ReviewJournal of the Royal Society, Interface2009
Designing and encoding models for synthetic biology.
Review in Journal of the Royal Society, Interface, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Teaching systematic, reproducible model development using synthetic biology.Chemical engineering education · 2023Article
- Model-Based Design of a Synthetic Oscillator Based on an Epigenetic Methylation Memory System.ACS synthetic biology · 2022Article
- GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems.ACS synthetic biology · 2022Article
- Principles of synthetic biology: a MOOC for an emerging field.Synthetic biology (Oxford, England) · 2019Article
- Scaling up genetic circuit design for cellular computing: advances and prospects.Natural computing · 2018Article
- Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.Bioinformatics (Oxford, England) · 2016Article
- Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.Frontiers in microbiology · 2016Review
- SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.BMC systems biology · 2015Article
- Identifying latent dynamic components in biological systems.IET systems biology · 2015Article
- DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.Scientific reports · 2015Article
- Combining computational models, semantic annotations and simulation experiments in a graph database.Database : the journal of biological databases and curation · 2015Article
- KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems.BMC systems biology · 2014Article
- Artificially constructed quorum-sensing circuits are used for subtle control of bacterial population density.PloS one · 2014Article
- Improving collaboration by standardization efforts in systems biology.Frontiers in bioengineering and biotechnology · 2014Review
- Systems approaches for synthetic biology: a pathway toward mammalian design.Frontiers in physiology · 2013Article
- Synthetic biology: mapping the scientific landscape.PloS one · 2012Article
- A strategy for building an amplified transcriptional switch to detect bacterial contamination of plants.Plant molecular biology · 2012Article
- Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes.Nature communications · 2011Article
- Integrating systems biology models and biomedical ontologies.BMC systems biology · 2011Article
- Model annotation for synthetic biology: automating model to nucleotide sequence conversion.Bioinformatics (Oxford, England) · 2011Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology 'loop'.
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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.