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Visualizing biological data—now and in the future

Methods and tools for visualizing biological data have improved considerably over the last decades, but they are still inadequate for some high-throughput data sets. For most users, a key challenge is to benefit from the deluge of data without being overwhelmed by it. This challenge is still largely unfulfilled and will require the development of truly integrated and highly useable tools.

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Figure 1: Possible integrated visualization environment.

References

  1. Nielsen, C.B., Cantor, M., Dubchak, I., Gordon, D. & Wang, T. Nat. Methods 7, S5–S15 (2010).

    Article  CAS  Google Scholar 

  2. Procter, J.B. et al. Nat. Methods 7, S16–S25 (2010).

    Article  CAS  Google Scholar 

  3. O'Donoghue, S.I. et al. Nat. Methods 7, S42–S55 (2010).

    Article  CAS  Google Scholar 

  4. Gehlenborg, N. et al. Nat. Methods 7, S56–S68 (2010).

    Article  CAS  Google Scholar 

  5. Walter, T. et al. Nat. Methods 7, S26–S41 (2010).

    Article  CAS  Google Scholar 

  6. Shannon, P. et al. Genome Res. 13, 2498–2504 (2003).

    Article  CAS  Google Scholar 

  7. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. & Barton, G.J. Bioinformatics 25, 1189–1191 (2009).

    Article  CAS  Google Scholar 

  8. Rhead, B. et al. Nucleic Acids Res. 38 (database issue), D613–D619 (2010).

    Article  CAS  Google Scholar 

  9. Berman, H., Henrick, K. & Nakamura, H. Nat. Struct. Biol. 10, 980 (2003).

    Article  CAS  Google Scholar 

  10. Martone, M.E. et al. J. Struct. Biol. 161, 220–231 (2008).

    Article  Google Scholar 

  11. Shneiderman, B. & Plaisant, C. Designing the User Interface: Strategies for Effective Human-Computer Interaction 5th edn. (Addison Wesley, Reading, Massachusetts, USA, 2009).

    Google Scholar 

  12. Thomas, J.J. & Cook, K.A. Illuminating the Path: The Research and Development Agenda for Visual Analytics (National Visual Analytics Center & IEEE, Richland, Washington, USA, 2005).

    Google Scholar 

  13. Saraiya, P., North, C. & Duca, K. IEEE Trans. Vis. Comput. Graph. 11, 443–456 (2005).

    Article  Google Scholar 

  14. Mirel, B. J. Biomed. Discov. Collab. 4, 2 (2009).

    Article  Google Scholar 

  15. Nielsen, C.B., Jackman, S.D., Birol, I. & Jones, S.J.M. IEEE Trans. Vis. Comput. Graph. 15, 881–888 (2009).

    Article  Google Scholar 

  16. Grasso, C., Quist, M., Ke, K. & Lee, C. Bioinformatics 19, 1446–1448 (2003).

    Article  CAS  Google Scholar 

  17. Le Novère, N. et al. Nat. Biotechnol. 27, 735–741 (2009).

    Article  Google Scholar 

  18. Ball, R. & North, C. Comput. Graph. 31, 380–400 (2007).

    Article  Google Scholar 

  19. Freeman, T.C. et al. PLOS Comput. Biol. 3, e206 (2007).

    Article  Google Scholar 

  20. Gillet, A., Sanner, M., Stoffler, D. & Olson, A. Structure 13, 483–491 (2005).

    Article  CAS  Google Scholar 

  21. Garcia-Ruiz, M.A. & Gutierrez-Pulido, J.R. Interact. Comput. 18, 853–868 (2006).

    Article  Google Scholar 

  22. Enright, A.J., Van Dongen, S. & Ouzounis, C.A. Nucleic Acids Res. 30, 1575–1584 (2002).

    Article  CAS  Google Scholar 

  23. Dowell, R.D., Jokerst, R.M., Day, A., Eddy, S.R. & Stein, L. BMC Bioinformatics 2, 7 (2001).

    Article  CAS  Google Scholar 

  24. Shannon, P.T., Reiss, D.J., Bonneau, R. & Baliga, N.S. BMC Bioinformatics 7, 176 (2006).

    Article  Google Scholar 

  25. Burrage, K., Hood, L. & Ragan, M.A. Brief. Bioinform. 7, 390–398 (2006).

    Article  CAS  Google Scholar 

  26. Suderman, M. & Hallett, M. Bioinformatics 23, 2651–2659 (2007).

    Article  CAS  Google Scholar 

  27. Saalfeld, S., Cardona, A., Hartenstein, V. & Tomancák, P. Bioinformatics 25, 1984–1986 (2009).

    Article  CAS  Google Scholar 

Download references

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Correspondence to Seán I O'Donoghue.

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O'Donoghue, S., Gavin, AC., Gehlenborg, N. et al. Visualizing biological data—now and in the future. Nat Methods 7 (Suppl 3), S2–S4 (2010). https://doi.org/10.1038/nmeth.f.301

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