BEW: Bioinformatics Workbench for Analysis of Biofilms Experimental Data

  • Gael Pérez RodríguezEmail author
  • Daniel Glez-Peña
  • Nuno F. Azevedo
  • Maria Olívia Pereira
  • Florentino Fdez-Riverola
  • Anália Lourenço
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 294)


Biofilms research has evolved considerably in the last decade and is now generating large volumes of heterogeneous data. MIABiE, the international initiative on Biofilms, is devising guidelines for data interchange, and some databases provide access to biofilms experiments. However, the field is lacking appropriate bioinformatics tools in support of increasing operational and analytical needs. This paper presents a flexible and extensible open-source workbench for the operation and analysis of biofilms experiments, as follows: (i) the creation of customised experiments, (ii) the collection of various analytical results, following community standardisation guidelines and (iii) on-demand reporting and statistical evaluation.


Biofilms standard operating procedures data interchange data analysis 


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  1. 1.
    Hall-Stoodley, L., Costerton, J.W., Stoodley, P.: Bacterial biofilms: from the natural environment to infectious diseases. Nat. Rev. Microbiol. 2, 95–108 (2004)CrossRefGoogle Scholar
  2. 2.
    Donlan, R.M.: Biofilms: microbial life on surfaces. Emerg. Infect. Dis. 8, 881–890 (2002)CrossRefGoogle Scholar
  3. 3.
    Davey, M.E., O’toole, G.A.: Microbial biofilms: from ecology to molecular genetics. Microbiol. Mol. Biol. Rev. 64, 847–867 (2000)CrossRefGoogle Scholar
  4. 4.
    Jain, A., Gupta, Y., Agrawal, R., Khare, P., Jain, S.K.: Biofilms–a microbial life perspective: a critical review. Crit. Rev. Ther. Drug Carrier Syst. 24, 393–443 (2007)CrossRefGoogle Scholar
  5. 5.
    Römling, U., Balsalobre, C.: Biofilm infections, their resilience to therapy and innovative treatment strategies. J. Intern. Med. 272, 541–561 (2012)CrossRefGoogle Scholar
  6. 6.
    Peters, B.M., Jabra-Rizk, M.A., O’May, G.A., Costerton, J.W., Shirtliff, M.E.: Polymicrobial interactions: impact on pathogenesis and human disease. Clin. Microbiol. Rev. 25, 193–213 (2012)CrossRefGoogle Scholar
  7. 7.
    Azevedo, N.F., Lopes, S.P., Keevil, C.W., Pereira, M.O., Vieira, M.J.: Time to “go large” on biofilm research: advantages of an omics approach. Biotechnol. Lett. 31, 477–485 (2009)CrossRefGoogle Scholar
  8. 8.
    Buckingham-Meyer, K., Goeres, D.M., Hamilton, M.A.: Comparative evaluation of biofilm disinfectant efficacy tests. J. Microbiol. Methods 70, 236–244 (2007)CrossRefGoogle Scholar
  9. 9.
    Hamilton, M.A.: KSA-SM-03 - Desirable attributes of a standardized method. Stand. METHODS Test. Surf. Disinfect (2010)Google Scholar
  10. 10.
    Lourenço, A., Ferreira, A., Veiga, N., Machado, I., Pereira, M.O., Azevedo, N.F.: BiofOmics: A Web Platform for the Systematic and Standardized Collection of High-Throughput Biofilm Data. PLoS One 7, e39960 (2012)Google Scholar
  11. 11.
    Sousa, A.M., Ferreira, A., Azevedo, N.F., Pereira, M.O., Lourenço, A.: Computational approaches to standard-compliant biofilm data for reliable analysis and integration. J. Integr. Bioinform. 9, 203 (2012)Google Scholar
  12. 12.
    Bray, T., Paoli, J., Sperberg-McQueen, C.M.: Extensible markup language, XML (1998),
  13. 13.
    Sreenivasaiah, P.K., Kim, D.H.: Current trends and new challenges of databases and web applications for systems driven biological research. Front. Physiol. 1, 147 (2010)CrossRefGoogle Scholar
  14. 14.
    Glez-Peña, D., Reboiro-Jato, M., Maia, P., Rocha, M., Díaz, F., Fdez-Riverola, F.: AIBench: a rapid application development framework for translational research in biomedicine. Comput. Methods Programs Biomed. 98, 191–203 (2010)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Gael Pérez Rodríguez
    • 1
    Email author
  • Daniel Glez-Peña
    • 1
  • Nuno F. Azevedo
    • 2
  • Maria Olívia Pereira
    • 3
  • Florentino Fdez-Riverola
    • 1
  • Anália Lourenço
    • 1
    • 2
  1. 1.ESEI - Escuela Superior de Ingeniería Informática, Edificio PolitécnicoOurenseSpain
  2. 2.LEPABE – Dep. of Chemical Engineering, Faculty of EngineeringUniversity of PortoPortoPortugal
  3. 3.IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of MinhoBragaPortugal

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