Team:ETH Zurich/Modeling/Download

From 2008.igem.org

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(→Genome Static Analysis)
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'''Download file:''' [[Image:ETHZ-iGEM2008-GenomeStaticAnalysis.zip]]
'''Download file:''' [[Image:ETHZ-iGEM2008-GenomeStaticAnalysis.zip]]
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''Compute:'' This simulation download the genome annotation of E.Coli K12 MG1655 from GenBank and restriction enzymes informations from REBASE. For each restriction enzyme, calculates the fragments generated by digesting the chromosome of the strain. It calculates statistics on various aspects, such as probability of having an essential gene per fragment.
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'''Compute:''' This simulation download the genome annotation of E.Coli K12 MG1655 from GenBank and restriction enzymes informations from REBASE. For each restriction enzyme, calculates the fragments generated by digesting the chromosome of the strain. It calculates statistics on various aspects, such as probability of having an essential gene per fragment.
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''Output:'' An array of records, each one containing statistical analysis for one of the restriction enzyme groups. Generates five plots that explain the statistical results.
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'''Output:''' An array of records, each one containing statistical analysis for one of the restriction enzyme groups. Generates five plots that explain the statistical results.
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''Softwared needed:'' MATLAB with BioInformatic Toolbox.
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'''Softwared needed:''' MATLAB with BioInformatic Toolbox.
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''Third part code:'' use of standard Bioinformatic Toolbox functions.
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'''Third part code:''' use of standard Bioinformatic Toolbox functions.
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''Files and descriptions:''
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'''Files and descriptions:'''
* convertCuttingSitesIntoGeneNames.m - convert informations on cutting sites for restriction enzymes in file names as Blattner Ids and alphanumeric gene names.
* convertCuttingSitesIntoGeneNames.m - convert informations on cutting sites for restriction enzymes in file names as Blattner Ids and alphanumeric gene names.
* createAtomicKnockoutsForRestEnzymes.m - construct the structure containing fragment patterns for all the selected restriction enzymes.
* createAtomicKnockoutsForRestEnzymes.m - construct the structure containing fragment patterns for all the selected restriction enzymes.
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* essentialGenes.mat - list of essential genes (single knockouts are mortal), obtained from different sources.
* essentialGenes.mat - list of essential genes (single knockouts are mortal), obtained from different sources.
   
   
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''Author(s):'' Luca and Georg.
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'''Author(s):''' Luca and Georg.
== Genome-scale Model ==
== Genome-scale Model ==

Revision as of 21:54, 25 October 2008


Contents


Genome Static Analysis

Download file: File:ETHZ-iGEM2008-GenomeStaticAnalysis.zip

Compute: This simulation download the genome annotation of E.Coli K12 MG1655 from GenBank and restriction enzymes informations from REBASE. For each restriction enzyme, calculates the fragments generated by digesting the chromosome of the strain. It calculates statistics on various aspects, such as probability of having an essential gene per fragment.

Output: An array of records, each one containing statistical analysis for one of the restriction enzyme groups. Generates five plots that explain the statistical results.

Softwared needed: MATLAB with BioInformatic Toolbox.

Third part code: use of standard Bioinformatic Toolbox functions.

Files and descriptions:

  • convertCuttingSitesIntoGeneNames.m - convert informations on cutting sites for restriction enzymes in file names as Blattner Ids and alphanumeric gene names.
  • createAtomicKnockoutsForRestEnzymes.m - construct the structure containing fragment patterns for all the selected restriction enzymes.
  • createAtomicKnockoutStruct.m - constructe a structure object containing fragment patterns for one restriction enzyme.
  • digestionSimulation.m - perform the digestion of chromosome using all the restriction enzymes.
  • genomeStaticAnalysis.m - main function, invoke the digestion and plots the five graphs.
  • essentialGenes.mat - list of essential genes (single knockouts are mortal), obtained from different sources.

Author(s): Luca and Georg.

Genome-scale Model

Chemostat Selection

Switch Circuit

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