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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 15, Issue 1

Issues

SBML Level 3 package: Render, Version 1, Release 1

Frank T. BergmannORCID iD: http://orcid.org/0000-0001-5553-4702 / Sarah M. KeatingORCID iD: https://orcid.org/0000-0002-3356-3542 / Ralph Gauges / Sven Sahle / Katja Wengler
  • University of Hertfordshire, Hertfordshire, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2018-04-02 | DOI: https://doi.org/10.1515/jib-2017-0078

Abstract

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram. The SBML Level 3 Render package provides a flexible approach to rendering that is independent of both the underlying SBML model and the Layout information. There can be one block of render information that applies to all layouts or an additional block for each layout. Many of the elements used in the current render specification are based on corresponding elements from the SVG specification. This allows us to easily convert a combination of layout information and render information into a SVG drawing.

Keywords: SBML; Render; Visualisation

About the article

Received: 2017-12-14

Accepted: 2018-02-01

Published Online: 2018-04-02


Citation Information: Journal of Integrative Bioinformatics, Volume 15, Issue 1, 20170078, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2017-0078.

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©2018 Frank T. Bergmann et al., published by De Gruyter, Berlin/Boston. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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