diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json
index 960ae50..86aa885 100644
--- a/.claude-plugin/marketplace.json
+++ b/.claude-plugin/marketplace.json
@@ -7,7 +7,7 @@
   },
   "metadata": {
     "description": "Claude scientific skills from K-Dense Inc",
-    "version": "2.1.0"
+    "version": "2.1.1"
   },
   "plugins": [
     {
diff --git a/scientific-skills/aeon/SKILL.md b/scientific-skills/aeon/SKILL.md
index a5fd1e9..5301375 100644
--- a/scientific-skills/aeon/SKILL.md
+++ b/scientific-skills/aeon/SKILL.md
@@ -23,7 +23,7 @@ Apply this skill when:
 ## Installation
 
 ```bash
-pip install aeon
+uv pip install aeon
 ```
 
 ## Core Capabilities
diff --git a/scientific-skills/alphafold-database/SKILL.md b/scientific-skills/alphafold-database/SKILL.md
index 6f8c3a8..bca3c86 100644
--- a/scientific-skills/alphafold-database/SKILL.md
+++ b/scientific-skills/alphafold-database/SKILL.md
@@ -195,7 +195,7 @@ For large-scale analyses, use Google Cloud datasets:
 
 ```bash
 # Install gsutil
-pip install gsutil
+uv pip install gsutil
 
 # List available data
 gsutil ls gs://public-datasets-deepmind-alphafold-v4/
@@ -359,16 +359,16 @@ print(df)
 
 ```bash
 # Install Biopython for structure access
-pip install biopython
+uv pip install biopython
 
 # Install requests for API access
-pip install requests
+uv pip install requests
 
 # For visualization and analysis
-pip install numpy matplotlib pandas scipy
+uv pip install numpy matplotlib pandas scipy
 
 # For Google Cloud access (optional)
-pip install google-cloud-bigquery gsutil
+uv pip install google-cloud-bigquery gsutil
 ```
 
 ### 3D-Beacons API Alternative
diff --git a/scientific-skills/anndata/SKILL.md b/scientific-skills/anndata/SKILL.md
index 2e40999..42dc505 100644
--- a/scientific-skills/anndata/SKILL.md
+++ b/scientific-skills/anndata/SKILL.md
@@ -23,10 +23,10 @@ Use this skill when:
 ## Installation
 
 ```bash
-pip install anndata
+uv pip install anndata
 
 # With optional dependencies
-pip install anndata[dev,test,doc]
+uv pip install anndata[dev,test,doc]
 ```
 
 ## Quick Start
diff --git a/scientific-skills/arboreto/SKILL.md b/scientific-skills/arboreto/SKILL.md
index a737fb3..454afa6 100644
--- a/scientific-skills/arboreto/SKILL.md
+++ b/scientific-skills/arboreto/SKILL.md
@@ -15,7 +15,7 @@ Arboreto is a computational library for inferring gene regulatory networks (GRNs
 
 Install arboreto:
 ```bash
-pip install arboreto
+uv pip install arboreto
 ```
 
 Basic GRN inference:
@@ -114,21 +114,8 @@ network = grnboost2(expression_data=matrix, client_or_address=client)
 
 ## Installation
 
-**Recommended (Conda)**:
 ```bash
-conda install -c bioconda arboreto
-```
-
-**Alternative (pip)**:
-```bash
-pip install arboreto
-```
-
-**For isolated environment**:
-```bash
-conda create --name arboreto-env
-conda activate arboreto-env
-conda install -c bioconda arboreto
+uv pip install arboreto
 ```
 
 **Dependencies**: scipy, scikit-learn, numpy, pandas, dask, distributed
diff --git a/scientific-skills/astropy/SKILL.md b/scientific-skills/astropy/SKILL.md
index 10b7492..10a7a24 100644
--- a/scientific-skills/astropy/SKILL.md
+++ b/scientific-skills/astropy/SKILL.md
@@ -185,10 +185,10 @@ Robust statistical functions including sigma clipping and outlier rejection.
 
 ```bash
 # Install astropy
-pip install astropy
+uv pip install astropy
 
 # With optional dependencies for full functionality
-pip install astropy[all]
+uv pip install astropy[all]
 ```
 
 ## Common Workflows
diff --git a/scientific-skills/benchling-integration/SKILL.md b/scientific-skills/benchling-integration/SKILL.md
index 988f18b..4a0cf7a 100644
--- a/scientific-skills/benchling-integration/SKILL.md
+++ b/scientific-skills/benchling-integration/SKILL.md
@@ -28,7 +28,7 @@ This skill should be used when:
 **Python SDK Installation:**
 ```python
 # Stable release
-pip install benchling-sdk
+uv pip install benchling-sdk
 # or with Poetry
 poetry add benchling-sdk
 ```
diff --git a/scientific-skills/biomni/SKILL.md b/scientific-skills/biomni/SKILL.md
index 3f96366..33a6268 100644
--- a/scientific-skills/biomni/SKILL.md
+++ b/scientific-skills/biomni/SKILL.md
@@ -32,17 +32,10 @@ Use biomni for:
 
 ### Installation and Setup
 
-Biomni requires conda environment setup and API keys for LLM providers:
+Install Biomni and configure API keys for LLM providers:
 
 ```bash
-# Clone repository and set up environment
-git clone https://github.com/snap-stanford/biomni
-cd biomni
-bash setup.sh
-
-# Or install via pip
-conda activate biomni_e1
-pip install biomni --upgrade
+uv pip install biomni --upgrade
 ```
 
 Configure API keys (store in `.env` file or environment variables):
diff --git a/scientific-skills/biopython/SKILL.md b/scientific-skills/biopython/SKILL.md
index 863149b..16fc6dd 100644
--- a/scientific-skills/biopython/SKILL.md
+++ b/scientific-skills/biopython/SKILL.md
@@ -43,7 +43,7 @@ Biopython is organized into modular sub-packages, each addressing specific bioin
 Install Biopython using pip (requires Python 3 and NumPy):
 
 ```python
-pip install biopython
+uv pip install biopython
 ```
 
 For NCBI database access, always set your email address (required by NCBI):
diff --git a/scientific-skills/biorxiv-database/SKILL.md b/scientific-skills/biorxiv-database/SKILL.md
index 0809e7e..440ed50 100644
--- a/scientific-skills/biorxiv-database/SKILL.md
+++ b/scientific-skills/biorxiv-database/SKILL.md
@@ -414,7 +414,7 @@ To verify that the bioRxiv database skill is working correctly, run the comprehe
 
 **Prerequisites:**
 ```bash
-pip install requests
+uv pip install requests
 ```
 
 **Run tests:**
diff --git a/scientific-skills/bioservices/SKILL.md b/scientific-skills/bioservices/SKILL.md
index 4205490..13bc348 100644
--- a/scientific-skills/bioservices/SKILL.md
+++ b/scientific-skills/bioservices/SKILL.md
@@ -342,7 +342,7 @@ Load references when working with specific services or complex integration tasks
 ## Installation
 
 ```bash
-pip install bioservices
+uv pip install bioservices
 ```
 
 Dependencies are automatically managed. Package is tested on Python 3.9-3.12.
diff --git a/scientific-skills/cellxgene-census/SKILL.md b/scientific-skills/cellxgene-census/SKILL.md
index 3adac4b..a769633 100644
--- a/scientific-skills/cellxgene-census/SKILL.md
+++ b/scientific-skills/cellxgene-census/SKILL.md
@@ -31,12 +31,12 @@ This skill should be used when:
 
 Install the Census API:
 ```bash
-pip install cellxgene-census
+uv pip install cellxgene-census
 ```
 
 For machine learning workflows, install additional dependencies:
 ```bash
-pip install cellxgene-census[experimental]
+uv pip install cellxgene-census[experimental]
 ```
 
 ## Core Workflow Patterns
diff --git a/scientific-skills/chembl-database/SKILL.md b/scientific-skills/chembl-database/SKILL.md
index fb61f07..afb919f 100644
--- a/scientific-skills/chembl-database/SKILL.md
+++ b/scientific-skills/chembl-database/SKILL.md
@@ -29,7 +29,7 @@ This skill should be used when:
 The ChEMBL Python client is required for programmatic access:
 
