Team:Calgary Software/Project

From 2008.igem.org

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=== Step I ===
=== Step I ===
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First off, we will characterize the parts that Kent has pulled from the registry as ideas to simulate.
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The systems Kent suggested are linked here:
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 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45120 BBa_J45120]
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45200 BBa_J45200]
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45250 BBa_J45250]
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_I0462 BBa_I0462]
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45996 BBa_J45996]
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Once these are simulated well we can begin inserting more systems to increase search space AND try and find more complex pathways
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 +
 +
'''When characterizing proteins, include a field in the parts file titled "sequence = " and the protein sequence using ONE LETTER AMINO ACID notation'''
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 +
Translate DNA code into amino acids with [http://www.vivo.colostate.edu/molkit/translate/index.html this program]
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 +
e.g.
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This DNA sequence:
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 +
atggaagttgttgaagttcttcacatgaatggaggaaatggagacagtagctatgcaaacaattctttggttcagcaaaaggtgattctcatgacaaagc
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caataactgagcaagccatgattgatctctacagcagcctctttccagaaaccttatgcattgcagatttgggttgttctttgggagctaacactttctt
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ggtggtctcacagcttgttaaaatagtagaaaaagaacgaaaaaagcatggttttaagtctccagagttttattttcacttcaatgatcttcctggcaat
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gattttaatacactttttcagtcactgggggcatttcaagaagatttgagaaagcatataggggaaagctttggtccatgttttttcagtggagtgcctg
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gttcattttatactagacttttcccttccaaaagtttacattttgtttactcctcctacagtctcatgtggctatctcaggtgcctaatgggattgaaaa
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taacaagggaaacatttacatggcaagaacaagccctctaagtgttattaaagcatactacaagcaatatgaaatagatttttcaaattttctcaagtac
 +
cgttcagaggaattgatgaaaggtggaaagatggtgttaacactcctaggtagagaaagtgaggatcctactagcaaagaatgctgttacatttgggagc
 +
ttctagccatggccctcaataagttggttgaagagggattgataaaagaagagaaagtagatgcattcaatattcctcaatacacaccatcaccagcaga
 +
agtaaagtacatagttgagaaggaaggatcattcaccattaatcgcttggaaacatcaagagttcattggaatgcttctaataatgagaagaatggtggt
 +
tacaatgtgtcaaggtgcatgagagctgtggctgagcctttgcttgtcagccactttgacaaggaattgatggatttagtgttccacaagtacgaagaga
 +
ttgtttctgattgcatgtccaaagagaatactgagtttataaatgtcatcatctccttgaccaaaataaattaa
 +
 +
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Translates into this amino acid sequence:
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 +
MEVVEVLHMNGGNGDSSYANNSLVQQKVILMTKPITEQAMIDLYSSLFPETLCIADLGCS
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LGANTFLVVSQLVKIVEKERKKHGFKSPEFYFHFNDLPGNDFNTLFQSLGAFQEDLRKHI
 +
GESFGPCFFSGVPGSFYTRLFPSKSLHFVYSSYSLMWLSQVPNGIENNKGNIYMARTSPL
 +
SVIKAYYKQYEIDFSNFLKYRSEELMKGGKMVLTLLGRESEDPTSKECCYIWELLAMALN
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KLVEEGLIKEEKVDAFNIPQYTPSPAEVKYIVEKEGSFTINRLETSRVHWNASNNEKNGG
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YNVSRCMRAVAEPLLVSHFDKELMDLVFHKYEEIVSDCMSKENTEFINVIISLTKIN-
=== Step II ===
=== Step II ===

Revision as of 19:03, 10 June 2008


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Contents

The Project

            EvoGEM is an agent based system which seeks to design iGEM "genetic circuits" by harnessing the power of evolutionary design. In this design methodology, the paradigm of evolution is harnessed in order to select for efficient designs. The survival criteria are determined by the purpose for which these circuits are built, and those that fulfill that purpose well survive and create even better offspring while those that fail to please the criteria, are thrown away from the gene pool. The powerful agent based logic which allows for minimal pre-assumptions about the overall behavior of the system, along with the empirically proven evolutionary design create superb system that is able to both emulate and develop iGEM circuits.

