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MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison
Song, Baoxing1; Su, Xiaoquan1; Xu, Jian1,2,3; Ning, Kang1,2,3
2012-11-08
发表期刊PLOS ONE
卷号7期号:11
摘要

The NGS (next generation sequencing)-based metagenomic data analysis is becoming the mainstream for the study of microbial communities. Faced with a large amount of data in metagenomic research, effective data visualization is important for scientists to effectively explore, interpret and manipulate such rich information. The visualization of the metagenomic data, especially multi-sample data, is one of the most critical challenges. The different data sample sources, sequencing approaches and heterogeneous data formats make robust and seamless data visualization difficult. Moreover, researchers have different focuses on metagenomic studies: taxonomical or functional, sample-centric or genome-centric, single sample or multiple samples, etc. However, current efforts in metagenomic data visualization cannot fulfill all of these needs, and it is extremely hard to organize all of these visualization effects in a systematic manner. An extendable, interactive visualization tool would be the method of choice to fulfill all of these visualization needs. In this paper, we have present MetaSee, an extendable toolbox that facilitates the interactive visualization of metagenomic samples of interests. The main components of MetaSee include: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. This integrative visualization tool not only provides the visualization effects, but also enables researchers to perform in-depth analysis of the metagenomic samples of interests. Moreover, its open-source portal allows for the design of plug-ins for MetaSee, which would facilitate the development of any additional visualization effects.

; The NGS (next generation sequencing)-based metagenomic data analysis is becoming the mainstream for the study of microbial communities. Faced with a large amount of data in metagenomic research, effective data visualization is important for scientists to effectively explore, interpret and manipulate such rich information. The visualization of the metagenomic data, especially multi-sample data, is one of the most critical challenges. The different data sample sources, sequencing approaches and heterogeneous data formats make robust and seamless data visualization difficult. Moreover, researchers have different focuses on metagenomic studies: taxonomical or functional, sample-centric or genome-centric, single sample or multiple samples, etc. However, current efforts in metagenomic data visualization cannot fulfill all of these needs, and it is extremely hard to organize all of these visualization effects in a systematic manner. An extendable, interactive visualization tool would be the method of choice to fulfill all of these visualization needs. In this paper, we have present MetaSee, an extendable toolbox that facilitates the interactive visualization of metagenomic samples of interests. The main components of MetaSee include: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. This integrative visualization tool not only provides the visualization effects, but also enables researchers to perform in-depth analysis of the metagenomic samples of interests. Moreover, its open-source portal allows for the design of plug-ins for MetaSee, which would facilitate the development of any additional visualization effects. Citation: Song B, Su X, Xu J, Ning K (2012) MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison. PLoS ONE 7(11): e48998. doi:10.1371/journal.pone.0048998
文章类型Article
学科领域功能基因组
WOS标题词Science & Technology
DOI10.1371/journal.pone.0048998
关键词[WOS]GUT MICROBIOME ; DIVERSITY ; RESOURCE ; GENOMES
收录类别SCI
语种英语
WOS研究方向Science & Technology - Other Topics
WOS类目Multidisciplinary Sciences
WOS记录号WOS:000312269500058
引用统计
文献类型期刊论文
条目标识符http://ir.qibebt.ac.cn/handle/337004/1416
专题单细胞中心组群
作者单位1.Chinese Acad Sci, BioEnergy Genome Ctr, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao, Shandong, Peoples R China
2.Chinese Acad Sci, Shandong Key Lab Energy Genet, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao, Shandong, Peoples R China
3.Chinese Acad Sci, CAS Key Lab Biofuels, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao, Shandong, Peoples R China
推荐引用方式
GB/T 7714
Song, Baoxing,Su, Xiaoquan,Xu, Jian,et al. MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison[J]. PLOS ONE,2012,7(11).
APA Song, Baoxing,Su, Xiaoquan,Xu, Jian,&Ning, Kang.(2012).MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison.PLOS ONE,7(11).
MLA Song, Baoxing,et al."MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison".PLOS ONE 7.11(2012).
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