Literature DB >> 29605822

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

Frank T Bergmann1,2, Sarah M Keating3, Ralph Gauges4, Sven Sahle1, Katja Wengler5.   

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:  Render; SBML; Visualisation

Mesh:

Year:  2018        PMID: 29605822      PMCID: PMC6167038          DOI: 10.1515/jib-2017-0078

Source DB:  PubMed          Journal:  J Integr Bioinform        ISSN: 1613-4516


  6 in total

1.  Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.

Authors:  Christopher Schölzel; Valeria Blesius; Gernot Ernst; Andreas Dominik
Journal:  NPJ Syst Biol Appl       Date:  2021-06-03

2.  Closing the gap between formats for storing layout information in systems biology.

Authors:  David Hoksza; Piotr Gawron; Marek Ostaszewski; Jan Hasenauer; Reinhard Schneider
Journal:  Brief Bioinform       Date:  2020-07-15       Impact factor: 11.622

Review 3.  Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.

Authors:  Falk Schreiber; Björn Sommer; Gary D Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M Keating; Matthias König; Chris Myers; David Nickerson; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2019-07-13

4.  COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Authors:  Marek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frishman; Luis Cristóbal Monraz Gómez; Julia Somers; Matti Hoch; Shailendra Kumar Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G Yamada; Andreas Dräger; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Francesco Messina; Daniela Börnigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E Ackerman; Jason E Shoemaker; Jeremy Zucker; Kristie Oxford; Jeremy Teuton; Ebru Kocakaya; Gökçe Yağmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; Devasahayam Arokia Balaya Rex; Denise Slenter; Marvin Martens; Nhung Pham; Robin Haw; Bijay Jassal; Lisa Matthews; Marija Orlic-Milacic; Andrea Senff Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek Varusai; Jean-Marie Ravel; Rupsha Fraser; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; Xiaoming Hu; Rupert W Overall; Dieter Maier; Angela Bauch; Benjamin M Gyori; John A Bachman; Carlos Vega; Valentin Grouès; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Peña-Chilet; Kinza Rian; Tomáš Helikar; Bhanwar Lal Puniya; Dezso Modos; Agatha Treveil; Marton Olbei; Bertrand De Meulder; Stephane Ballereau; Aurélien Dugourd; Aurélien Naldi; Vincent Noël; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C Freeman; Franck Augé; Jacques S Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon L Wilighagen; Alexander R Pico; Chris T Evelo; Marc E Gillespie; Lincoln D Stein; Henning Hermjakob; Peter D'Eustachio; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider
Journal:  Mol Syst Biol       Date:  2021-10       Impact factor: 11.429

5.  Specifications of standards in systems and synthetic biology: status and developments in 2021.

Authors:  Falk Schreiber; Padraig Gleeson; Martin Golebiewski; Thomas E Gorochowski; Michael Hucka; Sarah M Keating; Matthias König; Chris J Myers; David P Nickerson; Björn Sommer; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2021-10-22

6.  Specifications of standards in systems and synthetic biology: status and developments in 2020.

Authors:  Falk Schreiber; Björn Sommer; Tobias Czauderna; Martin Golebiewski; Thomas E Gorochowski; Michael Hucka; Sarah M Keating; Matthias König; Chris Myers; David Nickerson; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2020-06-29
  6 in total

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