Parallel Algorithms for Big Data from Mass Spectrometry based Proteomics
Parallel Algorithms for Big Data from Mass Spectrometry based Proteomics
批准号:
9301702
负责人:
Ajay Gupta
金额:
$41.85万
依托单位国家:
美国
项目类别:
财政年份:
2017
资助国家:
美国
项目状态:
已结题
起止时间:
2017-04-01 至 2021-03-31
关键词:
Algorithm DesignAlgorithmsArchitectureBig DataBioinformaticsBiologyCareer ChoiceCollaborationsCommunitiesComplexComputational BiologyComputational ScienceComputer softwareComputersDataData AnalysesData AnalyticsData SetDatabasesDevelopmentEngineeringEnvironmentEvaluationGalaxyGenerationsGoalsGrantGraphHigh Performance ComputingLibrariesMass Spectrum AnalysisMedicineMemoryMethodsModernizationPeptidesPerformanceProtein DatabasesProteomicsResearchResearch PersonnelRouteRunningSamplingScientistSeminalSoftware DesignStudentsSystemSystems BiologyTechniquesTestingTimebasebig biomedical datacluster computingcomputer sciencecostdesignexperimental studyfoothigh throughput analysismass spectrometermedical schoolsparallel computerparallel processingparallelizationpetabyteportabilityprogramsprotein aminoacid sequencetool
中文摘要
项目总结/文摘
英文摘要
Project Summary/Abstract
The goal of the proposed project is to develop core algorithms, techniques and software libraries
to enable scalable, efficient and parallel computing solutions for mass spectrometry (MS) based
high-throughput proteomics data sets. To empower the larger proteomics community and
experimental biologist the project seeks to 1) identify a set of core methods that are frequently
used by proteomics practitioners 2) develop efficient and scalable parallel algorithms and
implementations for these methods 3) pursue mapping of these parallel computing techniques to a
wide variety of architectures such as multicores, manycores, distributed clusters, GPU’s and
FPGA’s 4) design and implement big data analytic techniques that can be used in our HPC
implementation as well as used by other researchers for sequential and/or parallel algorithms 5)
design interfaces using Galaxy framework for these parallel programs so that they can be used by
non-experts and people who are not familiar with parallel processing. The research will be
conducted in collaboration with domain experts in systems biology and proteomics. The specific
problems that will be targeted are parallel algorithms for clustering of MS data sets, parallel
algorithms for identifying peptides using databases from these MS data sets using multicore and
GPU’s and high performance algorithms that can make sense out of these MS data sets in a denovo
fashion without a need for a database. The parallel algorithms will be tested using simulated as
well as real experimental data sets and will be available for free academic use.
期刊论文(8)
专著(0)
科研奖励(0)
会议论文
DOI:
10.3389/fninf.2019.00070
发表时间:
2019-11-27
期刊:
FRONTIERS IN NEUROINFORMATICS
影响因子:
3.5
作者:
[Eslami, Taban, Mirjalili, Vahid, Saeed, Fahad]
通讯作者:
Saeed, Fahad
DOI:
10.1109/bibm.2017.8217951
发表时间:
2017-11
期刊:
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine
影响因子:
--
作者:
[Maabreh M, Qolomany B, Alsmadi I, Gupta A]
通讯作者:
Gupta A
Deep vs. Shallow Learning-based Filters of MSMS Spectra in Support of Protein Search Engines.
深度与基于浅层学习的MSMS光谱过滤器支持蛋白质搜索引擎。
DOI:
10.1109/bibm.2017.8217824
发表时间:
2017-11
期刊:
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine
影响因子:
--
作者:
[Maabreh M, Qolomany B, Springstead J, Alsmadi I, Gupta A]
通讯作者:
Gupta A
Development of a dry powder inhalation product against Respiratory Syncytial Virus based on an endogenous anionic pulmonary surfactant lipid
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批准号:10697027
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项目类别:
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资助金额:$29.01万
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财政年份:2023
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负责人:Ajay Gupta
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依托单位:
Quantitative susceptibility mapping for stroke risk prediction of vulnerable carotid plaques
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批准号:10446087
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项目类别:
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资助金额:$69.78万
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财政年份:2022
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负责人:Ajay Gupta
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依托单位:
Quantitative Susceptibility Mapping for Stroke Risk Prediction of Vulnerable Carotid Plaques
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批准号:10609912
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项目类别:
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资助金额:$68.9万
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财政年份:2022
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负责人:Ajay Gupta
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依托单位:
Understanding the dynamic interactions between tau pathology and microgliamediated inflammation in Alzheimer's Disease
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批准号:10622513
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项目类别:
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资助金额:$120.31万
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财政年份:2021
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负责人:Ajay Gupta
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依托单位:
Understanding the dynamic interactions between tau pathology and microgliamediated inflammation in Alzheimer's Disease
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批准号:10317631
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项目类别:
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资助金额:$114.16万
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财政年份:2021
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负责人:Ajay Gupta
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依托单位:
Understanding the dynamic interactions between tau pathology and microgliamediated inflammation in Alzheimer's Disease
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批准号:10471976
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项目类别:
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资助金额:$131.97万
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财政年份:2021
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负责人:Ajay Gupta
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依托单位:
MRI Detection of CarotId Plaques as a mecHanism for Embolic strokes of undeteRmined source (MRI DECIPHER)
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批准号:10204095
-
项目类别:
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资助金额:$82.36万
-
财政年份:2019
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负责人:Ajay Gupta
-
依托单位:
A Machine Learning Approach For CTA-based Plaque Characterization and Stroke Risk Prediction in Carotid Artery Atherosclerosis
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批准号:9904175
-
项目类别:
-
资助金额:$12.2万
-
财政年份:2019
-
负责人:Ajay Gupta
-
依托单位:
MRI Detection of CarotId Plaques as a mecHanism for Embolic strokes of undeteRmined source (MRI DECIPHER)
-
批准号:10661676
-
项目类别:
-
资助金额:$69.39万
-
财政年份:2019
-
负责人:Ajay Gupta
-
依托单位:
MRI Detection of CarotId Plaques as a mecHanism for Embolic strokes of undeteRmined source (MRI DECIPHER)
-
批准号:10449116
-
项目类别:
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资助金额:$79.67万
-
财政年份:2019
-
负责人:Ajay Gupta
-
依托单位:
Predictive model of spread of Parkinson's pathology using network diffusion
-
批准号:9913596
-
项目类别:
-
资助金额:$58.77万
-
财政年份:2016
-
负责人:Ajay Gupta
-
依托单位:
Iron Delivery Via hemodialysate in ESRD
-
批准号:6845677
-
项目类别:
-
资助金额:$9.91万
-
财政年份:2004
-
负责人:Ajay Gupta
-
依托单位:
Iron Delivery Via hemodialysate in ESRD
-
批准号:6720078
-
项目类别:
-
资助金额:$29.6万
-
财政年份:2004
-
负责人:Ajay Gupta
-
依托单位:
海外基金