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Volumn 9656, Issue , 2016, Pages 587-601

The case for docker in multicloud enabled bioinformatics applications

Author keywords

Bioinformatics; Cloud computing; Docker; High performance computing; Sequence analysis

Indexed keywords

BIOMEDICAL ENGINEERING; CLOUD COMPUTING; VIRTUAL REALITY; VIRTUALIZATION;

EID: 84973912685     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-31744-1_52     Document Type: Conference Paper
Times cited : (13)

References (26)
  • 1
    • 84907854550 scopus 로고    scopus 로고
    • The road from next-generation sequencing to personalized medicine
    • Gonzalez-Garay, M.: The road from next-generation sequencing to personalized medicine. Pers. Med. 11(5), 523–544 (2014)
    • (2014) Pers. Med , vol.11 , Issue.5 , pp. 523-544
    • Gonzalez-Garay, M.1
  • 2
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M., Banks, E., et al.: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43(5), 491–498 (2011)
    • (2011) Nature Genet , vol.43 , Issue.5 , pp. 491-498
    • Depristo, M.1    Banks, E.2
  • 3
    • 84973926175 scopus 로고    scopus 로고
    • FASTX-Toolkit. http://hannonlab.cshl.edu/fastx toolkit
  • 4
    • 84973856766 scopus 로고    scopus 로고
    • FASTQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  • 5
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows and wheeler transform
    • Li, H., Durbin, R.: Fast and accurate short read alignment with burrows and wheeler transform. Bioinformatics 25(14), 1754–1760 (2009)
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 6
    • 84881018840 scopus 로고    scopus 로고
    • Isaac: Ultra-fast whole-genome secondary analysis on Illumina sequencing platforms
    • Oxford, England
    • Raczy, C., Petrovski, R., Saunders, C.T., et al.: Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics 29(16), 2041–2043 (2013). (Oxford, England)
    • (2013) Bioinformatics , vol.29 , Issue.16 , pp. 2041-2043
    • Raczy, C.1    Petrovski, R.2    Saunders, C.T.3
  • 7
    • 77956534324 scopus 로고    scopus 로고
    • Annovar: Functional annotation of genetic variants from high-throughput sequencing data
    • Wang, K., Li, M., Hakonarson, H.: Annovar: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38(16), e164 (2010)
    • (2010) Nucleic Acids Res , vol.38 , Issue.16 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 10
    • 80052121849 scopus 로고    scopus 로고
    • CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
    • Angiuoli, S., Matalka, M., Gussman, A., et al.: CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 12(1), 356+ (2011)
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 356+
    • Angiuoli, S.1    Matalka, M.2    Gussman, A.3
  • 11
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of highthroughput community sequencing data
    • Gregory, J., Kuczynski, J., Stombaugh, J., et al.: QIIME allows analysis of highthroughput community sequencing data. Nat. Meth. 7(5), 335–336 (2010)
    • (2010) Nat. Meth , vol.7 , Issue.5 , pp. 335-336
    • Gregory, J.1    Kuczynski, J.2    Stombaugh, J.3
  • 12
    • 84902540086 scopus 로고    scopus 로고
    • A performance/cost model for a cuda drug discovery application on physical and public cloud infrastructures
    • Guerrero, G., Wallace, R., Vázquez-Poletti, J., et al.: A performance/cost model for a cuda drug discovery application on physical and public cloud infrastructures. Concurrency Comput.: Pract. Experience 26(10), 1787–1798 (2014)
    • (2014) Concurrency Comput.: Pract. Experience , vol.26 , Issue.10 , pp. 1787-1798
