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EClerize: A Customized Force-Directed Layout Algorithm for Biological Networks with EC Attributes
Date
2017-05-10
Author
Danacı, Hasan Fehmi
Atalay, Rengül
Atalay, Mehmet Volkan
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https://www.iscb.org/glbio2017
https://hdl.handle.net/11511/80791
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EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes
Danaci, Hasan Fehmi; Atalay, Rengül; Atalay, Mehmet Volkan (2018-08-01)
Visualizing large-scale data produced by the high throughput experiments as a biological graph leads to better understanding and analysis. This study describes a customized force-directed layout algorithm, EClerize, for biological graphs that represent pathways in which the nodes are associated with Enzyme Commission (EC) attributes. The nodes with the same EC class numbers are treated as members of the same cluster. Positions of nodes are then determined based on both the biological similarity and the conn...
ECPred: An Automated Enzymatic Function Prediction Tool Based on Combination of Different Classifiers
Dalkıran, Alperen; Rifaioğlu, Ahmet Süreyya; Doğan, Tunca; Atalay, Mehmet Volkan; Martin, Maria Jesus; Atalay, Rengül (2017-05-10)
EwE-F 1.0: an implementation of Ecopath with Ecosim in Fortran 95/2003 for coupling and integration with other models
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Societal and scientific challenges foster the implementation of the ecosystem approach to marine ecosystem analysis and management, which is a comprehensive means of integrating the direct and indirect effects of multiple stressors on the different components of ecosystems, from physical to chemical and biological and from viruses to fishes and marine mammals. Ecopath with Ecosim (EwE) is a widely used software package, which offers capability for a dynamic description of the multiple interactions occurring...
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature
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Background: The automated prediction of the enzymatic functions of uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most of these studies are limited to specific functional classes and levels of the Enzyme Commission (EC) number hierarchy. Besides, most of the previous methods incorporated only a single input feature type, which limits the applicability to the wide functional space. Here, we proposed a novel enzymatic f...
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Diverse Density (DD) algorithm is a well-known multiple instance learning method, also known to be effective to automatically identify sub-goals and improve Reinforcement Learning (RL). Expectation-Maximization Diverse Density (EMDD) improves DD in terms of both speed and accuracy. This study adapts EMDD to automatically identify subgoals for RL which is shown to perform significantly faster (3 to 10 times) than its predecessor, without sacrificing solution quality. The performance of the proposed method na...
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H. F. Danacı, R. Atalay, and M. V. Atalay, “EClerize: A Customized Force-Directed Layout Algorithm for Biological Networks with EC Attributes,” 2017, Accessed: 00, 2021. [Online]. Available: https://www.iscb.org/glbio2017.