The iGEM PIPE
The iGEM PIPE
Here you can find the notebooks from Delielena.
Getting familiar with the databases (BiGG in particular). The iML1515 model of Escherichia coli and the universal model were obtained from BiGG and tested. The initialization of the models (i.e. setting the constraints) was automated.
The Gapfilling algorithm was tested for allowing consumption of methene first and production of L-lactate as the target later. The automatic addition of the identified reactions to the models was coded.
Flux balance analysis of the different models for evaluating the performance was automated as well. The themodynamic analysis with the MDF algorithm from eQuilibrator was tested on the test case and the scripts for its automation were written.
The Optknock algorithm was introduced in the workflow to delete reactions for coupling growth and production. The criteria for the evaluation of the strategies were defined. The scoring function was then coded and tested on the test case.
The Biobricks required by the design strategies of test case were searched in the BioParts wikibase by using their E. C. numbers. This step was automated and the percentage of available Biobricks was compared to the scores previously obtained by generating a function that displays the two scores in a graph.
The Codon Harmonizer was integrated in the workflow by adapting a recent python script and including it in the PIPE. The code was modified to make it check for the presence of restriction sites in the sequences of the Biobricks and eliminating them by substituting synonymous codons.
The three studies used to the validation were selected and the PIPE was used to ask similar engineering questions to the chosen studies of reference.