repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
claude-code-templates | cli-tool/components/skills/scientific/drugbank-database/scripts/drugbank_helper.py | .py | #!/usr/bin/env python3
"""
DrugBank Helper Functions
Utility functions for common DrugBank operations including:
- Drug information extraction
- Interaction analysis
- Target identification
- Chemical property extraction
Usage:
from drugbank_helper import DrugBankHelper
db = DrugBankHelper()
drug_info = ... | 351 | 11,822 |
claude-code-templates | cli-tool/components/skills/scientific/venue-templates/scripts/query_template.py | .py | #!/usr/bin/env python3
"""
Query Template Script
Search and retrieve venue-specific templates by name, type, or keywords.
Usage:
python query_template.py --venue "Nature" --type "article"
python query_template.py --keyword "machine learning"
python query_template.py --list-all
python query_template.py ... | 261 | 8,959 |
claude-code-templates | cli-tool/components/skills/scientific/venue-templates/scripts/validate_format.py | .py | #!/usr/bin/env python3
"""
Validate Format Script
Check if document meets venue-specific formatting requirements.
Usage:
python validate_format.py --file my_paper.pdf --venue "Nature" --check-all
python validate_format.py --file my_paper.pdf --venue "NeurIPS" --check page-count,margins
python validate_form... | 256 | 8,766 |
claude-code-templates | cli-tool/components/skills/scientific/treatment-plans/scripts/validate_treatment_plan.py | .py | #!/usr/bin/env python3
"""
Validate Treatment Plan Quality
Comprehensive validation of treatment plan content quality and compliance.
"""
import sys
import re
import argparse
from pathlib import Path
from typing import Dict, List, Tuple
# Validation criteria and patterns
VALIDATION_CHECKS = {
'smart_goals': {
... | 368 | 12,392 |
claude-code-templates | cli-tool/components/skills/scientific/treatment-plans/scripts/timeline_generator.py | .py | #!/usr/bin/env python3
"""
Treatment Timeline Generator
Generates visual treatment timelines from treatment plan files.
"""
import sys
import re
import argparse
from pathlib import Path
from datetime import datetime, timedelta
from typing import List, Dict, Tuple
# Try to import matplotlib, but make it optional
try:
... | 370 | 12,631 |
claude-code-templates | cli-tool/components/skills/scientific/treatment-plans/scripts/check_completeness.py | .py | #!/usr/bin/env python3
"""
Check Treatment Plan Completeness
Validates that all required sections are present in a treatment plan.
"""
import sys
import re
import argparse
from pathlib import Path
from typing import List, Tuple
# Required sections for all treatment plans
REQUIRED_SECTIONS = [
r'\\section\*\{.*Pat... | 319 | 9,919 |
claude-code-templates | cli-tool/components/skills/scientific/treatment-plans/scripts/generate_template.py | .py | #!/usr/bin/env python3
"""
Generate Treatment Plan Template
Interactive script to select and generate treatment plan templates.
"""
import os
import sys
import shutil
import argparse
from pathlib import Path
from datetime import datetime
# Template types and descriptions
TEMPLATES = {
'general_medical': {
... | 245 | 7,490 |
claude-code-templates | cli-tool/components/skills/scientific/get-available-resources/scripts/detect_resources.py | .py | #!/usr/bin/env python3
"""
System Resource Detection Script
Detects available compute resources including CPU, GPU, memory, and disk space.
Outputs a JSON file that Claude Code can use to make informed decisions about
computational approaches (e.g., whether to use Dask, Zarr, Joblib, etc.).
Supports: macOS, Linux, Wi... | 402 | 14,081 |
claude-code-templates | cli-tool/components/skills/scientific/biomni/scripts/generate_report.py | .py | #!/usr/bin/env python3
"""
Enhanced PDF report generation for biomni conversation histories.
This script provides additional customization options for biomni reports:
- Custom styling and branding
- Formatted code blocks
- Section organization
- Metadata inclusion
- Export format options (PDF, HTML, Markdown)
Usage:
... | 371 | 10,810 |
claude-code-templates | cli-tool/components/skills/scientific/biomni/scripts/setup_environment.py | .py | #!/usr/bin/env python3
"""
Interactive setup script for biomni environment configuration.
