Newcastle University Drylab/25 May 2008

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)