ArticleIEEE transactions on bio-medical engineering2016
Toward Community Standards and Software for Whole-Cell Modeling.
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 24 papers.
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Who cites it
24 citing papers in PubMed.
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- Systems Biology in ELIXIR: modelling in the spotlight.F1000Research · 2022Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
- Bayesian metamodeling of complex biological systems across varying representations.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- BiPSim: a flexible and generic stochastic simulator for polymerization processes.Scientific reports · 2021Article
- A biochemical network modeling of a whole-cell.Scientific reports · 2020Article
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.Frontiers in bioengineering and biotechnology · 2020Article
- Genome-driven cell engineering review:Essays in biochemistry · 2019Review
- BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data.Nucleic acids research · 2019Article
- CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Recent advances in biomedical simulations: a manifesto for model engineering.F1000Research · 2019Review
- HEPATOKIN1 is a biochemistry-based model of liver metabolism for applications in medicine and pharmacology.Nature communications · 2018Article
- Emerging whole-cell modeling principles and methods.Current opinion in biotechnology · 2018Review
- Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.Journal of integrative bioinformatics · 2018Article
- A blueprint for human whole-cell modeling.Current opinion in systems biology · 2018Article
- From word models to executable models of signaling networks using automated assembly.Molecular systems biology · 2017Article
- How to deal with parameters for whole-cell modelling.Journal of the Royal Society, Interface · 2017Review
- Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices.Cellular logistics · 2017Article
Corrections and comments
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Authors and funding
57 authors.
Funding
Abstract
objectiveWhole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.
methodsWe organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.
resultsOur analysis revealed several challenges to representing WC models using the current standards.
conclusionWe, therefore, propose several new WC modeling standards, software, and databases. SIGNIFICANCE: We anticipate that these new standards and software will enable more comprehensive models.
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Registered trials
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