Team:Calgary Software/Project
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Evolution involves the changes of inherited traits in a population for successive generations. Each generation carries genetic information, expressing certain characteristics. Mutation enables manipulation of these traits as well as genetic recombination. Evolution is a result of heritable traits becoming more prevalent or rare. | Evolution involves the changes of inherited traits in a population for successive generations. Each generation carries genetic information, expressing certain characteristics. Mutation enables manipulation of these traits as well as genetic recombination. Evolution is a result of heritable traits becoming more prevalent or rare. | ||
Agent-based modeling is a computational method that replicates the behavior and interaction of individual components of a network such that their overall effect on the system can be observed. This involves many different aspects, including: | Agent-based modeling is a computational method that replicates the behavior and interaction of individual components of a network such that their overall effect on the system can be observed. This involves many different aspects, including: | ||
- | + | * game theory | |
- | + | * evolutionary programming | |
- | + | * complex systems | |
- | + | * emergence | |
- | Multiple agents are simulated in an environment to simulate and hypothesize the actions of complex phenomena | + | Multiple agents are simulated in an environment to simulate and hypothesize the actions of complex phenomena. </div> |
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Revision as of 23:47, 28 October 2008
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Home | The Team | The Project | Modeling | Notebook |
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Evolutionary Algorithm | Data Retrieval | Modeling | Graphical User Interface |
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Contents |
Introduction
We use evolutionary and genetic strategies, which are useful modeling methods, especially when coupled with agent-based designs. We created EvoGEM, a design that is based on the registry of genetic parts provided by the iGEM competition.
This design uses the paradigm of evolution to select efficient designs and produce a product or output that is generated independently by the system. EvoGEM uses the strategies of genetics and evolution to simulate an environment inside of a prokaryotic cell. This entails various events and structures that are present inside of the organism, such as:
- RNA polymerase
- messenger RNA
- ribosomes
- transcription and translation.
We presented EvoGEM during the 2007 iGEM Jamboree, where it sparked a lot of interest amongst the different teams. This summer, our team has expanded EvoGEM by:
- improving EvoGEM's fitness function.
- introducing more complex pattern recognition.
- testing the system under a much larger search space.
- building Perl scripts that support EvoGEM's requirements of a flat file registry
- creating an Objective-C based graphical user interface (GUI) in order to make the software-user interaction easy
- developing the EvoGEM code to include the behaviors specified before, and create a simulation of the processes in the cell such as transcription and translation.
Evolutionary Algorithm
Evolution involves the changes of inherited traits in a population for successive generations. Each generation carries genetic information, expressing certain characteristics. Mutation enables manipulation of these traits as well as genetic recombination. Evolution is a result of heritable traits becoming more prevalent or rare. Agent-based modeling is a computational method that replicates the behavior and interaction of individual components of a network such that their overall effect on the system can be observed. This involves many different aspects, including:
- game theory
- evolutionary programming
- complex systems
- emergence
Data Retrieval and Storage
- its type. - its function. - whether it codes for a protein. - how well the parts work. If the part coded for a protein, we retrieved its DNA sequence. We, then, found the amino acid sequence (using the BLAST algorithm) from UniProt, which is a large database of proteins. If the protein catalyzed an associated prosthetic or a biochemical reaction, we retrieved additional information from ChemSpider - a chemical database - to find the data characterizing any compounds that the particular enzymatic protein catalyzes. Finally, we stored the data in a database during run-time of EvoGEM.
Modeling
Graphical User Interface
Evolutionary Algorithm | Data Retrieval | Modeling | Graphical User Interface |
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Home | The Team | The Project | Modeling | Notebook |
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