ArticleIET systems biology2008
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.
Article in IET systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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
13 citing papers in PubMed.
- A Systems Biology Approach Towards a Comprehensive Understanding of Ferroptosis.International journal of molecular sciences · 2024Article
- A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons.Frontiers in systems biology · 2023Article
- 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 Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle.International journal of molecular sciences · 2021Article
- Thoroughly Calibrated Modular Agent-Based Model of the Human Cardiovascular and Renal Systems for Blood Pressure Regulation in Health and Disease.Frontiers in physiology · 2021Article
- Model-driven engineering of supramolecular buffering by multivalency.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.Bioinformatics (Oxford, England) · 2016Article
- Toward modular biological models: defining analog modules based on referent physiological mechanisms.BMC systems biology · 2014Article
- CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation.Physical biology · 2012Article
- Using views of Systems Biology Cloud: application for model building.Theory in biosciences = Theorie in den Biowissenschaften · 2011Review
- Annotation of SBML models through rule-based semantic integration.Journal of biomedical semantics · 2010Article
- Molecular machines or pleiomorphic ensembles: signaling complexes revisited.Journal of biology · 2009Article
- The natural and engineered 3D microenvironment as a regulatory cue during stem cell fate determination.Tissue engineering. Part B, Reviews · 2009Review
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
Assembly of quantitative models of large complex networks brings about several challenges. One of them is the combinatorial complexity, where relatively few signalling molecules can combine to form thousands or millions of distinct chemical species. A receptor that has several separate phosphorylation sites can exist in hundreds of different states, many of which must be accounted for individually when simulating the time course of signalling. When assembly of protein complexes is being included, the number of distinct molecular species can easily increase by a few orders of magnitude. Validation, visualisation and understanding the network can become intractable. Another challenge appears when the modeller needs to recast or grow a model. Keeping track of changes and adding new elements present a significant difficulty. An approach to solve these challenges within the virtual cell (VCell) is described. Using (i) automatic extraction from pathway databases of model components (http://vcell.org/biopax) and (ii) rules of interactions that serve as reaction network generators (http://vcell.org/bionetgen), a way is provided for semi-automatic generation of quantitative mathematical models that also facilitates the reuse of model elements. In this approach, kinetic models of large, complex networks can be assembled from separately constructed modules, either directly or via rules. To implement this approach, the strength of several related technologies is combined: the BioPAX ontology, the BioNetGen rule-based description of molecular interactions and the VCell modelling and simulation framework.
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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.