BioVLAB-Cloud-based Bioinformatics Analysis Workbench

BioVLAB-클라우드 기반의 생물정보학 분석 시스템

  • Published : 2013.03.15

Abstract

Keywords

Acknowledgement

Supported by : 한국연구재단

References

  1. The Cancer Genome Atlas(TCGA), Comprehensive molecular characterization of human colon and rectal cancer, Nature 487, 330-337, 19 July 2012 https://doi.org/10.1038/nature11252
  2. ENCODE Project Consortium. The ENCODE(ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40. https://doi.org/10.1126/science.1105136
  3. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. NAR 2011 39(Database Issue):D152-D157 https://doi.org/10.1093/nar/gkq1027
  4. Ida S. et al. BRENDA, enzyme data and metabolic information. Nucleic Acids Res. 2002 January 1; 30(1), 47-49. https://doi.org/10.1093/nar/30.1.47
  5. Peter M., Timothy G. The NIST Definition of Cloud Computing. NIST Special Publication 800-145
  6. Jay S., Hanlee J. Next-generation DNA sequencing. Nature Biotechnology 26, 1135-1145, 9 October 2008 https://doi.org/10.1038/nbt1486
  7. Matsunaga, A. CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications. eScience '08. IEEE Fourth International Conference
  8. Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP: Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics 2006, 22:2044-2046. https://doi.org/10.1093/bioinformatics/btl286
  9. Krampis K, T B, Chapman B, Tiwari B, Bicak M, Field D, Nelson K: SNP detection for massively parallel whole-genome resequencing. BMC Bioinformatics 2012, 13:42. https://doi.org/10.1186/1471-2105-13-42
  10. AWS Public Data, http://aws.amazon.com/ko/publicdatasets/
  11. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005, 15:1451-1455. https://doi.org/10.1101/gr.4086505
  12. XBaya: A Graphical Workflow Composer for Web Services. http://www.extreme.indiana.edu/xbaya
  13. Hejoon et al. Bio and Health informatics meets Cloud : BioVLAB as an example. Health Information Science and Systems 2013
  14. Alameda, J., Christie, M., Fox, G., Futrelle, J., Gannon, D., Hategan, M., Kandaswamy, G., von Laszewski, G., Nacar, M. A., Pierce, M., Roberts, E., Severance, C. and Thomas, M.(2007), The Open Grid Computing Environments collaboration: portlets and services for science gateways. Concurrency Computat.: Pract. Exper., 19: 921-942. doi: 10.1002/cpe.1078
  15. BioVLAB의 구조, http://biohealth.snu.ac.kr/wiki/index.php/BioVLab_:_Biology_Virtual_Collaborative_Lab# Apache_Airavata_migration_of_BioVLAB
  16. Amazon Elastic Compute Cloud(EC2), http://aws.amazon.com/ec2/
  17. Amazon Simple Storage Service(S3), http://aws.amazon.com/s3/
  18. Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MicroRNA and mRNA integrated analysis(MMIA): a web tool for examining biological functions of micro- RNA expression. Nucleic Acids Res. 2009 May 6.
  19. Suresh et al. Apache airavata: a framework for distributed applications and computational workflows. GCE '11 Proceedings of the 2011 ACM workshop on Gateway computing environments, Pages 21-28