            EvoGEM was briefly presented during the 2007 iGEM jamboree and has sparked quite a lot of interest amongst the different teams. This summer, our team plans to further develop the fitness function EvoGEM employs, introduce more complex pattern recognition, and test the system under a much larger search space than before. The final goal is to produce a system sophisticated enough to rebuild working designs from previous years' teams' projects, as well as intelligent enough to simulate successes and failures of working and non-working systems, respectively.

            The main focus of this project is to build perl scripts that will support EvoGEM's requirements of a flat file registry, and develop the EvoGEM code to include the behaviors specified before.

Project Details

The focus of the first part of the project is to create a perl script to quarry the registry and other databases in order to retrieve critical information about different bio-bricks. After that, the goal will be to improve the EvoGEM code to introduce the changes discussed in the previous section

Step I

First off, we will characterize the parts that Kent has pulled from the registry as ideas to simulate.

The systems Kent suggested are linked here:

[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45120 BBa_J45120]

[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45200 BBa_J45200]

[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45250 BBa_J45250]

[http://partsregistry.org/wiki/index.php?title=Part:BBa_I0462 BBa_I0462]

[http://partsregistry.org/wiki/index.php?title=Part:BBa_J45996 BBa_J45996]

Once these are simulated well we can begin inserting more systems to increase search space AND try and find more complex pathways


When characterizing proteins, include a field in the parts file titled "sequence = " and the protein sequence using ONE LETTER AMINO ACID notation

Translate DNA code into amino acids with [http://www.vivo.colostate.edu/molkit/translate/index.html this program]

e.g.

This DNA sequence:

atggaagttgttgaagttcttcacatgaatggaggaaatggagacagtagctatgcaaacaattctttggttcagcaaaaggtgattctcatgacaaagc caataactgagcaagccatgattgatctctacagcagcctctttccagaaaccttatgcattgcagatttgggttgttctttgggagctaacactttctt ggtggtctcacagcttgttaaaatagtagaaaaagaacgaaaaaagcatggttttaagtctccagagttttattttcacttcaatgatcttcctggcaat gattttaatacactttttcagtcactgggggcatttcaagaagatttgagaaagcatataggggaaagctttggtccatgttttttcagtggagtgcctg gttcattttatactagacttttcccttccaaaagtttacattttgtttactcctcctacagtctcatgtggctatctcaggtgcctaatgggattgaaaa taacaagggaaacatttacatggcaagaacaagccctctaagtgttattaaagcatactacaagcaatatgaaatagatttttcaaattttctcaagtac cgttcagaggaattgatgaaaggtggaaagatggtgttaacactcctaggtagagaaagtgaggatcctactagcaaagaatgctgttacatttgggagc ttctagccatggccctcaataagttggttgaagagggattgataaaagaagagaaagtagatgcattcaatattcctcaatacacaccatcaccagcaga agtaaagtacatagttgagaaggaaggatcattcaccattaatcgcttggaaacatcaagagttcattggaatgcttctaataatgagaagaatggtggt tacaatgtgtcaaggtgcatgagagctgtggctgagcctttgcttgtcagccactttgacaaggaattgatggatttagtgttccacaagtacgaagaga ttgtttctgattgcatgtccaaagagaatactgagtttataaatgtcatcatctccttgaccaaaataaattaa


Translates into this amino acid sequence:

MEVVEVLHMNGGNGDSSYANNSLVQQKVILMTKPITEQAMIDLYSSLFPETLCIADLGCS LGANTFLVVSQLVKIVEKERKKHGFKSPEFYFHFNDLPGNDFNTLFQSLGAFQEDLRKHI GESFGPCFFSGVPGSFYTRLFPSKSLHFVYSSYSLMWLSQVPNGIENNKGNIYMARTSPL SVIKAYYKQYEIDFSNFLKYRSEELMKGGKMVLTLLGRESEDPTSKECCYIWELLAMALN KLVEEGLIKEEKVDAFNIPQYTPSPAEVKYIVEKEGSFTINRLETSRVHWNASNNEKNGG YNVSRCMRAVAEPLLVSHFDKELMDLVFHKYEEIVSDCMSKENTEFINVIISLTKIN-

Step II

Step III

The Experiments

Part 3

Results

The Project
Home The Team Parts Submitted to the Registry Modeling Notebook
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