Literature DB >> 28049131

SED-ML web tools: generate, modify and export standard-compliant simulation studies.

Frank T Bergmann1, David Nickerson2, Dagmar Waltemath3, Martin Scharm3.   

Abstract

Summary: The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The Web Tools implement all current SED-ML specifications and, thus, support complex modifications and co-simulation of models in SBML and CellML formats. Ultimately, the Web Tools lower the bar on working with SED-ML documents and help users create valid simulation descriptions. Availability and Implementation: http://sysbioapps.dyndns.org/SED-ML_Web_Tools/ . Contact: fbergman@caltech.edu .
© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Mesh:

Year:  2017        PMID: 28049131      PMCID: PMC5860579          DOI: 10.1093/bioinformatics/btw812

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  7 in total

1.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

2.  Web-based kinetic modelling using JWS Online.

Authors:  Brett G Olivier; Jacky L Snoep
Journal:  Bioinformatics       Date:  2004-04-08       Impact factor: 6.937

3.  Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Authors:  Frank T Bergmann; Jonathan Cooper; Nicolas Le Novère; David Nickerson; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2015-09-04

4.  COPASI--a COmplex PAthway SImulator.

Authors:  Stefan Hoops; Sven Sahle; Ralph Gauges; Christine Lee; Jürgen Pahle; Natalia Simus; Mudita Singhal; Liang Xu; Pedro Mendes; Ursula Kummer
Journal:  Bioinformatics       Date:  2006-10-10       Impact factor: 6.937

5.  Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

Authors:  Dagmar Waltemath; Richard Adams; Frank T Bergmann; Michael Hucka; Fedor Kolpakov; Andrew K Miller; Ion I Moraru; David Nickerson; Sven Sahle; Jacky L Snoep; Nicolas Le Novère
Journal:  BMC Syst Biol       Date:  2011-12-15

Review 6.  Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Authors:  Michael Hucka; David P Nickerson; Gary D Bader; Frank T Bergmann; Jonathan Cooper; Emek Demir; Alan Garny; Martin Golebiewski; Chris J Myers; Falk Schreiber; Dagmar Waltemath; Nicolas Le Novère
Journal:  Front Bioeng Biotechnol       Date:  2015-02-24

7.  COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Authors:  Frank T Bergmann; Richard Adams; Stuart Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K Miller; David P Nickerson; Brett G Olivier; Nicolas Rodriguez; Herbert M Sauro; Martin Scharm; Stian Soiland-Reyes; Dagmar Waltemath; Florent Yvon; Nicolas Le Novère
Journal:  BMC Bioinformatics       Date:  2014-12-14       Impact factor: 3.169

  7 in total
  3 in total

1.  Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.

Authors:  Natalie J Stanford; Martin Scharm; Paul D Dobson; Martin Golebiewski; Michael Hucka; Varun B Kothamachu; David Nickerson; Stuart Owen; Jürgen Pahle; Ulrike Wittig; Dagmar Waltemath; Carole Goble; Pedro Mendes; Jacky Snoep
Journal:  Methods Mol Biol       Date:  2019

2.  A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.

Authors:  Pei-Chi Yang; Shweta Purawat; Pek U Ieong; Mao-Tsuen Jeng; Kevin R DeMarco; Igor Vorobyov; Andrew D McCulloch; Ilkay Altintas; Rommie E Amaro; Colleen E Clancy
Journal:  PLoS Comput Biol       Date:  2019-03-08       Impact factor: 4.475

3.  Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

Authors:  J Kyle Medley; Kiri Choi; Matthias König; Lucian Smith; Stanley Gu; Joseph Hellerstein; Stuart C Sealfon; Herbert M Sauro
Journal:  PLoS Comput Biol       Date:  2018-06-15       Impact factor: 4.475

  3 in total

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