Abstract
Microarray experiments can provide molecular-level insight into a variety of biological processes, from yeast cell cycle to tumorogenesis. However, analysis of both genomic and protein microarray data requires interactive collaborative investigation by biology and bioinformatics researchers. To assist collaborative analysis, remote collaboration tools for integrative analysis and visualization of microarray data are necessary. Such tools should: (i) provide fast response times when used with visualization-intensive genomics applications over a low-bandwidth wide area network, (ii) eliminate transfer of large and often sensitive datasets, (iii) work with any analysis software, and (iv) be platform-independent. Existing visualization systems do not satisfy all requirements. We have developed a remote visualization system called Varg that extends the platform-independent remote desktop system VNC with a novel global compression method. Our evaluations show that the Varg system can support interactive visualization-intensive genomic applications in a remote environment by reducing bandwidth requirements from 30:1 to 289:1.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Lipshutz, R.J., Fodor, S.P.A., Gingeras, T.R., Lockhart, D.J.: High density synthetic oligonucleotide arrays. Nature Genetics 21, 20–24 (1999)
Schena, M., Shalon, D., Davis, R.W., Brown, P.O.: Quantitative Monitoring of Gene-Expression Patterns with a Complementary-DNA Microarray. Science 270(5235), 467–470 (1995)
Cahill, D.J., Nordhoff, E.: Protein arrays and their role in proteomics. Adv. Biochem. Eng. Biotechnol. 83, 177–187 (2003)
Sydor, J.R., Nock, S.: Protein expression profiling arrays: tools for the multiplexed high-throughput analysis of proteins. Proteome Sci. 1(1), 3 (2003)
Oleinikov, A.V., Gray, M.D., Zhao, J., Montgomery, D.D., Ghindilis, A.L., Dill, K.: Self-assembling protein arrays using electronic semiconductor microchips and in vitro translation. J. Proteome Res. 2(3), 313–319 (2003)
Huang, R.P.: Protein arrays, an excellent tool in biomedical research. Front Biosci. 8, d559–576 (2003)
Cutler, P.: Protein arrays: the current state-of-the-art. Proteomics 3(1), 3–18 (2003)
Kerr, M.K., Churchill, G.A.: Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. In: Proc Natl. Acad. Sci. 98(16) pp. 8961-8965, USA (2001)
Yeung, K.Y., Haynor, D.R., Ruzzo, W.L.: Validating clustering for gene expression data. Bioinformatics 17(4), 309–318 (2001)
Mendez, M.A., Hodar, C., Vulpe, C., Gonzalez, M., Cambiazo, V.: Discriminant analysis to evaluate clustering of gene expression data. FEBS Lett 522(1–3), 24–28 (2002)
Datta, S., Datta, S.: Comparisons and validation of statistical clustering techniques for microarray gene expression data. Bioinformatics 19(4), 459–466 (2003)
Richardson, T., Stafford-Fraser, Q., Wood, K.R., Hopper, A.: Virtual network computing. Ieee Internet Computing 2(1), 33–38 (1998)
Schmidt, B.K., Lam, M.S., Northcutt, J.D.: The interactive performance of SLIM: a stateless, thin-client architecture. In: Proceedings of the seventeenth ACM symposium on Operating systems principles, Charleston, South Carolina, United States, ACM Press (1999)
Baratto, R.A., Kim, L.N., Nieh, J.: THINC: a virtual display architecture for thin-client computing. In: Proceedings of the twentieth ACM symposium on Operating systems principles, Brighton,United Kingdom, ACM Press (2005)
Cumberland, B.C., Carius, G., Muir, A: Microsoft Windows NT Server 4.0, Terminal Server Edition: Technical Reference. In: Edited by Press M. Redmond. WA (1999)
Apple Remote Desktop, http://www.apple.com/remotedesktop
Spring, N.T., Wetherall, D.: A protocol-independent technique for eliminating redundant network traffic. In: Proceedings of the conference on Applications, Technologies, Architectures, and Protocols for Computer Communication, Stockholm, Sweden, ACM Press (2000)
Muthitacharoen, A., Chen, B., Mazières, D.: A low-bandwidth network file system. In: Proceedings of the eighteenth ACM symposium on Operating systems principles, Banff, Alberta, Canada, ACM Press (2001)
Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Transactions on Information Theory 23(3), 337–343 (1977)
Broder, A.: Some applications of Rabin’s fingerprinting method. In: Sequences II: Methods in Communications, Security, and Computer Science: 1993 (1993)
Broder, A.: On the Resemblance and Containment of Documents. In: Proceedings of the Compression and Complexity of Sequences 1997. IEEE Computer Society (1997)
Manber, U.: Finding similar files in a large file system. In: Proceedings of the Winter 1994 USENIX Technical Conference, San Francisco, CA (1994)
Rabin, M.O.: Fingerprinting by random polynomials. In: Technical Report TR-15-81. Center for Research in Computing Technology, Harvard University (1981)
DEFLATE Compressed Data Format Specification version 1.3. In: RFC 1951. The Internet Engineering Task Force (1996)
Secure Hash Standard. In: FIPS PUB 180-1. National Institute of Standards and Technology (1995)
Iperf webpage, http://dast.nlanr.net/Projects/Iperf
Saldanha, A.J.: Java Treeview–extensible visualization of microarray data. Bioinformatics 20(17), 3246–3248 (2004)
Wallace, G., Anshus, O.J., Bi, P., Chen, H.Q., Clark, D., Cook, P., Finkelstein, A., Funkhouser, T., Gupta, A., Hibbs, M. et al.: Tools and applications for large-scale display walls. Ieee Computer Graphics and Applications 25(4), 24–33 (2005)
Saeed, A.I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M.: TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34(2), 374–378 (2003)
Hibbs, M.A., Dirksen, N.C., Li, K., Troyanskaya, O.G.: Visualization methods for statistical analysis of microarray clusters. BMC Bioinformatics 6, 115 (2005)
Richardson, T.: The RFB Protocol version 3.8. In: RealVNC Ltd (2005)
Gregory, K.W.: The JPEG still picture compression standard. Commun. ACM 34(4), 30–44 (1991)
Lai, A.M., Nieh, J.: On the performance of wide-area thin-client computing. ACM Trans. Comput. Syst. 24(2), 175–209 (2006)
Gall, D.L.: MPEG: a video compression standard for multimedia applications. Commun. ACM 34(4), 46–58 (1991)
Christiansen, B.O., Schauser, K.E.: Fast Motion Detection for Thin Client Compression. In: Proceedings of the Data Compression Conference (DCC ’02), IEEE Computer Society (2002)
Access Grid, http://www.accessgrid.org
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Bongo, L.A., Wallace, G., Larsen, T., Li, K., Troyanskaya, O. (2007). Systems Support for Remote Visualization of Genomics Applications over Wide Area Networks. In: Dubitzky, W., Schuster, A., Sloot, P.M.A., Schroeder, M., Romberg, M. (eds) Distributed, High-Performance and Grid Computing in Computational Biology. GCCB 2007. Lecture Notes in Computer Science(), vol 4360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69968-2_12
Download citation
DOI: https://doi.org/10.1007/978-3-540-69968-2_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69841-8
Online ISBN: 978-3-540-69968-2
eBook Packages: Computer ScienceComputer Science (R0)