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 :doc:`colab_notebooks`.

CRISPR and Strain Engineering
-----------------------------

.. list-table::
   :widths: 18 52 30
   :header-rows: 1

   * - Name
     - Focus
     - Source
   * - ``05_terminator_library...``
     - Outline for designing terminator libraries for expression tuning.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/05_terminator_library_for_expression_tuning.ipynb>`__
   * - ``06_crispr_multiplex...``
     - Planning scaffold for multiplex CRISPR workflows.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/06_crispr_multiplex_editing_planner.ipynb>`__
   * - ``08_promoter_swap...``
     - Planning scaffold for promoter swap workflows in *Pichia*.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/08_promoter_swap_for_overexpression_library_in_pichia.ipynb>`__
   * - ``09_crispr_cas9...``
     - Worked Cas9 deletion example with combined-genome off-target scanning and repair oligo design.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/09_crispr_cas9_deletion_example_in_aspergillus_oryzae.ipynb>`__
   * - ``10_crispr_cas12a...``
     - Worked Cas12a deletion example with the same Aspergillus workflow structure.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/10_crispr_cas12a_deletion_example_in_aspergillus_oryzae.ipynb>`__

Library and Protein Engineering
-------------------------------

.. list-table::
   :widths: 18 52 30
   :header-rows: 1

   * - Name
     - Focus
     - Source
   * - ``00_Designing_primers...``
     - Example for designing primer sets for a Kozak library.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/00_Designing_primers_for_kozak_library.ipynb>`__
   * - ``01_HT_cazyme...``
     - High-throughput primer design workflow for CAZyme targets.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/01_HT_cazyme_primer_design.ipynb>`__
   * - ``02_primer_directed...``
     - Planning scaffold for primer-directed mutagenesis.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/02_primer_directed_mutagenesis.ipynb>`__
   * - ``03_investigate_plastic...``
     - Planning scaffold for enzyme discovery and prioritization.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/03_investigate_plastic_degrading_enzymes.ipynb>`__
   * - ``04_promoter_library...``
     - Planning scaffold for promoter library design in yeast.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/04_promoter_library_design_in_s_cerevisiae.ipynb>`__
   * - ``07_homolog_mining...``
     - Planning scaffold for homolog mining and expression panel generation.
     - `Open on GitHub <https://github.com/hiyama341/teemi/blob/main/teemi_cad_workflows/inspiration_notebooks/notebooks/07_homolog_mining_to_codon_optimized_expression_panel.ipynb>`__

Legacy Colab Notebooks
----------------------

For larger, end-to-end case studies, continue to :doc:`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