Abstract
Blotting turns out to be a rather common and effective approach in molecular information processing. An initial pool of molecules considered as sets of individual data becomes spatially separated according to the presence or absence of specific attributes like weight index or chemical groups and labels. In this connection, molecules with similar properties form a spot or blot. Finally, each blot can be visualised or analysed revealing a corresponding score index or count from the number of accumulated molecules. The entire variety of blots which emerge over time provides crucial and condensed information about the molecular system under study. Inspired by the idea to obtain significant data reduction while keeping the essential characteristics of the molecular system as output, we introduce blotting membrane systems as a modelling framework open for numerous applications in data mining. By means of three dedicated case studies, we demonstrate its descriptive capability from an explorative point of view. Our case studies address particle-based numerical integration, which suggests a model for the synchronised 17-year life cycle of Magicicadas. Furthermore, we exemplify electrophoresis as a way to carry out a variant of bucket sort.
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References
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Pardini, G., Tesei, L.: Spatial P Systems. Natural Computing 10, 3–16 (2011)
Bernardini, F., Gheorghe, M., Krasnogor, N.: Quorum sensing P systems. Theoretical Computer Science 371(1–2), 20–33 (2007)
Bowen, B., Steinberg, J., Laemmli, U.K., Weintraub, H.: The detection of DNA-binding proteins by protein blotting. Nucleic Acids Research 8(1), 1–20 (1980)
Chalfie, M., Tu, Y., Euskirchen, G., Ward, W.W., Prasher, D.C.: Green fluorescent protein as a marker for gene expression. Science 263(5148), 802–805 (1994)
Churchman, L.S., Ökten, Z., Rock, R.S., Dawson, J.F., Spudich, J.A.: Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. PNAS 102(5), 1419–1423 (2005)
Cohen, H., Lefebvre, C. (eds.): Handbook of Categorization in Cognitive Science. Elsevier (2005)
Dawson, T.E., Pate, J.S.: Seasonal water uptake and movement in root systems of plants of dimorphic root morphology: A stable isotope investigation. Oecologia 107, 13–20 (1996)
Fayyad, U., Piatetsky-Shapiro, G., Smyth, P.: From Data Mining to Knowledge Discovery in Databases. American Assoc. for Artificial Intelligence 3, 37–54 (1996)
Hames, D., Hooper, N.: Biochemistry, 3rd edn. Taylor & Francis (2005)
Han, J., Kamber, M., Pei, J.: Data Mining: Concepts and Techniques. Morgan Kaufmann (2011)
Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Series in Statistics. Springer Verlag (2009)
Hinze, T., Fassler, R., Lenser, T., Dittrich, P.: Register Machine Computations on Binary Numbers by Oscillating and Catalytic Chemical Reactions Modelled using Mass-Action Kinetics. International Journal of Foundations of Computer Science 20(3), 411–426 (2009)
Hinze, T., Schell, B., Schumann, M., Bodenstein, C.: Maintenance of Chronobiological Information by P System Mediated Assembly of Control Units for Oscillatory Waveforms and Frequency. In: Csuhaj-Varjú, E., Gheorghe, M., Rozenberg, G., Salomaa, A., Vaszil, Gy. (eds.) CMC 2012. LNCS, vol. 7762, pp. 208–227. Springer, Heidelberg (2013)
Hinze, T., Behre, J., Bodenstein, C., Escuela, G., Grünert, G., Hofstedt, P., Sauer, P., Hayat, S., Dittrich, P.: Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology. In: Frisco, P., Gheorghe, M., Perez-Jimenez, M.J. (eds.) Applications of Membrane Computing in Systems and Synthetic Biology. Series Emergence, Complexity, and Computation, vol. 7, pp. 133–173. Springer Verlag (2014)
Johannson, B.G.: Agarose Gel Electrophoresis. Scandinavian Journal of Clinical and Laboratory Investigation 29(s124), 7–19 (1972)
Kremers, G.J., Gilbert, S.G., Cranfill, P.J., Davidson, M.W., Piston, D.W.: Fluorescent proteins at a glance. Journal of Cell Science 124, 157–160 (2011)
Marchetti, L., Manca, V., Pagliarini, R., Bollig-Fischer, A.: MP Modelling for Systems Biology: Two Case Studies. In: Frisco, P., Gheorghe, M., Perez-Jimenez, M.J. (eds.) Applications of Membrane Computing in Systems and Synthetic Biology. Series Emergence, Complexity, and Computation, vol. 7, pp. 223–243. Springer Verlag (2014)
Marlatt, C.L.: The periodical cicada. Bull. U.S. Dept. Agri. Div. Entomol. Bull. 18, 52 (1907)
Miller, M.B., Bassler, B.L.: Quorum Sensing in Bacteria. Annu. Rev. Microbiol. 55, 165–199 (2001)
Păun, Gh.: Membrane Computing: An Introduction. Springer Verlag (2002)
Sabnis, R.W.: Handbook of biological dyes and stains: synthesis and industrial application. Wiley-VCH (2010)
Southern, E.M.: Detection of specific sequences among DNA fragments separated by gel electrophoresis. Journal of Molecular Biology 98(3), 503–517 (1975)
Sparmann, A., van Lohuizen, M.: Polycomb silencers control cell fate, development and cancer. Nature Reviews Cancer 6, 846–856 (2006)
Towbin, H., Staehelin, T., Gordon, J.: Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: Procedure and some applications. PNAS 76(9), 4350–4354 (1979)
Nüsslein-Volhard, C.: Determination of the embryonic axes of Drosophila. Development 113, 1–10 (1991)
Lizotte-Waniewski, M., Tawe, W., Guiliano, D.B., Lu, W., Liu, J., Williams, S.A., Lustigman, S.: Identification of Potential Vaccine and Drug Target Candidates by Expressed Sequence Tag Analysis and Immunoscreening of Onchocerca volvulus Larval cDNA Libraries. Infection and Immunity 68(6), 3491–3501 (2000)
Westermeier, R.: Electrophoresis in Practice. Wiley-VCH (2005)
Williams, K.S., Simon, C.: The ecology, behavior and evolution of periodical cicadas. Annual Review of Entomology 40, 269–295 (1995)
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Hinze, T., Grützmann, K., Höckner, B., Sauer, P., Hayat, S. (2014). Categorised Counting Mediated by Blotting Membrane Systems for Particle-Based Data Mining and Numerical Algorithms. In: Gheorghe, M., Rozenberg, G., Salomaa, A., Sosík, P., Zandron, C. (eds) Membrane Computing. CMC 2014. Lecture Notes in Computer Science(), vol 8961. Springer, Cham. https://doi.org/10.1007/978-3-319-14370-5_15
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