caa a22 4500 605468583 CHVBK 20210128100317.0 cr unu---uuuuu 210128e20150601xx s 000 0 eng 10.1007/s00500-014-1467-6 doi (NATIONALLICENCE)springer-10.1007/s00500-014-1467-6 An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems [Elektronische Daten] [Zujian Wu, Wei Pang, George Coghill] Computational modelling of biochemical systems based on top-down and bottom-up approaches has been well studied over the last decade. In this research, after illustrating how to generate atomic components by a set of given reactants and two user pre-defined component patterns, we propose an integrative top-down and bottom-up modelling approach for stepwise qualitative exploration of interactions among reactants in biochemical systems. Evolution strategy is applied to the top-down modelling approach to compose models, and simulated annealing is employed in the bottom-up modelling approach to explore potential interactions based on models constructed from the top-down modelling process. Both the top-down and bottom-up approaches support stepwise modular addition or subtraction for the model evolution. Experimental results indicate that our modelling approach is feasible to learn the relationships among biochemical reactants qualitatively. In addition, hidden reactants of the target biochemical system can be obtained by generating complex reactants in corresponding composed models. Moreover, qualitatively learned models with inferred reactants and alternative topologies can be used for further web-lab experimental investigations by biologists of interest, which may result in a better understanding of the system. The Author(s), 2014 Evolution strategy nationallicence Simulated annealing nationallicence Qualitative model learning nationallicence Top-down and bottom-up modelling nationallicence Systems biology nationallicence Wu Zujian College of Information Science and Technology, Jinan University, 510632, Guangzhou, People's Republic of China aut Pang Wei School of Natural and Computing Sciences, University of Aberdeen, AB24 3UE, Aberdeen, Scotland, UK aut Coghill George School of Natural and Computing Sciences, University of Aberdeen, AB24 3UE, Aberdeen, Scotland, UK aut Soft Computing Springer Berlin Heidelberg 19/6(2015-06-01), 1595-1610 1432-7643 19:6<1595 2015 19 500 https://doi.org/10.1007/s00500-014-1467-6 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00500-014-1467-6 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Wu Zujian College of Information Science and Technology, Jinan University, 510632, Guangzhou, People's Republic of China aut NATIONALLICENCE 700 1- Pang Wei School of Natural and Computing Sciences, University of Aberdeen, AB24 3UE, Aberdeen, Scotland, UK aut NATIONALLICENCE 700 1- Coghill George School of Natural and Computing Sciences, University of Aberdeen, AB24 3UE, Aberdeen, Scotland, UK aut NATIONALLICENCE 773 0- Soft Computing Springer Berlin Heidelberg 19/6(2015-06-01), 1595-1610 1432-7643 19:6<1595 2015 19 500