检索结果-内蒙古大学图书馆

Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

Journal of Proteomics 2025年 317卷

作者： Zheng, Ping Audain, Enrique Webel, Henry Dai, Chengxin Klein, Joshua Hitz, Marc-Phillip Sachsenberg, Timo Bai, Mingze Perez-Riverol, Yasset Chongqing Key Laboratory of Big Data for Bio Intelligence Chongqing University of Posts and Telecommunications Chongqing China Institute of Medical Genetics University Medicine Oldenburg Carl von Ossietzky University Oldenburg Germany The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Lyngby Denmark State Key Laboratory of Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Life Omics Beijing China Program for Bioinformatics Boston University Boston United States Department of Computer Science Applied Bioinformatics University of Tübingen Tübingen Germany Institute for Bioinformatics and Medical Informatics University of Tübingen Tübingen Germany European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Cambridge United Kingdom

Intensity-based absolute quantification (iBAQ) is essential in proteomics as it allows for the assessment of a protein's absolute abundance in various samples or conditions. However, the computation of these values for increasingly large-scale and high-throughput experiments, such as those using DIA, TMT, or LFQ workflows, poses significant challenges in scalability and reproducibility. Here, we present ibaqpy (https://***/bigbio/ibaqpy), a Python package designed to compute iBAQ values efficiently for experiments of any scale. Ibaqpy leverages the Sample and Data Relationship Format (SDRF) metadata standard to incorporate experimental metadata into the quantification workflow. This allows for automatic normalization and batch correction while accounting for key aspects of the experimental design, such as technical and biological replicates, fractionation strategies, and sample conditions. Designed for large-scale proteomics datasets, ibaqpy can also recompute iBAQ values for existing experiments when an SDRF is available. We showcased ibaqpy's capabilities by reanalyzing 17 public proteomics datasets from ProteomeXchange, covering HeLa cell lines with 4921 samples and 5766 MS runs, quantifying a total of 11,014 proteins. In our reanalysis, ibaqpy is a key component in automating reproducible quantification, reducing manual effort and making quantitative proteomics more accessible while supporting FAIR principles for data reuse. Significance: Proteomics studies often rely on intensity-based absolute quantification (iBAQ) to assess protein abundance across various biological conditions. Despite its widespread use, computing iBAQ values at scale remains challenging due to the increasing complexity and volume of proteomics experiments. Existing tools frequently lack metadata integration, limiting their ability to handle experimental design intricacies such as replicates, fractions, and batch effects. Our work introduces ibaqpy, a scalable Python package that lev

关键词： Big data Bioinformatics Data integration Proteomics Quantification

来源：评论

学校读者我要写书评

暂无评论

Parallel algorithms for verification and sensitivity analysis of minimum spanning trees

Parallel algorithms for verification and sensitivity analysi...

引用

International Conference on Parallel and Distributed Systems (ICPADS)

作者： Weifa Liang Xiaojun Shen Qing Hu Department of Computer Science Australian National University Canberra Australia Computer Science Telecommunications Program University of Missouri KS USA

ISBN: (纸本)0818665556

To verify whether a spanning tree T(V,E) of graph G(V,E') is a minimum spanning tree, two parallel algorithms are presented. The first algorithm requires O(log n) time and O(max{m/log n, n/sup 3/2//log n}) processors, where |E'|=m and |V|=n. The second algorithm requires O(log n) time and O(m) processors or O(log nloglog n) time and O(max{m/log n, n}) processors. The first algorithm is optimal when G is dense, compared with its O(m) time sequential version. The second algorithm has better performance when G is sparse. By using above results, we also present an efficient algorithm for sensitivity analysis of minimum spanning trees which requires O(log n) time and O(max{m, n/sup 2//log n}) processors. All proposed algorithms in this paper are based on the parallel computational model called CREW PRAM.

关键词： Parallel algorithms Sensitivity analysis Tree graphs Costs computer science Cities and towns Concurrent computing Computational modeling Phase change random access memory Computational complexity

来源：评论

学校读者我要写书评

暂无评论

Sensing as a service: An exploration into practical implementations of DSA

Sensing as a service: An exploration into practical implemen...