 ```bash
-pip install chembl_webresource_client
+uv pip install chembl_webresource_client
 ```
 
 ### Basic Usage Pattern
diff --git a/scientific-skills/clinpgx-database/SKILL.md b/scientific-skills/clinpgx-database/SKILL.md
index b50f074..e3aa7c0 100644
--- a/scientific-skills/clinpgx-database/SKILL.md
+++ b/scientific-skills/clinpgx-database/SKILL.md
@@ -31,7 +31,7 @@ This skill should be used when:
 The ClinPGx REST API provides programmatic access to all database resources. Basic setup:
 
 ```bash
-pip install requests
+uv pip install requests
 ```
 
 ### API Endpoint
diff --git a/scientific-skills/cosmic-database/SKILL.md b/scientific-skills/cosmic-database/SKILL.md
index 07355f8..4f4a854 100644
--- a/scientific-skills/cosmic-database/SKILL.md
+++ b/scientific-skills/cosmic-database/SKILL.md
@@ -30,7 +30,7 @@ COSMIC requires authentication for data downloads:
 
 ### Python Requirements
 ```bash
-pip install requests pandas
+uv pip install requests pandas
 ```
 
 ## Quick Start
diff --git a/scientific-skills/datacommons-client/SKILL.md b/scientific-skills/datacommons-client/SKILL.md
index d073e36..1617577 100644
--- a/scientific-skills/datacommons-client/SKILL.md
+++ b/scientific-skills/datacommons-client/SKILL.md
@@ -14,12 +14,12 @@ Provides comprehensive access to the Data Commons Python API v2 for querying sta
 Install the Data Commons Python client with Pandas support:
 
 ```bash
-pip install "datacommons-client[Pandas]"
+uv pip install "datacommons-client[Pandas]"
 ```
 
 For basic usage without Pandas:
 ```bash
-pip install datacommons-client
+uv pip install datacommons-client
 ```
 
 ## Core Capabilities
diff --git a/scientific-skills/datamol/SKILL.md b/scientific-skills/datamol/SKILL.md
index be4bc92..e9c6d61 100644
--- a/scientific-skills/datamol/SKILL.md
+++ b/scientific-skills/datamol/SKILL.md
@@ -26,11 +26,7 @@ Datamol is a Python library that provides a lightweight, Pythonic abstraction la
 Guide users to install datamol:
 
 ```bash
-# Via conda/mamba (recommended)
-conda install -c conda-forge datamol
-
-# Via pip
-pip install datamol
+uv pip install datamol
 ```
 
 **Import convention**:
diff --git a/scientific-skills/deepchem/SKILL.md b/scientific-skills/deepchem/SKILL.md
index 36484b6..557095e 100644
--- a/scientific-skills/deepchem/SKILL.md
+++ b/scientific-skills/deepchem/SKILL.md
@@ -528,11 +528,11 @@ model = dc.models.GCNModel(batch_size=32)  # Instead of 128
 **Problem**: Module not found errors.
 **Solution**: Ensure DeepChem is installed with required dependencies:
 ```bash
-pip install deepchem
+uv pip install deepchem
 # For PyTorch models
-pip install deepchem[torch]
+uv pip install deepchem[torch]
 # For all features
-pip install deepchem[all]
+uv pip install deepchem[all]
 ```
 
 ## Reference Documentation
@@ -568,17 +568,17 @@ Eight detailed end-to-end workflows:
 
 Basic installation:
 ```bash
-pip install deepchem
+uv pip install deepchem
 ```
 
 For PyTorch models (GCN, GAT, etc.):
 ```bash
-pip install deepchem[torch]
+uv pip install deepchem[torch]
 ```
 
 For all features:
 ```bash
-pip install deepchem[all]
+uv pip install deepchem[all]
 ```
 
 If import errors occur, the user may need specific dependencies. Check the DeepChem documentation for detailed installation instructions.
diff --git a/scientific-skills/deeptools/SKILL.md b/scientific-skills/deeptools/SKILL.md
index 3ee305c..4ee7ab1 100644
--- a/scientific-skills/deeptools/SKILL.md
+++ b/scientific-skills/deeptools/SKILL.md
@@ -65,20 +65,8 @@ See `assets/quick_reference.md` for frequently used commands and parameters.
 
 ## Installation
 
-Guide users to install deepTools using conda (recommended):
-
 ```bash
-# Standard installation
-conda install -c conda-forge -c bioconda deeptools
-
-# For M1 Macs
-CONDA_SUBDIR=osx-64 conda create -c conda-forge -c bioconda -n deeptools deeptools
-```
-
-Or using pip:
-
-```bash
-pip install deeptools
+uv pip install deeptools
 ```
 
 ## Core Workflows
diff --git a/scientific-skills/denario/SKILL.md b/scientific-skills/denario/SKILL.md
index e550e1d..044ecdc 100644
--- a/scientific-skills/denario/SKILL.md
+++ b/scientific-skills/denario/SKILL.md
@@ -31,7 +31,7 @@ uv add "denario[app]"
 Or using pip:
 
 ```bash
-pip install "denario[app]"
+uv pip install "denario[app]"
 ```
 
 For Docker deployment or building from source, see `references/installation.md`.
diff --git a/scientific-skills/denario/references/installation.md b/scientific-skills/denario/references/installation.md
index 8887b89..a1be99a 100644
--- a/scientific-skills/denario/references/installation.md
+++ b/scientific-skills/denario/references/installation.md
@@ -21,9 +21,9 @@ uv init
 uv add "denario[app]"
 ```
 
-### Method 2: Using pip
+### Method 2: Alternative Installation
 
-Standard pip installation:
+Alternative installation using pip:
 
 ```bash
 # Create virtual environment (recommended)
@@ -31,7 +31,7 @@ python3 -m venv denario_env
 source denario_env/bin/activate  # On Windows: denario_env\Scripts\activate
 
 # Install denario
-pip install "denario[app]"
+uv pip install "denario[app]"
 ```
 
 ### Method 3: Building from Source
@@ -48,7 +48,7 @@ python3 -m venv Denario_env
 source Denario_env/bin/activate
 
 # Install in editable mode
-pip install -e .
+uv pip install -e .
 ```
 
 ### Method 4: Docker Deployment
@@ -146,7 +146,7 @@ Ensure Python 3.12+:
 python --version
 ```
 
-If older, install a newer version or use pyenv/conda for version management.
+If older, install a newer version or use pyenv for version management.
 
 ### Virtual Environment Activation
 
@@ -164,7 +164,7 @@ venv\Scripts\activate
 
 Use `--user` flag or virtual environments:
 ```bash
-pip install --user "denario[app]"
+uv pip install --user "denario[app]"
 ```
 
 ### Docker Port Conflicts
@@ -187,7 +187,7 @@ uv add --upgrade denario
 
 ### pip
 ```bash
-pip install --upgrade "denario[app]"
+uv pip install --upgrade "denario[app]"
 ```
 
 ### Docker
@@ -204,7 +204,7 @@ uv remove denario
 
 ### pip
 ```bash
-pip uninstall denario
+uv pip uninstall denario
 ```
 
 ### Docker
diff --git a/scientific-skills/dnanexus-integration/SKILL.md b/scientific-skills/dnanexus-integration/SKILL.md
index b3a7e85..619c373 100644
--- a/scientific-skills/dnanexus-integration/SKILL.md
+++ b/scientific-skills/dnanexus-integration/SKILL.md
@@ -252,7 +252,7 @@ Often you'll need multiple capabilities together (e.g., app development + config
 ### Install dxpy
 
 ```bash
-pip install dxpy
+uv pip install dxpy
 ```
 
