Newcastle University Drylab/25 May 2008

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Newcastle University

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May
MTWTFSS
      [http://2008.igem.org/Newcastle_University_Drylab/1_May_2008 1] [http://2008.igem.org/Newcastle_University_Drylab/2_May_2008 2] [http://2008.igem.org/Newcastle_University_Drylab/3_May_2008 3] [http://2008.igem.org/Newcastle_University_Drylab/4_May_2008 4]
[http://2008.igem.org/Newcastle_University_Drylab/5_May_2008 5] [http://2008.igem.org/Newcastle_University_Drylab/6_May_2008 6] [http://2008.igem.org/Newcastle_University_Drylab/7_May_2008 7] [http://2008.igem.org/Newcastle_University_Drylab/8_May_2008 8] [http://2008.igem.org/Newcastle_University_Drylab/9_May_2008 9] [http://2008.igem.org/Newcastle_University_Drylab/10_May_2008 10] [http://2008.igem.org/Newcastle_University_Drylab/11_May_2008 11]
[http://2008.igem.org/Newcastle_University_Drylab/12_May_2008 12] [http://2008.igem.org/Newcastle_University_Drylab/13_May_2008 13] [http://2008.igem.org/Newcastle_University_Drylab/14_May_2008 14] [http://2008.igem.org/Newcastle_University_Drylab/15_May_2008 15] [http://2008.igem.org/Newcastle_University_Drylab/16_May_2008 16] [http://2008.igem.org/Newcastle_University_Drylab/17_May_2008 17] [http://2008.igem.org/Newcastle_University_Drylab/18_May_2008 18]
[http://2008.igem.org/Newcastle_University_Drylab/19_May_2008 19] [http://2008.igem.org/Newcastle_University_Drylab/20_May_2008 20] [http://2008.igem.org/Newcastle_University_Drylab/21_May_2008 21] [http://2008.igem.org/Newcastle_University_Drylab/22_May_2008 22] [http://2008.igem.org/Newcastle_University_Drylab/23_May_2008 23] [http://2008.igem.org/Newcastle_University_Drylab/24_May_2008 24] [http://2008.igem.org/Newcastle_University_Drylab/25_May_2008 25]
[http://2008.igem.org/Newcastle_University_Drylab/26_May_2008 26] [http://2008.igem.org/Newcastle_University_Drylab/27_May_2008 27] [http://2008.igem.org/Newcastle_University_Drylab/28_May_2008 28] [http://2008.igem.org/Newcastle_University_Drylab/29_May_2008 29] [http://2008.igem.org/Newcastle_University_Drylab/30_May_2008 30] [http://2008.igem.org/Newcastle_University_Drylab/31_May_2008 31]
June
MTWTFSS
            [http://2008.igem.org/Newcastle_University_Drylab/1_June_2008 1]
[http://2008.igem.org/Newcastle_University_Drylab/2_June_2008 2] [http://2008.igem.org/Newcastle_University_Drylab/3_June_2008 3] [http://2008.igem.org/Newcastle_University_Drylab/4_June_2008 4] [http://2008.igem.org/Newcastle_University_Drylab/5_June_2008 5] [http://2008.igem.org/Newcastle_University_Drylab/6_June_2008 6] [http://2008.igem.org/Newcastle_University_Drylab/7_June_2008 7] [http://2008.igem.org/Newcastle_University_Drylab/8_June_2008 8]
[http://2008.igem.org/Newcastle_University_Drylab/9_June_2008 9] [http://2008.igem.org/Newcastle_University_Drylab/10_June_2008 10] [http://2008.igem.org/Newcastle_University_Drylab/11_June_2008 11] [http://2008.igem.org/Newcastle_University_Drylab/12_June_2008 12] [http://2008.igem.org/Newcastle_University_Drylab/13_June_2008 13] [http://2008.igem.org/Newcastle_University_Drylab/14_June_2008 14] [http://2008.igem.org/Newcastle_University_Drylab/15_June_2008 15]
[http://2008.igem.org/Newcastle_University_Drylab/16_June_2008 16] [http://2008.igem.org/Newcastle_University_Drylab/17_June_2008 17] [http://2008.igem.org/Newcastle_University_Drylab/18_June_2008 18] [http://2008.igem.org/Newcastle_University_Drylab/19_June_2008 19] [http://2008.igem.org/Newcastle_University_Drylab/20_June_2008 20] [http://2008.igem.org/Newcastle_University_Drylab/21_June_2008 21] [http://2008.igem.org/Newcastle_University_Drylab/22_June_2008 22]
[http://2008.igem.org/Newcastle_University_Drylab/23_June_2008 23] [http://2008.igem.org/Newcastle_University_Drylab/24_June_2008 24] [http://2008.igem.org/Newcastle_University_Drylab/25_June_2008 25] [http://2008.igem.org/Newcastle_University_Drylab/26_June_2008 26] [http://2008.igem.org/Newcastle_University_Drylab/27_June_2008 27] [http://2008.igem.org/Newcastle_University_Drylab/28_June_2008 28] [http://2008.igem.org/Newcastle_University_Drylab/29_June_2008 29]
[http://2008.igem.org/Newcastle_University_Drylab/30_June_2008 30]
July
MTWTFSS
  [http://2008.igem.org/Newcastle_University_Drylab/1_July_2008 1] [http://2008.igem.org/Newcastle_University_Drylab/2_July_2008 2] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/3_July_2008&action=edit 3] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/4_July_2008&action=edit 4] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/5_July_2008&action=edit 5] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/6_July_2008&action=edit 6]
[http://2008.igem.org/Newcastle_University_Drylab/7_July_2008 7] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/8_July_2008&action=edit 8] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/9_July_2008&action=edit 9] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/10_July_2008&action=edit 10] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/11_July_2008&action=edit 11] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/12_July_2008&action=edit 12] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/13_July_2008&action=edit 13]
[http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/14_July_2008&action=edit 14] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/15_July_2008&action=edit 15] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/16_July_2008&action=edit 16] [http://2008.igem.org/Newcastle_University_Drylab/17_July_2008 17] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/18_July_2008&action=edit 18] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/19_July_2008&action=edit 19] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/20_July_2008&action=edit 20]
[http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/21_July_2008&action=edit 21] [http://2008.igem.org/Newcastle_University_Drylab/22_July_2008 22] [http://2008.igem.org/Newcastle_University_Drylab/23_July_2008 23] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/24_July_2008&action=edit 24] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/25_July_2008&action=edit 25] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/26_July_2008&action=edit 26] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/27_July_2008&action=edit 27]
[http://2008.igem.org/Newcastle_University_Drylab/28_July_2008 28] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/29_July_2008&action=edit 29] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/30_July_2008&action=edit 30] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/31_July_2008&action=edit 31]
August
MTWTFSS
        [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/1_August_2008&action=edit 1] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/2_August_2008&action=edit 2] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/3_August_2008&action=edit 3]
[http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/4_August_2008&action=edit 4] [http://2008.igem.org/Newcastle_University_Drylab/5_August_2008 5] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/6_August_2008&action=edit 6] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/7_August_2008&action=edit 7] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/8_August_2008&action=edit 8] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/9_August_2008&action=edit 9] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/10_August_2008&action=edit 10]
[http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/11_August_2008&action=edit 11] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/12_August_2008&action=edit 12] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/13_August_2008&action=edit 13] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/14_August_2008&action=edit 14] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/15_August_2008&action=edit 15] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/16_August_2008&action=edit 16] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/17_August_2008&action=edit 17]
[http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/18_August_2008&action=edit 18] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/19_August_2008&action=edit 19] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/20_August_2008&action=edit 20] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/21_August_2008&action=edit 21] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/22_August_2008&action=edit 22] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/23_August_2008&action=edit 23] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/24_August_2008&action=edit 24]
[http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/25_August_2008&action=edit 25] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/26_August_2008&action=edit 26] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/27_August_2008&action=edit 27] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/28_August_2008&action=edit 28] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/29_August_2008&action=edit 29] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/30_August_2008&action=edit 30] [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/31_August_2008&action=edit 31]

