BioImg.org: A catalog of virtual machine images for the life sciences

Bioinformatics and Biology Insights

Volumn 9, Issue , 2015, Pages 125-128

  Dahlö, Martin ^a   Haziza, Frédéric ^a   Kallio, Aleksi ^b   Korpelainen, Eija ^b   Bongcam Rudloff, Erik ^c   Spjuth, Ola ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b CSC Scientific Computing Ltd   (Finland)

^c SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Catalogue; Cloud computing; Container; Software repository; Virtual appliance; Virtual machine image

Indexed keywords

APPLICATION SERVICE PROVIDER; ARTICLE; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPUTER PROGRAM; COMPUTER SYSTEM; DATA PROCESSING; INFORMATION PROCESSING; INFORMATION SYSTEM; VIRTUAL MACHINE IMAGE;

EID: 84942790462     PISSN: None     EISSN: 11779322     Source Type: Journal    
DOI: 10.4137/BBI.S28636     Document Type: Article

References (29)

1. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11:31-46.
2. Nilsson T, Mann M, Aebersold R, Yates JR III, Bairoch A, Bergeron JJ. Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods. 2010;7:681-5.
3. Mardis ER. The $1,000 genome, the $100,000 analysis? Genome Med. 2010;2:84.
4. Baxevanis AD. The importance of biological databases in biological discovery. Curr Protoc Bioinformatics. 2011;Chapter 1:Unit1.1.
5. Zou D, Ma L, Yu J, Zhang Z. Biological databases for human research. Genomics Proteomics Bioinformatics. 2015;13:55-63.
6. McWilliam H, Li W, Uludag M, et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res. 2013;41:W597-600.
7. NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2014;42:D7-17.
8. Bhagat J, Tanoh F, Nzuobontane E, et al. BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res. 2010;38:W689-94.
9. Goble CA, Bhagat J, Aleksejevs S, et al. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res. 2010;38:W677-82.
10. Bolser DM, Chibon PY, Palopoli N, et al. MetaBase - the wiki-database of biological databases. Nucleic Acids Res. 2012;40:D1250-4.
11. Field D, Tiwari B, Booth T, et al. Open software for biologists: from famine to feast. Nat Biotechnol. 2006;24:801-3.
12. Amazon EC2 - Elastic Compute Cloud. 2015. Available at: https://aws.amazon.com/ec2/. Accessed April 09, 2015.
13. VirtualBox. Available at: https://www.virtualbox.org. Accessed June 26, 2015.
14. Nocq J, Celton M, Gendron P, Lemieux S, Wilhelm BT. Harnessing virtual machines to simplify next-generation DNA sequencing analysis. Bioinformatics. 2013;29:2075-83.
15. Krampis K, Booth T, Chapman B, et al. Cloud BioLinux: preconfigured and on-demand bioinformatics computing for the genomics community. BMC Bio-informatics. 2012;13:42.
16. Angiuoli SV, Matalka M, Gussman A, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011;12:356.
17. Ochoa R, Davies M, Papadatos G, Atkinson F, Overington JP. myChEMBL: a virtual machine implementation of open data and cheminformatics tools. Bio-informatics. 2014;30:298-300.
18. AWS Marketplace. Available at: https://aws.amazon.com/marketplace. Accessed June 25, 2015.
19. Django - The Web Framework for Perfectionists with Deadlines. Available at: Error! Hyperlink reference not valid. Accessed June 24, 2015.
20. The Cloud Market. Available at: http://thecloudmarket.com. Accessed April 09, 2015.
21. VirtualBoxImages.com - VirtualBox Virtual Appliances. Available at: https://virtu-alboximages.com/. Accessed June 26, 2015.
22. Docker - Build, Ship and Run Any App, Anywhere. Available at: https://www.docker.com/. Accessed April 09, 2015.
23. LinuxContainers.org - Infrastructure for Container Projects. Available at: https://linuxcontainers.org/. Accessed April 09, 2015.
24. Kallio MA, Tuimala JT, Hupponen T, et al. Chipster: user-friendly analysis software for microarray and other high-throughput data. BMC Genomics. 2011;12:507.
25. GitHub. Available at: https://github.com. Accessed June 26, 2015.
26. Synapse - Contribute to the Cure. Available at: https://www.synapse.org/. Accessed June 26, 2015.
27. Howe B. Virtual appliances, cloud computing, and reproducible research. Comput Sci Eng. 2012;14:36-41.
28. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
29. Rebooting review. Nat Biotechnol. 2015;33:319.