 ### Login to DNAnexus
diff --git a/scientific-skills/document-skills/docx/SKILL.md b/scientific-skills/document-skills/docx/SKILL.md
index 3fb8086..b219b8c 100644
--- a/scientific-skills/document-skills/docx/SKILL.md
+++ b/scientific-skills/document-skills/docx/SKILL.md
@@ -194,4 +194,4 @@ Required dependencies (install if not available):
 - **docx**: `npm install -g docx` (for creating new documents)
 - **LibreOffice**: `sudo apt-get install libreoffice` (for PDF conversion)
 - **Poppler**: `sudo apt-get install poppler-utils` (for pdftoppm to convert PDF to images)
-- **defusedxml**: `pip install defusedxml` (for secure XML parsing)
\ No newline at end of file
+- **defusedxml**: `uv pip install defusedxml` (for secure XML parsing)
\ No newline at end of file
diff --git a/scientific-skills/document-skills/pdf/SKILL.md b/scientific-skills/document-skills/pdf/SKILL.md
index 8ca8ea5..b8092b6 100644
--- a/scientific-skills/document-skills/pdf/SKILL.md
+++ b/scientific-skills/document-skills/pdf/SKILL.md
@@ -212,7 +212,7 @@ pdftk input.pdf rotate 1east output rotated.pdf
 
 ### Extract Text from Scanned PDFs
 ```python
-# Requires: pip install pytesseract pdf2image
+# Requires: uv pip install pytesseract pdf2image
 import pytesseract
 from pdf2image import convert_from_path
 
diff --git a/scientific-skills/document-skills/pptx/SKILL.md b/scientific-skills/document-skills/pptx/SKILL.md
index 8ab2db9..f10502a 100644
--- a/scientific-skills/document-skills/pptx/SKILL.md
+++ b/scientific-skills/document-skills/pptx/SKILL.md
@@ -474,11 +474,11 @@ pdftoppm -jpeg -r 150 -f 2 -l 5 template.pdf slide  # Converts only pages 2-5
 
 Required dependencies (should already be installed):
 
-- **markitdown**: `pip install "markitdown[pptx]"` (for text extraction from presentations)
+- **markitdown**: `uv pip install "markitdown[pptx]"` (for text extraction from presentations)
 - **pptxgenjs**: `npm install -g pptxgenjs` (for creating presentations via html2pptx)
 - **playwright**: `npm install -g playwright` (for HTML rendering in html2pptx)
 - **react-icons**: `npm install -g react-icons react react-dom` (for icons)
 - **sharp**: `npm install -g sharp` (for SVG rasterization and image processing)
 - **LibreOffice**: `sudo apt-get install libreoffice` (for PDF conversion)
 - **Poppler**: `sudo apt-get install poppler-utils` (for pdftoppm to convert PDF to images)
-- **defusedxml**: `pip install defusedxml` (for secure XML parsing)
\ No newline at end of file
+- **defusedxml**: `uv pip install defusedxml` (for secure XML parsing)
\ No newline at end of file
diff --git a/scientific-skills/drugbank-database/SKILL.md b/scientific-skills/drugbank-database/SKILL.md
index ec60181..488daa0 100644
--- a/scientific-skills/drugbank-database/SKILL.md
+++ b/scientific-skills/drugbank-database/SKILL.md
@@ -134,13 +134,13 @@ Perform structure-based analysis including molecular similarity searches, proper
 
 ### Python Packages
 ```bash
-pip install drugbank-downloader  # Core access
-pip install bioversions          # Latest version detection
-pip install lxml                 # XML parsing optimization
-pip install pandas               # Data manipulation
-pip install rdkit                # Chemical informatics (for similarity)
-pip install networkx             # Network analysis (for interactions)
-pip install scikit-learn         # ML/clustering (for chemical space)
+uv pip install drugbank-downloader  # Core access
+uv pip install bioversions          # Latest version detection
+uv pip install lxml                 # XML parsing optimization
+uv pip install pandas               # Data manipulation
+uv pip install rdkit                # Chemical informatics (for similarity)
+uv pip install networkx             # Network analysis (for interactions)
+uv pip install scikit-learn         # ML/clustering (for chemical space)
 ```
 
 ### Account Setup
diff --git a/scientific-skills/ensembl-database/SKILL.md b/scientific-skills/ensembl-database/SKILL.md
index 9038938..2359900 100644
--- a/scientific-skills/ensembl-database/SKILL.md
+++ b/scientific-skills/ensembl-database/SKILL.md
@@ -229,7 +229,7 @@ def query_ensembl(endpoint, params=None, max_retries=3):
 ### Python Package (Recommended)
 
 ```bash
-pip install ensembl_rest
+uv pip install ensembl_rest
 ```
 
 The `ensembl_rest` package provides a Pythonic interface to all Ensembl REST API endpoints.
@@ -239,7 +239,7 @@ The `ensembl_rest` package provides a Pythonic interface to all Ensembl REST API
 No installation needed - use standard HTTP libraries like `requests`:
 
 ```bash
-pip install requests
+uv pip install requests
 ```
 
 ## Resources
diff --git a/scientific-skills/esm/SKILL.md b/scientific-skills/esm/SKILL.md
index 3fbc606..9e205c1 100644
--- a/scientific-skills/esm/SKILL.md
+++ b/scientific-skills/esm/SKILL.md
@@ -226,20 +226,20 @@ See `references/forge-api.md` for detailed Forge API documentation, authenticati
 **Basic installation:**
 
 ```bash
-pip install esm
+uv pip install esm
 ```
 
 **With Flash Attention (recommended for faster inference):**
 
 ```bash
-pip install esm
-pip install flash-attn --no-build-isolation
+uv pip install esm
+uv pip install flash-attn --no-build-isolation
 ```
 
 **For Forge API access:**
 
 ```bash
-pip install esm  # SDK includes Forge client
+uv pip install esm  # SDK includes Forge client
 ```
 
 No additional dependencies needed. Obtain Forge API token at https://forge.evolutionaryscale.ai
diff --git a/scientific-skills/etetoolkit/SKILL.md b/scientific-skills/etetoolkit/SKILL.md
index 174a8ce..7686243 100644
--- a/scientific-skills/etetoolkit/SKILL.md
+++ b/scientific-skills/etetoolkit/SKILL.md
@@ -358,7 +358,7 @@ Install ETE toolkit:
 
 ```bash
 # Basic installation
-pip install ete3
+uv pip install ete3
 
 # With external dependencies for rendering (optional but recommended)
 # On macOS:
@@ -368,7 +368,7 @@ brew install qt@5
 sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg
 
 # For full features including GUI
-pip install ete3[gui]
+uv pip install ete3[gui]
 ```
 
 **First-time NCBI Taxonomy setup:**
@@ -536,10 +536,10 @@ Load these references when detailed information is needed:
 
 ```bash
 # If "ModuleNotFoundError: No module named 'ete3'"
-pip install ete3
+uv pip install ete3
 
 # For GUI and rendering issues
-pip install ete3[gui]
+uv pip install ete3[gui]
 ```
 
 **Rendering issues:**
diff --git a/scientific-skills/exploratory-data-analysis/SKILL.md b/scientific-skills/exploratory-data-analysis/SKILL.md
index 717f9c2..e6a23d4 100644
--- a/scientific-skills/exploratory-data-analysis/SKILL.md
+++ b/scientific-skills/exploratory-data-analysis/SKILL.md
@@ -347,7 +347,7 @@ Many scientific formats require specialized libraries:
 try:
     from Bio import SeqIO
 except ImportError:
-    print("Install Biopython: pip install biopython")
+    print("Install Biopython: uv pip install biopython")
 ```
 
 Common requirements by category:
diff --git a/scientific-skills/flowio/SKILL.md b/scientific-skills/flowio/SKILL.md
index 64cfa14..3d09045 100644
--- a/scientific-skills/flowio/SKILL.md
+++ b/scientific-skills/flowio/SKILL.md
@@ -26,7 +26,7 @@ This skill should be used when:
 ## Installation
 
 ```bash
-pip install flowio
+uv pip install flowio
 ```
 
 Requires Python 3.9 or later.
diff --git a/scientific-skills/fluidsim/SKILL.md b/scientific-skills/fluidsim/SKILL.md
index 5e3a736..cdf16a6 100644
--- a/scientific-skills/fluidsim/SKILL.md
+++ b/scientific-skills/fluidsim/SKILL.md
@@ -23,13 +23,13 @@ Install fluidsim using uv with appropriate feature flags:
 
 ```bash
 # Basic installation
-uv pip install fluidsim
+uv uv pip install fluidsim
 
 # With FFT support (required for most solvers)
-uv pip install "fluidsim[fft]"
+uv uv pip install "fluidsim[fft]"
 
 # With MPI for parallel computing
-uv pip install "fluidsim[fft,mpi]"
+uv uv pip install "fluidsim[fft,mpi]"
 ```
 
 Set environment variables for output directories (optional):
@@ -41,7 +41,7 @@ export FLUIDDYN_PATH_SCRATCH=/path/to/working/directory
 
 No API keys or authentication required.
 