This script helps users set up:
1. Conda environment with required dependencies
2. API keys for LLM providers
3. Data lake directory configuration
4. MCP server setup (optional)
Usage:
python setup_environment.py
"""
import... | 356 | 10,542 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-visualization/scripts/figure_export.py | .py | #!/usr/bin/env python3
"""
Figure Export Utilities for Publication-Ready Scientific Figures
This module provides utilities to export matplotlib figures in publication-ready
formats with appropriate settings for various journals.
"""
import matplotlib.pyplot as plt
from pathlib import Path
from typing import List, Opt... | 344 | 10,904 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-visualization/scripts/style_presets.py | .py | #!/usr/bin/env python3
"""
Matplotlib Style Presets for Publication-Ready Scientific Figures
This module provides pre-configured matplotlib styles optimized for
different journals and use cases.
"""
import matplotlib.pyplot as plt
import matplotlib as mpl
from typing import Optional, Dict, Any
# Okabe-Ito colorblin... | 417 | 12,199 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-visualization/assets/color_palettes.py | .py | """
Colorblind-Friendly Color Palettes for Scientific Visualization
This module provides carefully curated color palettes optimized for
scientific publications and accessibility.
Usage:
from color_palettes import OKABE_ITO, apply_palette
import matplotlib.pyplot as plt
apply_palette('okabe_ito')
plt.... | 198 | 5,754 |
claude-code-templates | cli-tool/components/skills/scientific/pymc/scripts/model_comparison.py | .py | """
PyMC Model Comparison Script
Utilities for comparing multiple Bayesian models using information criteria
and cross-validation metrics.
Usage:
from scripts.model_comparison import compare_models, plot_model_comparison
# Compare multiple models
comparison = compare_models(
{'model1': idata1, 'm... | 388 | 12,411 |
claude-code-templates | cli-tool/components/skills/scientific/pymc/scripts/model_diagnostics.py | .py | """
PyMC Model Diagnostics Script
Comprehensive diagnostic checks for PyMC models.
Run this after sampling to validate results before interpretation.
Usage:
from scripts.model_diagnostics import check_diagnostics, create_diagnostic_report
# Quick check
check_diagnostics(idata)
# Full report with plo... | 351 | 11,113 |
claude-code-templates | cli-tool/components/skills/scientific/pymc/assets/hierarchical_model_template.py | .py | """
PyMC Hierarchical/Multilevel Model Template
This template provides a complete workflow for Bayesian hierarchical models,
useful for grouped/nested data (e.g., students within schools, patients within hospitals).
Customize the sections marked with # TODO
"""
import pymc as pm
import arviz as az
import numpy as np... | 334 | 11,858 |
claude-code-templates | cli-tool/components/skills/scientific/pymc/assets/linear_regression_template.py | .py | """
PyMC Linear Regression Template
This template provides a complete workflow for Bayesian linear regression,
including data preparation, model building, diagnostics, and predictions.
Customize the sections marked with # TODO
"""
import pymc as pm
import arviz as az
import numpy as np
import pandas as pd
import mat... | 242 | 8,118 |
claude-code-templates | cli-tool/components/skills/scientific/diffdock/scripts/setup_check.py | .py | #!/usr/bin/env python3
"""
DiffDock Environment Setup Checker
This script verifies that the DiffDock environment is properly configured
and all dependencies are available.
Usage:
python setup_check.py
python setup_check.py --verbose
"""
import argparse
import sys
import os
from pathlib import Path
def chec... | 279 | 8,016 |
claude-code-templates | cli-tool/components/skills/scientific/diffdock/scripts/prepare_batch_csv.py | .py | #!/usr/bin/env python3
"""
DiffDock Batch CSV Preparation and Validation Script
This script helps prepare and validate CSV files for DiffDock batch processing.
It checks for required columns, validates file paths, and ensures SMILES strings
are properly formatted.
Usage:
python prepare_batch_csv.py input.csv --va... | 255 | 8,730 |
claude-code-templates | cli-tool/components/skills/scientific/diffdock/scripts/analyze_results.py | .py | #!/usr/bin/env python3
"""
DiffDock Results Analysis Script
This script analyzes DiffDock prediction results, extracting confidence scores,
ranking predictions, and generating summary reports.
Usage:
python analyze_results.py results/output_dir/
python analyze_results.py results/ --top 50 --threshold 0.0
... | 335 | 11,036 |
claude-code-templates | cli-tool/components/skills/scientific/ensembl-database/scripts/ensembl_query.py | .py | #!/usr/bin/env python3
"""
Ensembl REST API Query Script
Reusable functions for common Ensembl database queries with built-in rate limiting and error handling.