引用

2010 IEEE Symposium on New Frontiers in Dynamic Spectrum, DySPAN 2010

作者： Weiss, Martin B. H. Delaere, Simon Lehr, William H. Telecommunications Program School of Information Sciences University of Pittsburgh Pittsburgh PA 15260 United States IBBT-SMIT Vrije Universiteit Brussel Belgium Laboratory for Computer Science Massachusetts Institute of Technology United States

ISBN: (纸本)9781424451883

The cognitive radio literature generally assumes that the functions required for non-cooperative secondary DSA are integrated into a single radio system. It need not be so. In this paper, we model cognitive radio functions as a value chain and explore the implications of different forms of organization of this value chain. We initially explore the consequences of separating the sensing function from other cognitive radio functions. ©2010 IEEE.

关键词： Cognitive radio

来源：评论

学校读者我要写书评

暂无评论

Preparing programming teachers 94

Preparing programming teachers

引用

Proceedings of the twenty-fifth SIGCSE symposium on computer science education

作者： Barbara Kushan Computer Science Telecommunications Program University of Missouri--Kansas City Kansas City MO

来源：评论

学校读者我要写书评

暂无评论

An iterative solution to the four-peg Tower of Hanoi problem 90

引用

Proceedings of the 1990 ACM annual conference on Cooperation

作者： Appie van de Liefvoort Computer Science Telecommunications Program University of Missouri-Kansas City Kansas City Missouri

One of the variations of the Towers of Hanoi puzzle allows for p pegs, and for four pegs the solution to this variation is shown to have a simple structure which can be used to derive an iterative solution to the prob...

ISBN: (纸本)9780897913485

关键词：

来源：评论

学校读者我要写书评

暂无评论

Improved fast integer sorting in linear space 01

Improved fast integer sorting in linear space

引用

Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms

作者： Yijie Han Computer Science Telecommunications Program University of Missouri at Kansas City Kansas City MO

ISBN: (纸本)9780898714906

We present improved fast deterministic algorithm for integer sorting in linear space. Our algorithm sorts n integers in linear space in Ο(n log log n log log log n) time. This improves the Ο(n(log log n)3/2) time bound given in [6]. When the n integers in {0,1,…, m - 1} to be sorted satisfying log m ⪈(log n)2+∈, 0 < ∈ < 1, the time complexity for sorting can be further reduced to Ο(n log log n). These results are obtained by applying signature sorting on our previous result[6].

关键词：

来源：评论

学校读者我要写书评

暂无评论

A bandwidth adaptation scheme to support QoS requirements of mobile users in wireless environments

A bandwidth adaptation scheme to support QoS requirements of...

引用

International Conference on computer Communications and Networks (ICCCN)

作者： A. Aljadhai T.F. Znati Computer Technology Department Riyadh College of Telecommunications Riyadh Saudi Arabia Department of Computer Science Telecommunications Program University of Pittsburgh Pittsburgh PA USA

This paper presents an adaptive QoS management scheme to accommodate dynamic variations in network resources, due to the mobility of the users and location-dependent errors. The scheme ensures that satisfactory levels of QoS guarantees are met regardless of the user mobility. QoS adaptation is achieved based on the use of application specific quality satisfaction curves, while enforcing a fair allocation of bandwidth among the competing flows. The performance of the proposed scheme is evaluated and results indicate that the scheme yields fair adaptation under heavy loads.

关键词： Bandwidth Quality of service Degradation Resource management Mobile computing computer networks Telecommunication traffic Intelligent networks Educational institutions computer network management

来源：评论

学校读者我要写书评

暂无评论

EAR-Math: Evaluation of Audio Rendered Mathematics

EAR-Math: Evaluation of Audio Rendered Mathematics

引用

8th International Conference on Universal Access in Human-computer Interaction, UAHCI 2014 - Held as Part of 16th International Conference on Human-computer Interaction, HCI International 2014

作者： Kacorri, Hernisa Riga, Paraskevi Kouroupetroglou, Georgios National and Kapodistrian University of Athens Department of Informatics and Telecommunications Panepistimiopolis Ilisia 15784 Athens Greece Doctoral Program in Computer Science Graduate Center 365 Fifth Ave New York NY 10016 United States

ISBN: (纸本)9783319074399

Audio rendering of mathematical expressions has accessibility benefits for people with visual impairment. Seeking a systematic way to measure participants' perception of the rendered formulae with audio cues, we investigate the design of performance metrics to capture the distance between reference and perceived math expressions. We propose EAR-Math, a methodological approach for user-based evaluation of math rendering against a baseline. EAR-Math measures systems' performance using three fine-grained error rates based on the structural elements, arithmetic operators, numbers and identifiers in a formula. The proposed methodology and metrics were successfully applied in a pilot study, where 5 sighted and 2 blind participants evaluated 39 stimuli rendered by MathPlayer in Greek. In the obtained results, we observed that structural elements had the highest mean and variance of errors, which improved from 18% in the first attempt to 10% and 7% in two following attempts. © 2014 Springer International Publishing.