-See `references/installation.md` for complete installation instructions, conda/mamba alternatives, and environment configuration.
+See `references/installation.md` for complete installation instructions and environment configuration.
 
 ### 2. Running Simulations
 
diff --git a/scientific-skills/fluidsim/references/installation.md b/scientific-skills/fluidsim/references/installation.md
index 3b9e19a..d25a644 100644
--- a/scientific-skills/fluidsim/references/installation.md
+++ b/scientific-skills/fluidsim/references/installation.md
@@ -35,20 +35,6 @@ uv pip install "fluidsim[fft,mpi]"
 
 Note: This triggers local compilation of mpi4py.
 
-### Conda/Mamba Installation
-
-For sequential simulations:
-
-```bash
-conda install fluidsim
-```
-
-For MPI-enabled environment:
-
-```bash
-conda create -n env-fluidsim fluidsim "h5py[build=mpi*]" fluidfft-mpi_with_fftw fluidfft-fftwmpi
-```
-
 ## Environment Configuration
 
 ### Output Directories
diff --git a/scientific-skills/geniml/SKILL.md b/scientific-skills/geniml/SKILL.md
index 8ba5b43..c369f99 100644
--- a/scientific-skills/geniml/SKILL.md
+++ b/scientific-skills/geniml/SKILL.md
@@ -14,19 +14,19 @@ Geniml is a Python package for building machine learning models on genomic inter
 Install geniml using uv:
 
 ```bash
-uv pip install geniml
+uv uv pip install geniml
 ```
 
 For ML dependencies (PyTorch, etc.):
 
 ```bash
-uv pip install 'geniml[ml]'
+uv uv pip install 'geniml[ml]'
 ```
 
 Development version from GitHub:
 
 ```bash
-uv pip install git+https://github.com/databio/geniml.git
+uv uv pip install git+https://github.com/databio/geniml.git
 ```
 
 ## Core Capabilities
diff --git a/scientific-skills/geo-database/SKILL.md b/scientific-skills/geo-database/SKILL.md
index e99ca94..09890e1 100644
--- a/scientific-skills/geo-database/SKILL.md
+++ b/scientific-skills/geo-database/SKILL.md
@@ -139,7 +139,7 @@ results = advanced_geo_search(search_terms)
 
 **Installation:**
 ```bash
-pip install GEOparse
+uv pip install GEOparse
 ```
 
 **Basic Usage:**
@@ -642,19 +642,19 @@ print(meta_results)
 
 ```bash
 # Primary GEO access library (recommended)
-pip install GEOparse
+uv pip install GEOparse
 
 # For E-utilities and programmatic NCBI access
-pip install biopython
+uv pip install biopython
 
 # For data analysis
-pip install pandas numpy scipy
+uv pip install pandas numpy scipy
 
 # For visualization
-pip install matplotlib seaborn
+uv pip install matplotlib seaborn
 
 # For statistical analysis
-pip install statsmodels scikit-learn
+uv pip install statsmodels scikit-learn
 ```
 
 ### Configuration
diff --git a/scientific-skills/get-available-resources/SKILL.md b/scientific-skills/get-available-resources/SKILL.md
index 8321a92..82a3efa 100644
--- a/scientific-skills/get-available-resources/SKILL.md
+++ b/scientific-skills/get-available-resources/SKILL.md
@@ -234,7 +234,7 @@ model = model.to(device)
 The detection script requires the following Python packages:
 
 ```bash
-pip install psutil
+uv pip install psutil
 ```
 
 All other functionality uses Python standard library modules (json, os, platform, subprocess, sys, pathlib).
@@ -261,7 +261,7 @@ All other functionality uses Python standard library modules (json, os, platform
 - Verify GPU is not in use by other processes
 
 **Script execution fails:**
-- Ensure psutil is installed: `pip install psutil`
+- Ensure psutil is installed: `uv pip install psutil`
 - Check Python version compatibility (Python 3.6+)
 - Verify script has execute permissions: `chmod +x scripts/detect_resources.py`
 
diff --git a/scientific-skills/gget/SKILL.md b/scientific-skills/gget/SKILL.md
index b5ef2a3..7e4ecff 100644
--- a/scientific-skills/gget/SKILL.md
+++ b/scientific-skills/gget/SKILL.md
@@ -17,10 +17,10 @@ Install gget in a clean virtual environment to avoid conflicts:
 
 ```bash
 # Using uv (recommended)
-uv pip install gget
+uv uv pip install gget
 
 # Or using pip
-pip install --upgrade gget
+uv pip install --upgrade gget
 
 # In Python/Jupyter
 import gget
@@ -302,13 +302,8 @@ Predict 3D protein structures using simplified AlphaFold2.
 
 **Setup Required**:
 ```bash
-# Install OpenMM first (version depends on Python version)
-# Python < 3.10:
-conda install -qy conda==4.13.0 && conda install -qy -c conda-forge openmm=7.5.1
-# Python 3.10:
-conda install -qy conda==24.1.2 && conda install -qy -c conda-forge openmm=7.7.0
-# Python 3.11:
-conda install -qy conda==24.11.1 && conda install -qy -c conda-forge openmm=8.0.0
+# Install OpenMM first
+uv pip install openmm
 
 # Then setup AlphaFold
 gget setup alphafold
@@ -835,7 +830,7 @@ gget ref -w dna -d homo_sapiens
 - Check PDB database first before running AlphaFold predictions
 
 ### Error Handling
-- Database structures change; update gget regularly: `pip install --upgrade gget`
+- Database structures change; update gget regularly: `uv pip install --upgrade gget`
 - Process max ~1000 Ensembl IDs at once with gget info
 - For large-scale analyses, implement rate limiting for API queries
 - Use virtual environments to avoid dependency conflicts
diff --git a/scientific-skills/gtars/SKILL.md b/scientific-skills/gtars/SKILL.md
index c45af42..bdbc967 100644
--- a/scientific-skills/gtars/SKILL.md
+++ b/scientific-skills/gtars/SKILL.md
@@ -24,7 +24,7 @@ Use this skill when working with:
 Install gtars Python bindings:
 
 ```bash
-uv pip install gtars
+uv uv pip install gtars
 ```
 
 ### CLI Installation
diff --git a/scientific-skills/histolab/SKILL.md b/scientific-skills/histolab/SKILL.md
index 1e52ea8..74d233b 100644
--- a/scientific-skills/histolab/SKILL.md
+++ b/scientific-skills/histolab/SKILL.md
@@ -11,13 +11,8 @@ Histolab is a Python library for processing whole slide images (WSI) in digital
 
 ## Installation
 
-Install histolab using pip or conda:
-
 ```bash
-pip install histolab
-
-# Or via conda
-conda install -c conda-forge histolab
+uv pip install histolab
 ```
 
