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Title:The Pathway Editor: A tool for managing complex biological networks
Authors: Anatoly Sorokin ; Kirill Paly ; Alexey Selkov ; Oleg Demin ; Serge Dronov ; Peter Ghazal ; Igor Goryanin
Date:Nov 2006
Publication Title:IBM Journal of research and Development
Publication Type:Journal Article Publication Status:Published
Volume No:50(6) Page Nos:561-573
Biological networks are systems of biochemical processes inside a cell that involve cellular constituents such as DNA, RNA, proteins, and various small molecules. Pathway maps are often used to represent the structure of such networks with associated biological information. Several pathway editors exist, and they vary according to specific domains of knowledge. This paper presents a review of existing pathway editors, along with an introduction to the Edinburgh Pathway Editor (EPE). EPE was designed for the annotation, visualization, and presentation of a wide variety of biological networks that include metabolic, genetic, and signal transduction pathways. EPE is based on a metadata-driven architecture. The editor supports the presentation and annotation of maps, in addition to the storage and retrieval of reaction kinetics information in relational databases that are either local or remote. EPE also has facilities for linking graphical objects to external databases and Web resources, and is capable of reproducing most existing graphical notations and visual representations of pathway maps. In summary, EPE provides a highly flexible tool for combining visualization, editing, and database manipulation of information relating to biological networks. EPE is open-source software, distributed under the Eclipse open-source application platform license.
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Bibtex format
author = { Anatoly Sorokin and Kirill Paly and Alexey Selkov and Oleg Demin and Serge Dronov and Peter Ghazal and Igor Goryanin },
title = {The Pathway Editor: A tool for managing complex biological networks},
journal = {IBM Journal of research and Development},
year = 2006,
month = {Nov},
volume = {50(6)},
pages = {561-573},
url = {},

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