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2 changes: 1 addition & 1 deletion source/web-app/opmodels/uploading-your-data.rst
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Expand Up @@ -55,7 +55,7 @@ Alternatively, you can assign replicates after uploading your CSV file:

- Set the **Column type** of each replicate column to ``Property``.
- Assign the same **Property name** to columns that represent replicates of the same measurement.
For example, to group ``Luminosity (Rep 1)`` and ``Luminosity (Rep 2)``, assign both the property name ``Replicate Luminosity``.
For example, to group ``mutation_effect_prediction_vae_1`` and ``mutation_effect_prediction_vae_2``, assign both the property name ``mutation_effect_prediction_vae``.

.. image:: /_static/opmodels/uploading-your-data/replicate-mapping.png

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9 changes: 6 additions & 3 deletions source/web-app/poet/prompts.rst
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Expand Up @@ -82,10 +82,10 @@ You can create a prompt context in three ways:
If you've previously uploaded prompts, you can reuse them. In the **Choose from project**,
select an existing prompt. The sequences from that prompt will automatically load.

.. image:: /_static/tools/poet/prompt-contenxt-use-existing-1.png
.. image:: /_static/tools/poet/prompt-context-use-existing-1.png
:alt: Use existing prompt

.. image:: /_static/tools/poet/prompt-contenxt-use-existing-2.png
.. image:: /_static/tools/poet/prompt-context-use-existing-2.png
:alt: Use existing prompt

2. Create Custom Context
Expand Down Expand Up @@ -182,7 +182,10 @@ Without a Project
^^^^^^^^^^^^^^^^^^^
Navigate to any PoET tool under **Prompt Definition**. You can either input the MSA directly or upload an existing `.fa`, `.fasta`, or `.csv` file.

.. image:: /_static/tools/poet/prompt-6.png
.. image:: /_static/tools/poet/prompt-6-1.png
:alt: Uploading MSA without a project

.. image:: /_static/tools/poet/prompt-6-2.png
:alt: Uploading MSA without a project

Within a Project
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2 changes: 1 addition & 1 deletion source/web-app/poet/substitution-analysis.rst
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Expand Up @@ -93,7 +93,7 @@ Your highest scoring variants and sites are also displayed in tables below the h
.. image:: /_static/tools/poet/sub-analysis-1.png
:alt: Substitution Analysis Heatmap

Refer to the **Details** tab to see the parameters you used to run the Substitution Analysis.
Refer to the **Input** tab to see the parameters you used to run the Substitution Analysis.

Fine-tuning your results
------------------------
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