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Biosystems

Title:		PhDSeeker: Pheromone-Directed Seeker for metabolic pathways
Author(s):		Gerard MF; Comelli RN;
Address:		"Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina. Electronic address: mgerard@sinc.unl.edu.ar. Departamento de Medio Ambiente, Fac. de Ingenieria y Ciencias Hidricas (FICH), Univ. Nacional del Litoral (UNL), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET). Ciudad Universitaria CC 242 Paraje El Pozo, 3000, Santa Fe, Argentina. Electronic address: rcomelli@fich.unl.edu.ar"
Journal Title:		Biosystems
Year:		2020
Volume:		20200922
Issue:
Page Number:		104259 -
DOI:		10.1016/j.biosystems.2020.104259
ISSN/ISBN:		1872-8324 (Electronic) 0303-2647 (Linking)
Abstract:		"Manually finding relationship networks among compounds can be a hard and time-consuming task. However, this process is fundamental when looking for a metabolic pathway that explains how multiple compounds are related, to identify relevant pathways in organisms, filling gaps on metabolic networks, or when new mechanisms for the synthesis of important compounds are sought. Here, we present PhDSeeker, a new tool for the automatic search of metabolic pathways. This tool is able to relate simultaneously several compounds. Furthermore, its flexibility allows it to be easily configured for addressing a wide range of situations. Solutions found are provided not only in plain text but also as interactive representations that can be analyzed in a web browser. Source code is available at https://github.com/sinc-lab/phdseeker. A web service is also available at https://sinc.unl.edu.ar/web-demo/phds/. Several fully documented study cases, including their settings and solutions files, are also provided as Supplementary Material"
Keywords:		*Algorithms Computational Biology/*methods Data Mining/*methods Internet *Metabolic Networks and Pathways Metabolomics/*methods Software Ant colony optimization Metabolic network representation Metabolic pathway searching Pathways synthesis;
Notes:		"MedlineGerard, Matias F Comelli, Raul N eng Ireland 2020/09/26 Biosystems. 2020 Dec; 198:104259. doi: 10.1016/j.biosystems.2020.104259. Epub 2020 Sep 22"