25 May 2008

Mark

Megan

Morgan

Nina

Compatibility Matrix

I completed a types of parts compatibility matrix to compare to the parts compatibility matrix. This matrix allows one to see which repressors or promoters are compatible with which regulators etc. To work out compatibility, the following factors of each of the parts will be considered;

a) Synthetic biology, genetic engineering or naturally occurring literary evidence of the exact associate parts interacting, or having a desired effect/control of gene expression of one or either of each other.

b) Already established compatibilities on the BioBricks parts registry http://partsregistry.org/Main_Page|parts_registry

c) If no specific literature on a particular part and its compatibility with another part exists and it does not appear to have been constructed as a biobrick, I will look into structures similar to the part in question to deduce that the interactions may be similar to the relationship of parts that have already been established. This deduction can only be carried out if the two parts function an effect on each other by actually interacting.

Once compatibility for each part and each target part (all other parts) has been established in each given I should store the compatible groups of parts together in a database. This database should also include models to the string of parts and should end up being "BioBricks" specifically designed to be inserted into our B. subtilis chassis. The models should be designed in CellML. They should join together the individual part models designed by Megan. The database should have unique Ids for the individual parts, the joined parts, the types of parts and the associated models (see ERD). This will allow Mark and the EA to sift through the models to identify the "fittest" order

Pseudocode

I have also attempted to write a pseudocode for my constraints database. I have started this off by drawing an ERD. The entities shall form the java classes that I shall use. I can use the structure of the ERD to establish how to structure the query and java that will obtain the list of parts from the parts repository and the database (Henkel et al., 2007)

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