ArticleIEEE transactions on bio-medical engineering2016
Guidelines for Reproducibly Building and Simulating Systems Biology Models.
Article in IEEE transactions on bio-medical engineering, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)Autophagy · 2021Guideline
- A Practical Guide to Reproducible Modeling for Biochemical Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models.Entropy (Basel, Switzerland) · 2022Article
- Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.NPJ systems biology and applications · 2021Article
- Isolating structural errors in reaction networks in systems biology.Bioinformatics (Oxford, England) · 2021Article
- Article
- Best Practices for Making Reproducible Biochemical Models.Cell systems · 2020Review
- Towards reproducible computational drug discovery.Journal of cheminformatics · 2020Review
- Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate.Wellcome open research · 2020Article
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.Frontiers in bioengineering and biotechnology · 2020Article
- Robust latent-variable interpretation of in vivo regression models by nested resampling.Scientific reports · 2019Article
- Parameter Estimation and Uncertainty Quantification for Systems Biology Models.Current opinion in systems biology · 2019Article
- Article
- Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.PLoS computational biology · 2018Article
- Emerging whole-cell modeling principles and methods.Current opinion in biotechnology · 2018Review
- Synthetic Biology: Engineering Living Systems from Biophysical Principles.Biophysical journal · 2017Review
- Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices.Cellular logistics · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
objectiveReproducibility is the cornerstone of the scientific method. However, currently, many systems biology models cannot easily be reproduced. This paper presents methods that address this problem.
methodsWe analyzed the recent Mycoplasma genitalium whole-cell (WC) model to determine the requirements for reproducible modeling.
resultsWe determined that reproducible modeling requires both repeatable model building and repeatable simulation.
conclusionNew standards and simulation software tools are needed to enhance and verify the reproducibility of modeling. New standards are needed to explicitly document every data source and assumption, and new deterministic parallel simulation tools are needed to quickly simulate large, complex models. SIGNIFICANCE: We anticipate that these new standards and software will enable researchers to reproducibly build and simulate more complex models, including WC models.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.