 ## Quick Start
diff --git a/scientific-skills/hypogenic/SKILL.md b/scientific-skills/hypogenic/SKILL.md
index e3cbf7e..05c5b97 100644
--- a/scientific-skills/hypogenic/SKILL.md
+++ b/scientific-skills/hypogenic/SKILL.md
@@ -15,7 +15,7 @@ Get started with Hypogenic in minutes:
 
 ```bash
 # Install the package
-pip install hypogenic
+uv pip install hypogenic
 
 # Clone example datasets
 git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
@@ -118,7 +118,7 @@ Mechanistically combine literature-only hypotheses with framework outputs.
 
 Install via pip:
 ```bash
-pip install hypogenic
+uv pip install hypogenic
 ```
 
 **Optional dependencies:**
diff --git a/scientific-skills/labarchive-integration/SKILL.md b/scientific-skills/labarchive-integration/SKILL.md
index fd98950..aafa95d 100644
--- a/scientific-skills/labarchive-integration/SKILL.md
+++ b/scientific-skills/labarchive-integration/SKILL.md
@@ -219,7 +219,7 @@ Install the `labarchives-py` wrapper for simplified API access:
 ```bash
 git clone https://github.com/mcmero/labarchives-py
 cd labarchives-py
-pip install .
+uv pip install .
 ```
 
 Alternatively, use direct HTTP requests via Python's `requests` library for custom implementations.
diff --git a/scientific-skills/lamindb/SKILL.md b/scientific-skills/lamindb/SKILL.md
index 40b756b..a9341bc 100644
--- a/scientific-skills/lamindb/SKILL.md
+++ b/scientific-skills/lamindb/SKILL.md
@@ -156,8 +156,8 @@ LaminDB provides six interconnected capability areas, each documented in detail
 ### 6. Setup and Deployment
 
 **Installation:**
-- Basic: `pip install lamindb`
-- With extras: `pip install 'lamindb[gcp,zarr,fcs]'`
+- Basic: `uv pip install lamindb`
+- With extras: `uv pip install 'lamindb[gcp,zarr,fcs]'`
 - Modules: bionty, wetlab, clinical
 
 **Instance types:**
diff --git a/scientific-skills/latchbio-integration/SKILL.md b/scientific-skills/latchbio-integration/SKILL.md
index 27173d2..36d837d 100644
--- a/scientific-skills/latchbio-integration/SKILL.md
+++ b/scientific-skills/latchbio-integration/SKILL.md
@@ -47,7 +47,7 @@ The Latch platform provides four main areas of functionality:
 
 ```bash
 # Install Latch SDK
-python3 -m pip install latch
+python3 -m uv pip install latch
 
 # Login to Latch
 latch login
diff --git a/scientific-skills/literature-review/SKILL.md b/scientific-skills/literature-review/SKILL.md
index e012e9b..75f36c5 100644
--- a/scientific-skills/literature-review/SKILL.md
+++ b/scientific-skills/literature-review/SKILL.md
@@ -512,7 +512,7 @@ This skill works seamlessly with other scientific skills:
 
 ### Required Python Packages
 ```bash
-pip install requests  # For citation verification
+uv pip install requests  # For citation verification
 ```
 
 ### Required System Tools
diff --git a/scientific-skills/markitdown/SKILL.md b/scientific-skills/markitdown/SKILL.md
index 92c6f8d..958f862 100644
--- a/scientific-skills/markitdown/SKILL.md
+++ b/scientific-skills/markitdown/SKILL.md
@@ -167,17 +167,17 @@ See `scripts/batch_convert.py` for implementation details.
 
 **Full installation (all features):**
 ```bash
-pip install 'markitdown[all]'
+uv pip install 'markitdown[all]'
 ```
 
 **Modular installation (specific features):**
 ```bash
-pip install 'markitdown[pdf]'           # PDF support
-pip install 'markitdown[docx]'          # Word support
-pip install 'markitdown[pptx]'          # PowerPoint support
-pip install 'markitdown[xlsx]'          # Excel support
-pip install 'markitdown[audio]'         # Audio transcription
-pip install 'markitdown[youtube]'       # YouTube transcripts
+uv pip install 'markitdown[pdf]'           # PDF support
+uv pip install 'markitdown[docx]'          # Word support
+uv pip install 'markitdown[pptx]'          # PowerPoint support
+uv pip install 'markitdown[xlsx]'          # Excel support
+uv pip install 'markitdown[audio]'         # Audio transcription
+uv pip install 'markitdown[youtube]'       # YouTube transcripts
 ```
 
 **Requirements:**
diff --git a/scientific-skills/matchms/SKILL.md b/scientific-skills/matchms/SKILL.md
index daa1fdd..002d83b 100644
--- a/scientific-skills/matchms/SKILL.md
+++ b/scientific-skills/matchms/SKILL.md
@@ -178,12 +178,12 @@ Consult `references/workflows.md` for detailed examples.
 ## Installation
 
 ```bash
-pip install matchms
+uv pip install matchms
 ```
 
 For molecular structure processing (SMILES, InChI):
 ```bash
-pip install matchms[chemistry]
+uv pip install matchms[chemistry]
 ```
 
 ## Reference Documentation
diff --git a/scientific-skills/medchem/SKILL.md b/scientific-skills/medchem/SKILL.md
index b1091d5..6fd59aa 100644
--- a/scientific-skills/medchem/SKILL.md
+++ b/scientific-skills/medchem/SKILL.md
@@ -21,14 +21,8 @@ This skill should be used when:
 
 ## Installation
 
-Install medchem via conda or pip:
-
 ```bash
-# Via conda
-micromamba install -c conda-forge medchem
-
-# Via pip
-pip install medchem
+uv pip install medchem
 ```
 
 ## Core Capabilities
diff --git a/scientific-skills/modal/SKILL.md b/scientific-skills/modal/SKILL.md
index b01181b..1850e54 100644
--- a/scientific-skills/modal/SKILL.md
+++ b/scientific-skills/modal/SKILL.md
@@ -29,7 +29,7 @@ Modal requires authentication via API token.
 
 ```bash
 # Install Modal
-uv pip install modal
+uv uv pip install modal
 
 # Authenticate (opens browser for login)
 modal token new
diff --git a/scientific-skills/molfeat/SKILL.md b/scientific-skills/molfeat/SKILL.md
index e7e278f..7ae2192 100644
--- a/scientific-skills/molfeat/SKILL.md
+++ b/scientific-skills/molfeat/SKILL.md
@@ -23,14 +23,10 @@ This skill should be used when working with:
 ## Installation
 
 ```bash
-# Recommended: Using conda/mamba
-mamba install -c conda-forge molfeat
-
-# Alternative: Using pip
-pip install molfeat
+uv pip install molfeat
 
 # With all optional dependencies
-pip install "molfeat[all]"
+uv pip install "molfeat[all]"
 ```
 
 **Optional dependencies for specific featurizers:**
@@ -489,8 +485,8 @@ Process in chunks or use streaming approaches for datasets > 100K molecules.
 ### Pretrained Model Dependencies
 Some models require additional packages. Install specific extras:
 ```bash
-pip install "molfeat[transformer]"  # For ChemBERTa/ChemGPT
-pip install "molfeat[dgl]"          # For GIN models
+uv pip install "molfeat[transformer]"  # For ChemBERTa/ChemGPT
+uv pip install "molfeat[dgl]"          # For GIN models
 ```
 
 ### Reproducibility
diff --git a/scientific-skills/networkx/SKILL.md b/scientific-skills/networkx/SKILL.md
index 253adde..89a07de 100644
--- a/scientific-skills/networkx/SKILL.md
+++ b/scientific-skills/networkx/SKILL.md
@@ -258,8 +258,8 @@ import networkx as nx
 print(nx.__version__)
 
 # Install if needed (via bash)
-# pip install networkx
-# pip install networkx[default]  # With optional dependencies
+# uv pip install networkx
+# uv pip install networkx[default]  # With optional dependencies
 ```
 
