From f91e6fbc32d79f759a0092f414d9e297ffd6790f Mon Sep 17 00:00:00 2001 From: Ali Ghareeb <198827622+ghareea@users.noreply.github.com> Date: Mon, 20 Apr 2026 17:20:14 -0700 Subject: [PATCH 1/3] Update README with running instructions for Robin Clarify instructions for running Robin in Jupyter Notebook. --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 627525e..5c49a8e 100644 --- a/README.md +++ b/README.md @@ -86,6 +86,7 @@ For a fully self-contained environment that avoids OS-level dependency conflicts Robin will automatically load this `.env` file at startup. Alternatively, you can export the variables in your shell, or pass them directly when creating the `RobinConfiguration` object. ## Running Robin via `robin_demo.ipynb` +*In order to run Robin as used in the manuscript, a user must only input the name of a disease, with no other text. If a user wishes to optimize how Robin searches for experimental models and therapeutic candidates, we suggest changing the internal prompts of Robin (via prompts.py), not the initial input to the pipeline.* 1. **Launch Jupyter Notebook or JupyterLab:** Navigate to the `robin` directory in your terminal (ensure your virtual environment is activated) and run: From 6a9d1646cdce558b9b609483516ca8734143a7d9 Mon Sep 17 00:00:00 2001 From: Ali Ghareeb <198827622+ghareea@users.noreply.github.com> Date: Mon, 20 Apr 2026 17:29:28 -0700 Subject: [PATCH 2/3] Update README for clarity on disease input Clarified instructions for running Robin with disease name input. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5c49a8e..09b8c41 100644 --- a/README.md +++ b/README.md @@ -86,7 +86,7 @@ For a fully self-contained environment that avoids OS-level dependency conflicts Robin will automatically load this `.env` file at startup. Alternatively, you can export the variables in your shell, or pass them directly when creating the `RobinConfiguration` object. ## Running Robin via `robin_demo.ipynb` -*In order to run Robin as used in the manuscript, a user must only input the name of a disease, with no other text. If a user wishes to optimize how Robin searches for experimental models and therapeutic candidates, we suggest changing the internal prompts of Robin (via prompts.py), not the initial input to the pipeline.* +*In order to run Robin as used in the manuscript, only input the name of a disease, with no other text. If you wish to optimize how Robin searches for experimental models and therapeutic candidates, we suggest changing the internal prompts of Robin (via prompts.py), not the initial input to the pipeline.* 1. **Launch Jupyter Notebook or JupyterLab:** Navigate to the `robin` directory in your terminal (ensure your virtual environment is activated) and run: From ac2a865e3e1ce875f54da33a3a76cc5e4d2dd251 Mon Sep 17 00:00:00 2001 From: Sam Cox Date: Tue, 21 Apr 2026 16:49:14 -0700 Subject: [PATCH 3/3] running precommit to fix --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 09b8c41..6da24fa 100644 --- a/README.md +++ b/README.md @@ -86,7 +86,8 @@ For a fully self-contained environment that avoids OS-level dependency conflicts Robin will automatically load this `.env` file at startup. Alternatively, you can export the variables in your shell, or pass them directly when creating the `RobinConfiguration` object. ## Running Robin via `robin_demo.ipynb` -*In order to run Robin as used in the manuscript, only input the name of a disease, with no other text. If you wish to optimize how Robin searches for experimental models and therapeutic candidates, we suggest changing the internal prompts of Robin (via prompts.py), not the initial input to the pipeline.* + +_In order to run Robin as used in the manuscript, only input the name of a disease, with no other text. If you wish to optimize how Robin searches for experimental models and therapeutic candidates, we suggest changing the internal prompts of Robin (via prompts.py), not the initial input to the pipeline._ 1. **Launch Jupyter Notebook or JupyterLab:** Navigate to the `robin` directory in your terminal (ensure your virtual environment is activated) and run: