ReviewCell systems2020
Best Practices for Making Reproducible Biochemical Models.
Review in Cell systems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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
21 citing papers in PubMed.
- A standardized workflow for kinetic metabolic model curation and dissemination.PLoS computational biology · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- A Roadmap for the Future of Systems Biology in Cancer Research.Cancer research · 2025Review
- SIMPROV: Provenance capturing for simulation studies.PloS one · 2025Article
- Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Article
- Adapting modeling and simulation credibility standards to computational systems biology.Journal of translational medicine · 2023Review
- Standards, dissemination, and best practices in systems biology.Current opinion in biotechnology · 2023Review
- Article
- Reproducibility and FAIR principles: the case of a segment polarity network model.Frontiers in cell and developmental biology · 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
- Physiologically Based Pharmacokinetic Modeling of Nanoparticle Biodistribution: A Review of Existing Models, Simulation Software, and Data Analysis Tools.International journal of molecular sciences · 2022Review
- A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.Nature communications · 2022Article
- GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems.ACS synthetic biology · 2022Article
- Kinetic Modeling ofMetabolites · 2022Review
- A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle.International journal of molecular sciences · 2021Article
- Programmatic modeling for biological systems.Current opinion in systems biology · 2021Article
- Relating simulation studies by provenance-Developing a family of Wnt signaling models.PLoS computational biology · 2021Article
- To Sobol or not to Sobol? The effects of sampling schemes in systems biology applications.Mathematical biosciences · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Like many scientific disciplines, dynamical biochemical modeling is hindered by irreproducible results. This limits the utility of biochemical models by making them difficult to understand, trust, or reuse. We comprehensively list the best practices that biochemical modelers should follow to build reproducible biochemical model artifacts-all data, model descriptions, and custom software used by the model-that can be understood and reused. The best practices provide advice for all steps of a typical biochemical modeling workflow in which a modeler collects data; constructs, trains, simulates, and validates the model; uses the predictions of a model to advance knowledge; and publicly shares the model artifacts. The best practices emphasize the benefits obtained by using standard tools and formats and provides guidance to modelers who do not or cannot use standards in some stages of their modeling workflow. Adoption of these best practices will enhance the ability of researchers to reproduce, understand, and reuse biochemical 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.