Literature DB >> 30191472

Reproducible Research Using Biomodels.

Pedro Mendes1.   

Abstract

Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area of research could easily be achieved by making use of existing resources, such as supplying models in standard formats and depositing code, models, and results in public repositories.

Entities:  

Keywords:  Biomodels; Reproducibility; Standards

Mesh:

Year:  2018        PMID: 30191472      PMCID: PMC6234049          DOI: 10.1007/s11538-018-0498-z

Source DB:  PubMed          Journal:  Bull Math Biol        ISSN: 0092-8240            Impact factor:   1.758


  31 in total

1.  Reproducible research in computational science.

Authors:  Roger D Peng
Journal:  Science       Date:  2011-12-02       Impact factor: 47.728

2.  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

3.  Computer science. Accessible reproducible research.

Authors:  Jill P Mesirov
Journal:  Science       Date:  2010-01-22       Impact factor: 47.728

4.  Reproducible research and Biostatistics.

Authors:  Roger D Peng
Journal:  Biostatistics       Date:  2009-07       Impact factor: 5.899

5.  SBRML: a markup language for associating systems biology data with models.

Authors:  Joseph O Dada; Irena Spasić; Norman W Paton; Pedro Mendes
Journal:  Bioinformatics       Date:  2010-02-21       Impact factor: 6.937

6.  Reproducibility of research in biophysics.

Authors:  Les Loew; Dorothy Beckett; Edward H Egelman; Suzanne Scarlata
Journal:  Biophys J       Date:  2015-04-07       Impact factor: 4.033

7.  1,500 scientists lift the lid on reproducibility.

Authors:  Monya Baker
Journal:  Nature       Date:  2016-05-26       Impact factor: 49.962

8.  Enhancing reproducibility for computational methods.

Authors:  Victoria Stodden; Marcia McNutt; David H Bailey; Ewa Deelman; Yolanda Gil; Brooks Hanson; Michael A Heroux; John P A Ioannidis; Michela Taufer
Journal:  Science       Date:  2016-12-09       Impact factor: 47.728

9.  Minimum Information About a Simulation Experiment (MIASE).

Authors:  Dagmar Waltemath; Richard Adams; Daniel A Beard; Frank T Bergmann; Upinder S Bhalla; Randall Britten; Vijayalakshmi Chelliah; Michael T Cooling; Jonathan Cooper; Edmund J Crampin; Alan Garny; Stefan Hoops; Michael Hucka; Peter Hunter; Edda Klipp; Camille Laibe; Andrew K Miller; Ion Moraru; David Nickerson; Poul Nielsen; Macha Nikolski; Sven Sahle; Herbert M Sauro; Henning Schmidt; Jacky L Snoep; Dominic Tolle; Olaf Wolkenhauer; Nicolas Le Novère
Journal:  PLoS Comput Biol       Date:  2011-04-28       Impact factor: 4.475

10.  BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

Authors:  Nicolas Le Novère; Benjamin Bornstein; Alexander Broicher; Mélanie Courtot; Marco Donizelli; Harish Dharuri; Lu Li; Herbert Sauro; Maria Schilstra; Bruce Shapiro; Jacky L Snoep; Michael Hucka
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

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  3 in total

Review 1.  Computational models in systems biology: standards, dissemination, and best practices.

Authors:  Luis Sordo Vieira; Reinhard C Laubenbacher
Journal:  Curr Opin Biotechnol       Date:  2022-02-23       Impact factor: 10.279

Review 2.  Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review.

Authors:  Sherli Koshy-Chenthittayil; Linda Archambault; Dhananjai Senthilkumar; Reinhard Laubenbacher; Pedro Mendes; Anna Dongari-Bagtzoglou
Journal:  Microorganisms       Date:  2021-02-17

Review 3.  Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways.

Authors:  Richard Fitzpatrick; Melanie I Stefan
Journal:  Neuroinformatics       Date:  2022-05-11
  3 in total

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