 ### Common Workflow Pattern
diff --git a/scientific-skills/neurokit2/SKILL.md b/scientific-skills/neurokit2/SKILL.md
index 19c736a..2874fac 100644
--- a/scientific-skills/neurokit2/SKILL.md
+++ b/scientific-skills/neurokit2/SKILL.md
@@ -268,12 +268,12 @@ Most `*_analyze()` functions automatically choose the appropriate mode.
 ## Installation
 
 ```bash
-pip install neurokit2
+uv pip install neurokit2
 ```
 
 For development version:
 ```bash
-pip install https://github.com/neuropsychology/NeuroKit/zipball/dev
+uv pip install https://github.com/neuropsychology/NeuroKit/zipball/dev
 ```
 
 ## Common Workflows
diff --git a/scientific-skills/omero-integration/SKILL.md b/scientific-skills/omero-integration/SKILL.md
index 7a4ae60..c668cc5 100644
--- a/scientific-skills/omero-integration/SKILL.md
+++ b/scientific-skills/omero-integration/SKILL.md
@@ -115,14 +115,8 @@ Covers permissions, filesets, cross-group queries, delete operations, and other
 
 ## Installation
 
-Install the OMERO Python bindings using pip or conda:
-
 ```bash
-# Using pip
-pip install omero-py
-
-# Using conda
-conda install -c conda-forge omero-py
+uv pip install omero-py
 ```
 
 **Requirements:**
@@ -130,8 +124,6 @@ conda install -c conda-forge omero-py
 - Zeroc Ice 3.6+
 - Access to an OMERO server (host, port, credentials)
 
-**Best practice:** Use a Python virtual environment (venv, conda, or mamba) to isolate dependencies.
-
 ## Quick Start
 
 Basic connection pattern:
diff --git a/scientific-skills/paper-2-web/SKILL.md b/scientific-skills/paper-2-web/SKILL.md
index b3d5b65..c545ba4 100644
--- a/scientific-skills/paper-2-web/SKILL.md
+++ b/scientific-skills/paper-2-web/SKILL.md
@@ -95,9 +95,7 @@ Creates print-ready academic posters with professional layouts and visual design
    ```bash
    git clone https://github.com/YuhangChen1/Paper2All.git
    cd Paper2All
-   conda create -n paper2all python=3.11
-   conda activate paper2all
-   pip install -r requirements.txt
+   uv pip install -r requirements.txt
    ```
 
 2. **Configure API Keys** (create `.env` file):
diff --git a/scientific-skills/paper-2-web/references/installation.md b/scientific-skills/paper-2-web/references/installation.md
index 37dce01..dd8d1e4 100644
--- a/scientific-skills/paper-2-web/references/installation.md
+++ b/scientific-skills/paper-2-web/references/installation.md
@@ -9,7 +9,6 @@
 
 ### Software Requirements
 - **Python**: 3.11 or higher
-- **Conda**: Environment manager for dependency isolation
 - **LibreOffice**: Required for document format conversion (PDF to PPTX, etc.)
 - **Poppler utilities**: Required for PDF processing and manipulation
 
@@ -21,18 +20,12 @@ git clone https://github.com/YuhangChen1/Paper2All.git
 cd Paper2All
 ```
 
-### 2. Create Conda Environment
+### 2. Install Dependencies
 ```bash
-conda create -n paper2all python=3.11
-conda activate paper2all
+uv pip install -r requirements.txt
 ```
 
-### 3. Install Dependencies
-```bash
-pip install -r requirements.txt
-```
-
-### 4. Install System Dependencies
+### 3. Install System Dependencies
 
 **Ubuntu/Debian:**
 ```bash
diff --git a/scientific-skills/pathml/SKILL.md b/scientific-skills/pathml/SKILL.md
index 53f139c..a1e40c4 100644
--- a/scientific-skills/pathml/SKILL.md
+++ b/scientific-skills/pathml/SKILL.md
@@ -78,10 +78,10 @@ Efficiently store and manage large pathology datasets using HDF5 format. PathML
 
 ```bash
 # Install PathML
-pip install pathml
+uv pip install pathml
 
 # With optional dependencies for all features
-pip install pathml[all]
+uv pip install pathml[all]
 ```
 
 ### Basic Workflow Example
diff --git a/scientific-skills/pdb-database/SKILL.md b/scientific-skills/pdb-database/SKILL.md
index df11f4b..f199de9 100644
--- a/scientific-skills/pdb-database/SKILL.md
+++ b/scientific-skills/pdb-database/SKILL.md
@@ -233,10 +233,10 @@ Install the official RCSB PDB Python API client:
 
 ```bash
 # Current recommended package
-pip install rcsb-api
+uv pip install rcsb-api
 
 # For legacy code (deprecated, use rcsb-api instead)
-pip install rcsbsearchapi
+uv pip install rcsbsearchapi
 ```
 
 The `rcsb-api` package provides unified access to both Search and Data APIs through the `rcsbapi.search` and `rcsbapi.data` modules.
diff --git a/scientific-skills/polars/SKILL.md b/scientific-skills/polars/SKILL.md
index ad68833..a2f48e7 100644
--- a/scientific-skills/polars/SKILL.md
+++ b/scientific-skills/polars/SKILL.md
@@ -15,7 +15,7 @@ Polars is a lightning-fast DataFrame library for Python and Rust built on Apache
 
 Install Polars:
 ```python
-pip install polars
+uv pip install polars
 ```
 
 Basic DataFrame creation and operations:
diff --git a/scientific-skills/pubchem-database/SKILL.md b/scientific-skills/pubchem-database/SKILL.md
index 8551065..bae7f5d 100644
--- a/scientific-skills/pubchem-database/SKILL.md
+++ b/scientific-skills/pubchem-database/SKILL.md
@@ -280,19 +280,19 @@ url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON?
 Install PubChemPy for Python-based access:
 
 ```bash
-pip install pubchempy
+uv pip install pubchempy
 ```
 
 For direct API access and bioactivity queries:
 
 ```bash
-pip install requests
+uv pip install requests
 ```
 
 Optional for data analysis:
 
 ```bash
-pip install pandas
+uv pip install pandas
 ```
 
 ## Helper Scripts
diff --git a/scientific-skills/pufferlib/SKILL.md b/scientific-skills/pufferlib/SKILL.md
index 5824f63..cbb2702 100644
--- a/scientific-skills/pufferlib/SKILL.md
+++ b/scientific-skills/pufferlib/SKILL.md
@@ -420,7 +420,7 @@ env = pufferlib.make(
 ## Installation
 
 ```bash
-pip install pufferlib
+uv pip install pufferlib
 ```
 
 ## Documentation
diff --git a/scientific-skills/pydeseq2/SKILL.md b/scientific-skills/pydeseq2/SKILL.md
index 56cbfdf..111b8fb 100644
--- a/scientific-skills/pydeseq2/SKILL.md
+++ b/scientific-skills/pydeseq2/SKILL.md
@@ -529,14 +529,8 @@ Load these references into context when users need:
 
 ## Installation and Requirements
 
-PyDESeq2 can be installed via pip or conda:
-
 ```bash
-# Via pip
-pip install pydeseq2
-
-# Via conda
-conda install -c bioconda pydeseq2
+uv pip install pydeseq2
 ```
 
 **System requirements:**
diff --git a/scientific-skills/pydicom/SKILL.md b/scientific-skills/pydicom/SKILL.md
index 0fefe4c..9d3ccc6 100644
--- a/scientific-skills/pydicom/SKILL.md
+++ b/scientific-skills/pydicom/SKILL.md
@@ -27,17 +27,17 @@ Use this skill when working with:
 Install pydicom and common dependencies:
 
 ```bash
-pip install pydicom
-pip install pillow  # For image format conversion
-pip install numpy   # For pixel array manipulation
-pip install matplotlib  # For visualization
+uv pip install pydicom
+uv pip install pillow  # For image format conversion
+uv pip install numpy   # For pixel array manipulation
+uv pip install matplotlib  # For visualization
 ```
 
