, Naoyuki Japan Aerosp Explorat Agcy JAXA Chofu Tokyo 1828522 Japan

ISBN: (纸本)9789806560680

In this paper, we studied if tools are available for FORTRAN user to use the FPGA-based custom computer, and the feasibility to improve CFD code execution time using FPGA-based custom computer. By designing pipeline structure using FPGA, 38.1 to 468.3 times execution time acceleration will be expected by doing logical circuit simulation.

关键词： computational fluid dynamics FORTRAN programming tool FPGA custom computer pipeline

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Canica: An ide for the Java Modeling Language

Canica: An ide for the Java Modeling Language

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10th IASTED International Conference on Software Engineering and Applications

作者： Perez, Angelica B. Cheon, Yoonsik Gates, Ann Q. Univ Texas Dept Comp Sci El Paso TX 79968 USA

ISBN: (纸本)9780889866423

Canica is an integrated development environment for the Java Modeling Language (JML), a formal behavioral interface specification language for Java. The JML distribution includes several support tools, such as a syntax checker, a compiler, and a document generator, and there are several third-party tools available for JML. However, most of these tools are command-line-based and work in isolation. Canica glues and streamlines these tools to provide a GUI-based, integrated environment for JML;for example, it automates unit testing including test data generation, test execution, and test result determination. In this paper, we describe the key features of Canica and explain its design and implementation. We also discuss the lessons that we learned from our development effort.

关键词： integrated development environment specification tool programming tool unit test Java Modeling Language

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