Related Experiment Video
Updated: May 11, 2026
11:23
A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression
Published on: October 6, 2019
Hierarchical modeling for synthetic biology.
Deepak Chandran1, Herbert M Sauro
1Department of Bioengineering, University of Washington, Box 355061, William H. Foege Building, Room N210E, Seattle, WA 98195-5061, USA. deepakc@uw.edu
ACS Synthetic Biology
|May 9, 2013
Summary
Synthetic biology needs a way to link mathematical models and experimental data. TinkerCell
Area of Science:
- Synthetic biology
- Computational biology
- Bioinformatics
Background:
- Synthetic biology integrates mathematical modeling and experimental work.
- Current methods lack a unified way to connect conceptual biological system descriptions with mathematical models and experimental data, particularly DNA sequence annotations.
- Different mathematical models of the same biological system can lead to inconsistent mapping of sequence annotations.
Purpose of the Study:
- To develop a software framework for representing conceptual biological system descriptions independent of specific mathematical models.
- To enable automatic mapping of conceptual diagrams to multiple mathematical models.
- To facilitate the integration of modeling and experimental data in synthetic biology.
Main Methods:
- Utilized hierarchical modeling within the TinkerCell software.
- Developed a "conceptual diagram" representation for biological systems.
- Implemented automatic mapping of conceptual diagrams to various underlying mathematical models.
Main Results:
- TinkerCell provides a software solution for creating model-agnostic conceptual diagrams of biological systems.
- These diagrams can incorporate quantitative values relevant for both modeling and experimental work.
- The approach allows for automatic mapping to different mathematical models.
Conclusions:
- The developed conceptual diagram approach in TinkerCell addresses the need for a unified representation in synthetic biology.
- This facilitates the connection between conceptual understanding, mathematical modeling, and experimental data.
- This work is a step towards practical computer-aided design (CAD) systems for synthetic biology.
Related Concept Videos
02:55Synthetic Biology
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
02:00Molecular Models
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
01:20Applications of Molecular Taxonomy
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
01:23Phylogeny
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.