GuidelineJournal of integrative bioinformatics2015
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.
Guideline in Journal of integrative bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it.
- SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.Journal of integrative bioinformatics · 2015Guideline
- Metabolic modeling elucidates phenformin and atpenin A5 as broad-spectrum antiviral drugs against RNA viruses.Communications biology · 2025Article
- Immune digital twins for complex human pathologies: applications, limitations, and challenges.NPJ systems biology and applications · 2024Review
- Article
- Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.Journal of integrative bioinformatics · 2024Article
- Hierarchical modelling of microbial communities.Bioinformatics (Oxford, England) · 2023Article
- Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.Bioinformatics advances · 2023Article
- A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.Nature communications · 2022Article
- BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts.PLoS computational biology · 2022Article
- NOT Gates Based on Protein Degradation as a Case Study for a New Modular Modeling via SBML Level 3-Comp Package.Frontiers in bioengineering and biotechnology · 2022Article
- Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan.Frontiers in pharmacology · 2022Article
- Article
- Specifications of standards in systems and synthetic biology: status and developments in 2021.Journal of integrative bioinformatics · 2021Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
- A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle.International journal of molecular sciences · 2021Article
- Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease.Database : the journal of biological databases and curation · 2021Article
- Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function.Frontiers in physiology · 2021Review
- SBML Level 3: an extensible format for the exchange and reuse of biological models.Molecular systems biology · 2020Review
- BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint.BMC bioinformatics · 2020Article
- The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).Journal of integrative bioinformatics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling. The package enables a modeler to include submodels within an enclosing SBML model, delete unneeded or redundant elements of that submodel, replace elements of that submodel with element of the containing model, and replace elements of the containing model with elements of the submodel. In addition, the package defines an optional "port" construct, allowing a model to be defined with suggested interfaces between hierarchical components; modelers can chose to use these interfaces, but they are not required to do so and can still interact directly with model elements if they so chose. Finally, the SBML Hierarchical Model Composition package is defined in such a way that a hierarchical model can be "flattened" to an equivalent, non-hierarchical version that uses only plain SBML constructs, thus enabling software tools that do not yet support hierarchy to nevertheless work with SBML hierarchical models.
Indexed as
Identifiers
What OpenQuestion holds
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.