 For handling compressed DICOM files, additional packages may be needed:
 
 ```bash
-pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg  # JPEG compression
-pip install python-gdcm  # Alternative compression handler
+uv pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg  # JPEG compression
+uv pip install python-gdcm  # Alternative compression handler
 ```
 
 ## Core Workflows
@@ -397,7 +397,7 @@ Detailed reference information is available in the `references/` directory:
 ## Common Issues and Solutions
 
 **Issue: "Unable to decode pixel data"**
-- Solution: Install additional compression handlers: `pip install pylibjpeg pylibjpeg-libjpeg python-gdcm`
+- Solution: Install additional compression handlers: `uv pip install pylibjpeg pylibjpeg-libjpeg python-gdcm`
 
 **Issue: "AttributeError" when accessing tags**
 - Solution: Check if attribute exists with `hasattr(ds, 'AttributeName')` or use `ds.get('AttributeName', default)`
diff --git a/scientific-skills/pyhealth/SKILL.md b/scientific-skills/pyhealth/SKILL.md
index fd18860..bde84c9 100644
--- a/scientific-skills/pyhealth/SKILL.md
+++ b/scientific-skills/pyhealth/SKILL.md
@@ -205,7 +205,7 @@ This skill includes comprehensive reference documentation organized by functiona
 ## Installation
 
 ```bash
-pip install pyhealth
+uv pip install pyhealth
 ```
 
 **Requirements:**
diff --git a/scientific-skills/pylabrobot/SKILL.md b/scientific-skills/pylabrobot/SKILL.md
index dc3ff9d..92cd9ba 100644
--- a/scientific-skills/pylabrobot/SKILL.md
+++ b/scientific-skills/pylabrobot/SKILL.md
@@ -84,7 +84,7 @@ To get started with PyLabRobot, install the package and initialize a liquid hand
 
 ```python
 # Install PyLabRobot
-# pip install pylabrobot
+# uv pip install pylabrobot
 
 # Basic liquid handling setup
 from pylabrobot.liquid_handling import LiquidHandler
diff --git a/scientific-skills/pymatgen/SKILL.md b/scientific-skills/pymatgen/SKILL.md
index 05dd129..667e6cb 100644
--- a/scientific-skills/pymatgen/SKILL.md
+++ b/scientific-skills/pymatgen/SKILL.md
@@ -29,14 +29,14 @@ This skill should be used when:
 
 ```bash
 # Core pymatgen
-pip install pymatgen
+uv pip install pymatgen
 
 # With Materials Project API access
-pip install pymatgen mp-api
+uv pip install pymatgen mp-api
 
 # Optional dependencies for extended functionality
-pip install pymatgen[analysis]  # Additional analysis tools
-pip install pymatgen[vis]       # Visualization tools
+uv pip install pymatgen[analysis]  # Additional analysis tools
+uv pip install pymatgen[vis]       # Visualization tools
 ```
 
 ### Basic Structure Operations
@@ -646,7 +646,7 @@ Pymatgen integrates seamlessly with:
 
 **Import errors**: Install missing dependencies
 ```bash
-pip install pymatgen[analysis,vis]
+uv pip install pymatgen[analysis,vis]
 ```
 
 **API key not found**: Set MP_API_KEY environment variable
diff --git a/scientific-skills/pymoo/SKILL.md b/scientific-skills/pymoo/SKILL.md
index 96d9a12..955b18b 100644
--- a/scientific-skills/pymoo/SKILL.md
+++ b/scientific-skills/pymoo/SKILL.md
@@ -548,7 +548,7 @@ python3 scripts/decision_making_example.py
 
 **Installation:**
 ```bash
-pip install pymoo
+uv pip install pymoo
 ```
 
 **Dependencies:** NumPy, SciPy, matplotlib, autograd (optional for gradient-based)
diff --git a/scientific-skills/pyopenms/SKILL.md b/scientific-skills/pyopenms/SKILL.md
index 2806039..9e2723f 100644
--- a/scientific-skills/pyopenms/SKILL.md
+++ b/scientific-skills/pyopenms/SKILL.md
@@ -14,7 +14,7 @@ PyOpenMS provides Python bindings to the OpenMS library for computational mass s
 Install using uv:
 
 ```bash
-uv pip install pyopenms
+uv uv pip install pyopenms
 ```
 
 Verify installation:
diff --git a/scientific-skills/pysam/SKILL.md b/scientific-skills/pysam/SKILL.md
index 33ae787..7dda627 100644
--- a/scientific-skills/pysam/SKILL.md
+++ b/scientific-skills/pysam/SKILL.md
@@ -24,10 +24,8 @@ This skill should be used when:
 ## Quick Start
 
 ### Installation
-```python
-# Pysam is typically installed via conda or pip
-# conda install -c bioconda pysam
-# pip install pysam
+```bash
+uv pip install pysam
 ```
 
 ### Basic Examples
diff --git a/scientific-skills/pytdc/SKILL.md b/scientific-skills/pytdc/SKILL.md
index 2970d53..dd53a4d 100644
--- a/scientific-skills/pytdc/SKILL.md
+++ b/scientific-skills/pytdc/SKILL.md
@@ -25,13 +25,13 @@ This skill should be used when:
 Install PyTDC using pip:
 
 ```bash
-pip install PyTDC
+uv pip install PyTDC
 ```
 
 To upgrade to the latest version:
 
 ```bash
-pip install PyTDC --upgrade
+uv pip install PyTDC --upgrade
 ```
 
 Core dependencies (automatically installed):
diff --git a/scientific-skills/reactome-database/reactome-database/SKILL.md b/scientific-skills/reactome-database/reactome-database/SKILL.md
index 0d08000..0d7f464 100644
--- a/scientific-skills/reactome-database/reactome-database/SKILL.md
+++ b/scientific-skills/reactome-database/reactome-database/SKILL.md
@@ -54,7 +54,7 @@ Python client library that wraps Reactome API calls for easier programmatic acce
 
 **Installation:**
 ```bash
-pip install reactome2py
+uv pip install reactome2py
 ```
 
 **Note:** The reactome2py package (version 3.0.0, released January 2021) is functional but not actively maintained. For the most up-to-date functionality, consider using direct REST API calls.
diff --git a/scientific-skills/reportlab/SKILL.md b/scientific-skills/reportlab/SKILL.md
index c953bc1..c48a6ca 100644
--- a/scientific-skills/reportlab/SKILL.md
+++ b/scientific-skills/reportlab/SKILL.md
@@ -593,16 +593,16 @@ style = TableStyle([
 ## Installation
 
 ```bash
-pip install reportlab
+uv pip install reportlab
 
 # For image support
-pip install pillow
+uv pip install pillow
 
 # For charts
-pip install reportlab[renderPM]
+uv pip install reportlab[renderPM]
 
 # For barcode support (included in reportlab)
-# QR codes require: pip install qrcode
+# QR codes require: uv pip install qrcode
 ```
 
 ## When to Use This Skill
diff --git a/scientific-skills/scikit-bio/SKILL.md b/scientific-skills/scikit-bio/SKILL.md
index ee1afa0..c792e42 100644
--- a/scientific-skills/scikit-bio/SKILL.md
+++ b/scientific-skills/scikit-bio/SKILL.md
@@ -393,9 +393,7 @@ df = embedding.to_dataframe()
 
 ### Installation
 ```bash
-pip install scikit-bio
-# Or with conda:
-conda install -c conda-forge scikit-bio
+uv pip install scikit-bio
 ```
 