    • Guerrero, G.1    Wallace, R.2    Vázquez-Poletti, J.3
  • 13
    • 84911371466 scopus 로고    scopus 로고
    • Cloud4Psi: Cloud computing for 3D protein structure similarity searching
    • Mrozek, D., Malysiak-Mrozek, B., Klapcinski, A.: Cloud4Psi: cloud computing for 3D protein structure similarity searching. Bioinformatics 30(19), 2822–2825 (2014)
    • (2014) Bioinformatics , vol.30 , Issue.19 , pp. 2822-2825
    • Mrozek, D.1    Malysiak-Mrozek, B.2    Klapcinski, A.3
  • 14
    • 84958164302 scopus 로고    scopus 로고
    • Scaling ab initio predictions of 3D protein structures in Microsoft Azure cloud
    • Mrozek, D., Gosk, P., Malysiak-Mrozek, B.: Scaling ab initio predictions of 3D protein structures in Microsoft Azure cloud. J. Grid Comp. 13(4), 561–585 (2015)
    • (2015) J. Grid Comp , vol.13 , Issue.4 , pp. 561-585
    • Mrozek, D.1    Gosk, P.2    Malysiak-Mrozek, B.3
  • 15
    • 84878717921 scopus 로고    scopus 로고
    • Cloud computing for protein-ligand binding site comparison
    • Hung, C.-L., Hua, G.-J.: Cloud computing for protein-ligand binding site comparison. Biomed. Res. Int. 2013, Article ID 170356, 1–7 (2013)
    • (2013) Biomed. Res. Int , pp. 1-7
    • Hung, C.-L.1    Hua, G.-J.2
  • 16
    • 84973859224 scopus 로고    scopus 로고
    • Oracle VirtualBox. http://www.virtualbox.org/
  • 17
    • 84973918463 scopus 로고    scopus 로고
    • Kernel Virtual Machine. http://www.linux-kvm.org
  • 18
    • 84973888635 scopus 로고    scopus 로고
    • Xen Project. http://www.xenproject.org/
  • 19
    • 84973918492 scopus 로고    scopus 로고
    • VMware. http://www.vmware.com/
  • 20
    • 84973918262 scopus 로고    scopus 로고
    • Docker. http://docker.com/
  • 21
    • 84973886308 scopus 로고    scopus 로고
    • NGSeasy: A next generation sequencing pipeline in Docker containers
    • Folarin, A., Dobson, R., Newhouse, S.: NGSeasy: a next generation sequencing pipeline in Docker containers. F1000Research 4, 997 (2015)
    • (2015) F1000research , vol.4 , pp. 997
    • Folarin, A.1    Dobson, R.2    Newhouse, S.3
  • 22
    • 84944472830 scopus 로고    scopus 로고
    • Supporting bioinformatics applications with hybrid multi-cloud services
    • In: Ortuño, F., Rojas, I. (eds.), Springer, Heidelberg
    • Ali, A.A., El-Kalioby, M., Abouelhoda, M.: Supporting bioinformatics applications with hybrid multi-cloud services. In: Ortuño, F., Rojas, I. (eds.) IWBBIO 2015, Part I. LNCS, vol. 9043, pp. 415–425. Springer, Heidelberg (2015)
    • (2015) IWBBIO 2015, Part I. LNCS , vol.9043 , pp. 415-425
    • Ali, A.A.1    El-Kalioby, M.2    Abouelhoda, M.3
  • 23
    • 84973881286 scopus 로고    scopus 로고
    • Pods. http://cloud.google.com/container-engine/docs/pods
  • 24
    • 84973882139 scopus 로고    scopus 로고
    • Docker Compose. https://www.docker.com/docker-compose
  • 25
    • 70349882144 scopus 로고    scopus 로고
    • Frodock: A new approach for fast rotational protein-protein docking
    • Garzon, J., Lopéz-Blanco, J., Pons, C., et al.: Frodock: a new approach for fast rotational protein-protein docking. Bioinformatics 25(19), 2544–2551 (2009)
    • (2009) Bioinformatics , vol.25 , Issue.19 , pp. 2544-2551
    • Garzon, J.1    Lopéz-Blanco, J.2    Pons, C.3
  • 26
    • 84860503874 scopus 로고    scopus 로고
    • Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support
    • Abouelhoda, M., Issa, S., Ghanem, M.: Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support. BMC Bioinformatics 13(1), 77 (2012)
    • (2012) BMC Bioinformatics , vol.13 , Issue.1 , pp. 77
    • Abouelhoda, M.1    Issa, S.2    Ghanem, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.