DOI: 10.1186/1471-2105-13-42. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

10.1186/1471-2105-13-42

Crossref journal-article

Springer Science and Business Media LLC

BMC Bioinformatics (297)

Bibliography

Krampis, K., Booth, T., Chapman, B., Tiwari, B., Bicak, M., Field, D., & Nelson, K. E. (2012). Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics, 13(1).

Authors 7

Konstantinos Krampis (first)
Tim Booth (additional)
Brad Chapman (additional)
Bela Tiwari (additional)
Mesude Bicak (additional)
Dawn Field (additional)
Karen E Nelson (additional)

References 33 Referenced 129

Illumina MiSeq[ http://www.illumina.com/systems/miseq.ilmn ]
Schatz MC, Langmead B, Salzberg SL: Cloud computing and the DNA data race. Nat Biotechnol 2010, 28: 691–693. 10.1038/nbt0710-691 (10.1038/nbt0710-691) / Nat Biotechnol by MC Schatz (2010)
Stein L: The case for cloud computing in genome informatics. Genome Biol 2010, 11: 207–211. 10.1186/gb-2010-11-5-207 (10.1186/gb-2010-11-5-207) / Genome Biol by L Stein (2010)
Sansom C: Up in a cloud? Nat Biotechnol 2010, 28: 13–15. 10.1038/nbt0110-13 (10.1038/nbt0110-13) / Nat Biotechnol by C Sansom (2010)
Dudley JT, Butte AJ: In silico research in the era of cloud computing. Nat Biotechnol 2010, 28: 1181–1185. 10.1038/nbt1110-1181 (10.1038/nbt1110-1181) / Nat Biotechnol by JT Dudley (2010)
Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M: Open software for biologists: from famine to feast. Nat Biotechnol 2006, 24: 801–803. 10.1038/nbt0706-801 (10.1038/nbt0706-801) / Nat Biotechnol by D Field (2006)
NoMachine/FreeNX remote desktop client[ http://www.nomachine.com/ ]
Cloud BioLinux source code repository[ https://github.com/chapmanb/cloudbiolinux ]
Amazon EC2 cloud service[ http://aws.amazon.com/ec2 ]
Nurmi D, Wolski R, Grzegorczyk C, Obertelli , Soman S, Youseff L, Zagorodnov D: The Eucalyptus Open-Source Cloud-Computing System. Proceedings of the 9th IEEE/ACM International Symposium on Cluster Computing and the Grid 2009. / Proceedings of the 9th IEEE/ACM International Symposium on Cluster Computing and the Grid by D Nurmi (2009)
OpenStack cloud platform[ http://www.openstack.org/ ]
Fabric software management[ http://fabfile.org/ ]
Debian Aptitude[ http://en.wikipedia.org/wiki/Advanced_Packaging_Tool ]
Alestic VMs[ http://alestic.com ]
Ubuntu Enterprize Cloud images[ https://help.ubuntu.com/community/UEC/Images ]
Ubuntu VM builder[ https://wiki.ubuntu.com/EC2Vmbuilder ]
Möller S, Krabbenhoft H, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C: Community-driven computational biology with Debian Linux. BMC Bioinformatics 2010, 11(Suppl 12):S5. 10.1186/1471-2105-11-S12-S5 (10.1186/1471-2105-11-S12-S5) / BMC Bioinformatics by S Möller (2010)
Ubuntu Science page[ http://tinyurl.com/4l7mfy6 ]
CPAN: Comprehensive Perl Archive Network[ http://www.cpan.org ]
Amazon EC2 pricing[ http://aws.amazon.com/ec2/pricing/ ]
Amazon cloud console[ http://aws.amazon.com/ ]
Oracle VirtualBox[ http://www.virtualbox.org ]
Angiuoli SV, Maralka M, Gussman A, Galens K, Vangala M, Riley Dr, Arze C, White JR, White O, CloVR FrickeWF: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 2011, 12: 356. 10.1186/1471-2105-12-356 (10.1186/1471-2105-12-356) / BMC Bioinformatics by SV Angiuoli (2011)
Bioconductor Cloud VM[ http://bioconductor.org/help/bioconductor-cloud-ami/ ]
Qiime[ http://qiime.sourceforge.net/install/virtual_box.html ]
GMOD[ http://gmod.org/wiki/GMOD_virtual_machine_project ]
Cloud BioLinux - based sequencing data analysis pipeline[ https://github.com/chapmanb/bcbb/tree/master/nextgen ]
Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J: Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 2010, 11: S4. ± ± (10.1186/1471-2105-11-S12-S4) / BMC Bioinformatics by E Afgan (2010)
Iosup A, Ostermann S, Yigitbasi M, Prodan R, Fahringer R, Epema D: Performance Analysis of Cloud Computing Services for Many-Tasks Scientific Computing. IEEE Transactions on Parallel and Distributed Systems 2011, 30: 931–945. (10.1109/TPDS.2011.66) / IEEE Transactions on Parallel and Distributed Systems by A Iosup (2011)
Apache Hadoop[ http://hadoop.apache.org ]
Langmead B, Schatz M, Lin J, Pop M, Salzberg S: Searching for SNPs with cloud computing. Genome Biol 2010, 10: R134. ± ± (10.1186/gb-2009-10-11-r134) / Genome Biol by B Langmead (2010)
Schatz MC: CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 2009, 25: 1363–1369. 10.1093/bioinformatics/btp236 (10.1093/bioinformatics/btp236) / Bioinformatics by MC Schatz (2009)
Contrail genome assembler[ http://contrail-bio.sf.net ]

Dates

Type	When
Created	13 years, 5 months ago (March 19, 2012, 11:14 a.m.)
Deposited	6 years, 7 months ago (Jan. 23, 2019, 12:52 a.m.)
Indexed	4 months ago (April 19, 2025, 6:09 a.m.)
Issued	13 years, 5 months ago (March 19, 2012)
Published	13 years, 5 months ago (March 19, 2012)
Published Online	13 years, 5 months ago (March 19, 2012)
Published Print	12 years, 8 months ago (Dec. 1, 2012)

Funders 0

None

BibTeX

@article{Krampis_2012, title={Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community}, volume={13}, ISSN={1471-2105}, url={http://dx.doi.org/10.1186/1471-2105-13-42}, DOI={10.1186/1471-2105-13-42}, number={1}, journal={BMC Bioinformatics}, publisher={Springer Science and Business Media LLC}, author={Krampis, Konstantinos and Booth, Tim and Chapman, Brad and Tiwari, Bela and Bicak, Mesude and Field, Dawn and Nelson, Karen E}, year={2012}, month=mar }

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