Reproducible Research Using Biomodels
- 1 December 2018
- journal article
- research article
- Published by Springer Science and Business Media LLC in Bulletin of Mathematical Biology
- Vol. 80 (12), 3081-3087
- https://doi.org/10.1007/s11538-018-0498-z
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.Keywords
Funding Information
- National Institute of General Medical Sciences (GM080219)
This publication has 33 references indexed in Scilit:
- Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup LanguageBMC Systems Biology, 2011
- Reproducible Research in Computational ScienceScience, 2011
- Minimum Information About a Simulation Experiment (MIASE)PLoS Computational Biology, 2011
- NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological DetailPLoS Computational Biology, 2010
- Accessible Reproducible ResearchScience, 2010
- The Systems Biology Graphical NotationNature Biotechnology, 2009
- Virtual Cell modelling and simulation software environmentIET Systems Biology, 2008
- COPASI—a COmplex PAthway SImulatorBioinformatics, 2006
- Minimum information requested in the annotation of biochemical models (MIRIAM)Nature Biotechnology, 2005
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsBioinformatics, 2003