Biocompute 2.0: An improved collaborative workspace for data intensive bio-science

Concurrency and Computation: Practice and Experience

Volumn 23, Issue 17, 2011, Pages 2305-2314

  Carmichael, Rory ^a   Braga Henebry, Patrick ^b   Thain, Douglas ^a   Emrich, Scott ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b IMC Financial Markets   (United States)

Author keywords

bioinformatics; interface design; makeflow; web portal

Indexed keywords

BIOINFORMATICS; PORTALS;

BIOINFORMATICS APPLICATIONS; BIOLOGICAL COMMUNITY; COLLABORATIVE RESOURCES; COLLABORATIVE WORKSPACE; DATA DISTRIBUTION; DATA INTENSIVE SCIENCE; INTERFACE DESIGNS; MAKEFLOW;

USER INTERFACES;

EID: 80054955975     PISSN: 15320626     EISSN: 15320634     Source Type: Journal    
DOI: 10.1002/cpe.1782     Document Type: Article

References (16)

1. Carmichael R, Braga-Henebry P, et al. Biocompute: towards a collaborative workspace for data-intensive bio-science. WORKSHOP SESSION: Emerging Computational Methods for Life Sciences, 2010.
2. Johnson M, Zaretskaya I, et al. NCBI BLAST: a better web interface. Nucleic Acids Research 2008; 36: W5.
3. Lawson D, Arensburger P, et al. VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Research 2006; 35: D503.
4. Thain D, Moretti C, et al. Chirp: a practical global filesystem for cluster and grid computing. Journal of Grid Computing 2009; 7: 51-72.
5. Litzkow M, Livny M, et al. Condor-A Hunter of Idle Workstations. Proceedings of the 8th International Conference of Distributed Computing Systems, 1998.
6. Raman R, Livny M, et al. Resource management through multilateral matchmaking. International Symposium on High Performance and Distributed Computing, 2000.
7. Yu L, Moretti C, et al. Harnessing Parallelism in Multicore Clusters with the All-Pairs, Wavefront, and Makeflow Abstractions. Journal of Cluster Computing 2010: 1-14.
8. Altschul SF, Gish W, et al. Basic local alignment search tool. Journal of Molecular Biology 1990; 215: 402-410.
9. Moreau L, Ludascher B, et al. The first provenance challenge. Concurrency and Computation: Practice and Experience 2007; 20: 400-418.
10. Darling AE, Carey L, et al. The design, implementation, and evaluation of mpiBLAST. Proceedings of ClusterWorld, 2003.
11. Dumontier M, Hogue CWV,. NBLAST: a cluster variant of BLAST for NxN comparisons. BMC Bioinformatics 2002; 3: 13.
12. Giardine B, Riemer C, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Research 3005; 15: 1451.
13. Oinn T, Addis M, et al. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004.
14. Li H, Durbin R,. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 2009; 25: 1754-60.
15. Ning Z, Cox AJ, et al. SSAHA: a fast search method for large DNA databases. Genome Research 2001; 11: 1725.
16. Rumble SM, Lacroute P, et al. SHRiMP: accurate mapping of short color-space reads. PLoS Computational Biology 2009; 5: e1000386.