 ### Performance Considerations
diff --git a/scientific-skills/scikit-learn/SKILL.md b/scientific-skills/scikit-learn/SKILL.md
index 784f677..f3715ea 100644
--- a/scientific-skills/scikit-learn/SKILL.md
+++ b/scientific-skills/scikit-learn/SKILL.md
@@ -13,13 +13,13 @@ This skill provides comprehensive guidance for machine learning tasks using scik
 
 ```bash
 # Install scikit-learn using uv
-uv pip install scikit-learn
+uv uv pip install scikit-learn
 
 # Optional: Install visualization dependencies
-uv pip install matplotlib seaborn
+uv uv pip install matplotlib seaborn
 
 # Commonly used with
-uv pip install pandas numpy
+uv uv pip install pandas numpy
 ```
 
 ## When to Use This Skill
diff --git a/scientific-skills/scvi-tools/SKILL.md b/scientific-skills/scvi-tools/SKILL.md
index c8aca95..165ff77 100644
--- a/scientific-skills/scvi-tools/SKILL.md
+++ b/scientific-skills/scvi-tools/SKILL.md
@@ -168,9 +168,9 @@ See `references/theoretical-foundations.md` for detailed background on the mathe
 ## Installation
 
 ```bash
-pip install scvi-tools
+uv pip install scvi-tools
 # For GPU support
-pip install scvi-tools[cuda]
+uv pip install scvi-tools[cuda]
 ```
 
 ## Best Practices
diff --git a/scientific-skills/shap/SKILL.md b/scientific-skills/shap/SKILL.md
index 81de6c6..b011249 100644
--- a/scientific-skills/shap/SKILL.md
+++ b/scientific-skills/shap/SKILL.md
@@ -537,13 +537,13 @@ Includes: Mathematical foundations, proofs, comparisons, advanced topics.
 
 ```bash
 # Basic installation
-pip install shap
+uv pip install shap
 
 # With visualization dependencies
-pip install shap matplotlib
+uv pip install shap matplotlib
 
 # Latest version
-pip install -U shap
+uv pip install -U shap
 ```
 
 **Dependencies**: numpy, pandas, scikit-learn, matplotlib, scipy
diff --git a/scientific-skills/stable-baselines3/SKILL.md b/scientific-skills/stable-baselines3/SKILL.md
index 877876f..c689332 100644
--- a/scientific-skills/stable-baselines3/SKILL.md
+++ b/scientific-skills/stable-baselines3/SKILL.md
@@ -267,7 +267,7 @@ model.learn(total_timesteps=10000)
 - **Memory errors**: Reduce `buffer_size` for off-policy algorithms or use fewer parallel environments
 - **Slow training**: Consider SubprocVecEnv for parallel environments
 - **Unstable training**: Try different algorithms, tune hyperparameters, or check reward scaling
-- **Import errors**: Ensure `stable_baselines3` is installed: `pip install stable-baselines3[extra]`
+- **Import errors**: Ensure `stable_baselines3` is installed: `uv pip install stable-baselines3[extra]`
 
 ## Resources
 
@@ -286,8 +286,8 @@ model.learn(total_timesteps=10000)
 
 ```bash
 # Basic installation
-pip install stable-baselines3
+uv pip install stable-baselines3
 
 # With extra dependencies (Tensorboard, etc.)
-pip install stable-baselines3[extra]
+uv pip install stable-baselines3[extra]
 ```
diff --git a/scientific-skills/tooluniverse/SKILL.md b/scientific-skills/tooluniverse/SKILL.md
index 110dfd6..fb05fb0 100644
--- a/scientific-skills/tooluniverse/SKILL.md
+++ b/scientific-skills/tooluniverse/SKILL.md
@@ -286,5 +286,5 @@ Run examples to understand typical usage patterns and workflow composition.
 - **Official Website**: https://aiscientist.tools
 - **GitHub**: https://github.com/mims-harvard/ToolUniverse
 - **Documentation**: https://zitniklab.hms.harvard.edu/ToolUniverse/
-- **Installation**: `uv pip install tooluniverse`
+- **Installation**: `uv uv pip install tooluniverse`
 - **MCP Server**: `tooluniverse-smcp`
diff --git a/scientific-skills/tooluniverse/references/installation.md b/scientific-skills/tooluniverse/references/installation.md
index 17063a3..6395521 100644
--- a/scientific-skills/tooluniverse/references/installation.md
+++ b/scientific-skills/tooluniverse/references/installation.md
@@ -2,16 +2,10 @@
 
 ## Installation
 
-### Using uv (Recommended)
 ```bash
 uv pip install tooluniverse
 ```
 
-### Using pip
-```bash
-pip install tooluniverse
-```
-
 ## Basic Setup
 
 ### Python SDK
diff --git a/scientific-skills/torch_geometric/SKILL.md b/scientific-skills/torch_geometric/SKILL.md
index b320fc3..23d966d 100644
--- a/scientific-skills/torch_geometric/SKILL.md
+++ b/scientific-skills/torch_geometric/SKILL.md
@@ -25,12 +25,12 @@ This skill should be used when working with:
 ### Installation
 
 ```bash
-pip install torch_geometric
+uv pip install torch_geometric
 ```
 
 For additional dependencies (sparse operations, clustering):
 ```bash
-pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html
+uv pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html
 ```
 
 ### Basic Graph Creation
diff --git a/scientific-skills/torchdrug/SKILL.md b/scientific-skills/torchdrug/SKILL.md
index e504ac8..ab746db 100644
--- a/scientific-skills/torchdrug/SKILL.md
+++ b/scientific-skills/torchdrug/SKILL.md
@@ -40,9 +40,9 @@ This skill should be used when working with:
 ### Installation
 
 ```bash
-pip install torchdrug
+uv pip install torchdrug
 # Or with optional dependencies
-pip install torchdrug[full]
+uv pip install torchdrug[full]
 ```
 
 ### Quick Example
diff --git a/scientific-skills/umap-learn/SKILL.md b/scientific-skills/umap-learn/SKILL.md
index 3c3768b..411e2f5 100644
--- a/scientific-skills/umap-learn/SKILL.md
+++ b/scientific-skills/umap-learn/SKILL.md
@@ -14,11 +14,7 @@ UMAP (Uniform Manifold Approximation and Projection) is a dimensionality reducti
 ### Installation
 
 ```bash
-# Via conda
-conda install -c conda-forge umap-learn
-
-# Via pip
-pip install umap-learn
+uv pip install umap-learn
 ```
 
 ### Basic Usage
@@ -339,7 +335,7 @@ Parametric UMAP replaces direct embedding optimization with a learned neural net
 
 **Installation:**
 ```bash
-pip install umap-learn[parametric_umap]
+uv pip install umap-learn[parametric_umap]
 # Requires TensorFlow 2.x
 ```
 
diff --git a/scientific-skills/uspto-database/SKILL.md b/scientific-skills/uspto-database/SKILL.md
index 259a251..9e036d5 100644
--- a/scientific-skills/uspto-database/SKILL.md
+++ b/scientific-skills/uspto-database/SKILL.md
@@ -205,7 +205,7 @@ PEDS provides comprehensive prosecution history including transaction events, st
 #### Installation
 
 ```bash
-pip install uspto-opendata-python
+uv pip install uspto-opendata-python
 ```
 
 #### Basic PEDS Usage
diff --git a/scientific-skills/zarr-python/SKILL.md b/scientific-skills/zarr-python/SKILL.md
index a0aeff8..acefa67 100644
--- a/scientific-skills/zarr-python/SKILL.md
+++ b/scientific-skills/zarr-python/SKILL.md
@@ -13,18 +13,14 @@ Zarr is a Python library for storing large N-dimensional arrays with chunking an
 
 ### Installation
 
-```python
-# Using pip
-pip install zarr
-
-# Using conda
-conda install --channel conda-forge zarr
+```bash
+uv pip install zarr
 ```
 
 Requires Python 3.11+. For cloud storage support, install additional packages:
 ```python
-pip install s3fs  # For S3
-pip install gcsfs  # For Google Cloud Storage
+uv pip install s3fs  # For S3
+uv pip install gcsfs  # For Google Cloud Storage
 ```
 
 ### Basic Array Creation