Workflow Gallery#
The workflow gallery highlights the lighter, workflow-oriented notebooks in
teemi_cad_workflows/inspiration_notebooks/notebooks. These examples are a good
fit when you want a focused starting point rather than a long end-to-end case study.
The current direction of the repository is to expand this gallery while keeping the larger strictosidine notebooks available under Colab Notebooks.
CRISPR and Strain Engineering#
Name |
Focus |
Source |
|---|---|---|
|
Outline for designing terminator libraries for expression tuning. |
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Planning scaffold for multiplex CRISPR workflows. |
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Planning scaffold for promoter swap workflows in Pichia. |
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Worked Cas9 deletion example with combined-genome off-target scanning and repair oligo design. |
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Worked Cas12a deletion example with the same Aspergillus workflow structure. |
Library and Protein Engineering#
Name |
Focus |
Source |
|---|---|---|
|
Example for designing primer sets for a Kozak library. |
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High-throughput primer design workflow for CAZyme targets. |
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Planning scaffold for primer-directed mutagenesis. |
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Planning scaffold for enzyme discovery and prioritization. |
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Planning scaffold for promoter library design in yeast. |
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Planning scaffold for homolog mining and expression panel generation. |
Legacy Colab Notebooks#
For larger, end-to-end case studies, continue to Colab Notebooks. Those notebooks document the strictosidine DBTL campaign across two iterative cycles and remain the best place to launch the full Google Colab workflows.
Recommended Next Examples#
The next useful workflow additions for the repo are:
Cas12a multiplex deletion planning in Aspergillus oryzae
genotyping planner for CRISPR edits
Cas9 vs Cas12a guide comparison notebook
signal peptide swapping workflow
homolog mining to expression panel