关键词： Artificial intelligence

来源：评论

学校读者我要写书评

暂无评论

Improved Metaheuristics with Machine Learning Enabled Medical Decision Support System

引用

computers, Materials & Continua 2022年第11期73卷 2423-2439页

作者： Sara A.Althubiti JoséEscorcia-Gutierrez Margarita Gamarra Roosvel Soto-Diaz Romany F.Mansour Fayadh Alenezi Department of Computer Science College of Computer and Information SciencesMajmaah UniversityAl-Majmaah11952Saudi Arabia Research Center-CIENS Escuela Naval de Suboficiales A.R.C.“Barranquilla”BarranquillaColombia Electronics and Telecommunications Engineering Program Universidad Autónoma del CaribeBarranquilla080001Colombia Departament of Computational Science and Electronic Universidad de la CostaCUCBarranquilla080001Colombia Biomedical Engineering Program Universidad Simón BolívarBarranquilla080001Colombia Department of Mathematics Faculty of ScienceNew Valley UniversityEl-Kharga 72511Egypt Department of Electrical Engineering College of EngineeringJouf UniversitySaudi Arabia

Smart healthcare has become a hot research topic due to the contemporary developments of Internet of Things(IoT),sensor technologies,cloud computing,and ***,the latest advances of Artificial Intelligence(AI)tools find helpful for decision-making in innovative healthcare to diagnose several *** Cancer(OC)is a kind of cancer that affects women’s ovaries,and it is tedious to identify OC at the primary stages with a high mortality *** OC data produced by the Internet of Medical Things(IoMT)devices can be utilized to differentiate *** this aspect,this paper introduces a new quantum black widow optimization with a machine learningenabled decision support system(QBWO-MLDSS)for smart *** primary intention of the QBWO-MLDSS technique is to detect and categorize the OC rapidly and ***,the QBWO-MLDSS model involves a Z-score normalization approach to pre-process the *** addition,the QBWO-MLDSS technique derives a QBWO algorithm as a feature selection to derive optimum feature ***,symbiotic organisms search(SOS)with extreme learning machine(ELM)model is applied as a classifier for the detection and classification of ELM model,thereby improving the overall classification *** design of QBWO and SOS for OC detection and classification in the smart healthcare environment shows the study’s *** experimental result analysis of the QBWO-MLDSS model is conducted using a benchmark dataset,and the comparative results reported the enhanced outcomes of the QBWO-MLDSS model over the recent approaches.

关键词： Ovarian cancer decision support system smart healthcare IoMT deep learning feature selection

来源：评论

学校读者我要写书评

暂无评论

A dual-hybrid adaptive routing strategy for wireless ad-hoc networks

A dual-hybrid adaptive routing strategy for wireless ad-hoc ...

引用

2000 IEEE Wireless Communications and Networking Conference

作者： McDonald, A. Bruce Znati, Taieb University of Pittsburgh Telecommunications Program Pittsburgh PA United States University of Pittsburgh Department of Computer Science Pittsburgh PA United States Children's Hospital of Pittsburgh Department of Neurophysiology Pittsburgh PA United States

ISBN: (纸本)0780365968

Recent debate in the research community has focused around the following question: should the design of routing algorithms for ad-hoc networks be predicated upon the minimization of routing overhead, or the optimization of network paths? The answer to this question depends upon the mobility and traffic characteristics present in the network. It is doubtful that any one approach by itself can be optimal, or even sufficient when there are temporal and spatial changes in the network dynamics. Most proposed solutions have adopt a fixed approach. To address this shortcoming we propose a dynamic cluster-based routing strategy that shifts the characteristics of its routing approach according to localized network dynamics. This is achieved by dividing routing into intra-cluster and inter-cluster components utilizing a strategy that is hybrid in terms of both its route acquisition and path computation approaches. By adapting the cluster organization to node mobility the strategy senses the network and balances optimality and overhead. The reason for doing this is to achieve the best possible performance subject to a wide range of operating environments.

关键词： Wireless telecommunication systems

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：