Colab notebooks

Welcome to the Colab notebook section. Here we will show how ConStrain can be used in the DBTL cycle.

DESIGN:

  1. The HomologSelection notebook describes how we automatically can fetch homologs from NCBI from a query in a standardizable and repeatable way.

  2. The PromoterSelection notebook describes how promoters can be selected from RNAseq data and fetched from online database with various quality measurements implemented.

  3. The Combinatorial_library_with_DesignAssembly notebook describes how a combinatorial library can be generated with the DesignAssembly class along with robot executable intructions.

BUILD:

  1. The USER_gRNA_plasmid notebook describes the assembly of a CRISPR plasmid with USER cloning.

  2. The Background_strain notebook describes the construction of the background strain by K/O of G8H and CPR

  3. The croStrains_test_build notebook describes how a smaller combinatorial library was build and test the method before moving on to a larger library.

  4. The CombinatorialLibrary notebook shows how the first large combinatorial library was generated for 1440 possible combinations.

TEST:

  1. The LibraryCharacterisation notebook describes Con data processing of LC-MS data and genotyping of the generated strains.

LEARN:

  1. The DataAnalysisML notebook describes how we use AutoML to predict the best combinations for a targeted second round of library construction.

For more information head over to our publication describing the use of ConStrain in a literate programming context.