癌症基因组学云：协作、可重复且民主化——大规模计算研究的新范式
The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.
作者信息
Lau Jessica W, Lehnert Erik, Sethi Anurag, Malhotra Raunaq, Kaushik Gaurav, Onder Zeynep, Groves-Kirkby Nick, Mihajlovic Aleksandar, DiGiovanna Jack, Srdic Mladen, Bajcic Dragan, Radenkovic Jelena, Mladenovic Vladimir, Krstanovic Damir, Arsenijevic Vladan, Klisic Djordje, Mitrovic Milan, Bogicevic Igor, Kural Deniz, Davis-Dusenbery Brandi
机构信息
Seven Bridges Genomics, Cambridge, Massachusetts.
出版信息
Cancer Res. 2017 Nov 1;77(21):e3-e6. doi: 10.1158/0008-5472.CAN-17-0387.
Abstract
The Seven Bridges Cancer Genomics Cloud (CGC; www.cancergenomicscloud.org) enables researchers to rapidly access and collaborate on massive public cancer genomic datasets, including The Cancer Genome Atlas. It provides secure on-demand access to data, analysis tools, and computing resources. Researchers from diverse backgrounds can easily visualize, query, and explore cancer genomic datasets visually or programmatically. Data of interest can be immediately analyzed in the cloud using more than 200 preinstalled, curated bioinformatics tools and workflows. Researchers can also extend the functionality of the platform by adding their own data and tools via an intuitive software development kit. By colocalizing these resources in the cloud, the CGC enables scalable, reproducible analyses. Researchers worldwide can use the CGC to investigate key questions in cancer genomics. .
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本文引用的文献
1
Integrated genomic and molecular characterization of cervical cancer.宫颈癌的综合基因组和分子特征分析
Nature. 2017 Mar 16;543(7645):378-384. doi: 10.1038/nature21386. Epub 2017 Jan 23.
2
Making sense of replications.理解重复实验结果。
Elife. 2017 Jan 19;6:e23383. doi: 10.7554/eLife.23383.
3
RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.RABIX：一个支持工作流描述的可重新计算性和互操作性的开源工作流执行器。
Pac Symp Biocomput. 2017;22:154-165. doi: 10.1142/9789813207813_0016.
4
Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration.乳腺肿瘤相关RNA影响肿瘤细胞的增殖、侵袭和迁移。
Cell Rep. 2016 Sep 27;17(1):261-274. doi: 10.1016/j.celrep.2016.08.081.
5
Data analysis: Create a cloud commons.数据分析：创建一个云共享空间。
Nature. 2015 Jul 9;523(7559):149-51. doi: 10.1038/523149a.
6
The future of cancer genomics.癌症基因组学的未来。
Nat Med. 2015 Feb;21(2):99. doi: 10.1038/nm.3801.
7
An open investigation of the reproducibility of cancer biology research.一项关于癌症生物学研究可重复性的公开调查。
Elife. 2014 Dec 10;3:e04333. doi: 10.7554/eLife.04333.
8
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.癌症细胞系百科全书使对抗癌药物敏感性的预测建模成为可能。
Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003.
9
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.整合基因组分析确定了具有 PDGFRA、IDH1、EGFR 和 NF1 异常的胶质母细胞瘤的临床相关亚型。
Cancer Cell. 2010 Jan 19;17(1):98-110. doi: 10.1016/j.ccr.2009.12.020.
10
The increasing dominance of teams in production of knowledge.团队在知识生产中日益占据主导地位。
Science. 2007 May 18;316(5827):1036-9. doi: 10.1126/science.1136099. Epub 2007 Apr 12.
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