Usage:
python ensembl_query.py --gene BRCA2 --species human
python ensembl_query.py --variant rs699 --species human
python ensembl_query.py --regio... | 428 | 13,595 |
claude-code-templates | cli-tool/components/skills/scientific/generate-image/scripts/generate_image.py | .py | #!/usr/bin/env python3
"""
Generate and edit images using OpenRouter API with various image generation models.
Supports models like:
- google/gemini-3-pro-image-preview (generation and editing)
- black-forest-labs/flux.2-pro (generation and editing)
- black-forest-labs/flux.2-flex (generation)
- And more image generat... | 282 | 8,787 |
claude-code-templates | cli-tool/components/skills/scientific/etetoolkit/scripts/tree_operations.py | .py | #!/usr/bin/env python3
"""
Tree operations helper script for common ETE toolkit tasks.
Provides command-line interface for basic tree operations like:
- Format conversion
- Rooting (outgroup, midpoint)
- Pruning
- Basic statistics
- ASCII visualization
"""
import argparse
import sys
from pathlib import Path
try:
... | 230 | 8,235 |
claude-code-templates | cli-tool/components/skills/scientific/etetoolkit/scripts/quick_visualize.py | .py | #!/usr/bin/env python3
"""
Quick tree visualization script with common customization options.
Provides command-line interface for rapid tree visualization with
customizable styles, layouts, and output formats.
"""
import argparse
import sys
from pathlib import Path
try:
from ete3 import Tree, TreeStyle, NodeStyl... | 215 | 7,156 |
claude-code-templates | cli-tool/components/skills/scientific/pymatgen/scripts/phase_diagram_generator.py | .py | #!/usr/bin/env python3
"""
Phase diagram generator using Materials Project data.
This script generates phase diagrams for chemical systems using data from the
Materials Project database via pymatgen's MPRester.
Usage:
python phase_diagram_generator.py chemical_system [options]
Examples:
python phase_diagram_... | 234 | 7,353 |
claude-code-templates | cli-tool/components/skills/scientific/pymatgen/scripts/structure_analyzer.py | .py | #!/usr/bin/env python3
"""
Structure analysis tool using pymatgen.
Analyzes crystal structures and provides comprehensive information including:
- Composition and formula
- Space group and symmetry
- Lattice parameters
- Density
- Coordination environment
- Bond lengths and angles
Usage:
python structure_analyzer... | 267 | 8,452 |
claude-code-templates | cli-tool/components/skills/scientific/pymatgen/scripts/structure_converter.py | .py | #!/usr/bin/env python3
"""
Structure file format converter using pymatgen.
This script converts between different structure file formats supported by pymatgen.
Supports automatic format detection and batch conversion.
Usage:
python structure_converter.py input_file output_file
python structure_converter.py in... | 170 | 5,179 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-slides/scripts/pdf_to_images.py | .py | #!/usr/bin/env python3
"""
PDF to Images Converter for Presentations
Converts presentation PDFs to images for visual inspection and review.
Supports multiple output formats and resolutions.
Uses PyMuPDF (fitz) as the primary conversion method - no external
dependencies required (no poppler, ghostscript, or ImageMagic... | 222 | 6,644 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-slides/scripts/generate_slide_image_ai.py | .py | #!/usr/bin/env python3
"""
AI-powered slide image generation using Nano Banana Pro.
This script generates presentation slides or slide visuals using AI:
- full_slide mode: Generate complete slides with title, content, and visuals (for PDF workflow)
- visual_only mode: Generate just images/figures to place on slides (f... | 764 | 29,060 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-slides/scripts/validate_presentation.py | .py | #!/usr/bin/env python3
"""
Presentation Validation Script
Validates scientific presentations for common issues:
- Slide count vs. duration
- LaTeX compilation
- File size checks
- Basic format validation
"""
import sys
import os
import argparse
import subprocess
from pathlib import Path
from typing import Dict, List,... | 404 | 13,115 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-slides/scripts/slides_to_pdf.py | .py | #!/usr/bin/env python3
"""
Combine slide images into a single PDF presentation.
This script takes multiple slide images (PNG, JPG) and combines them
into a single PDF file, maintaining aspect ratio and quality.
Usage:
# Combine all PNG files in a directory
python slides_to_pdf.py slides/*.png -o presentation.... | 236 | 7,423 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-slides/scripts/generate_slide_image.py | .py | #!/usr/bin/env python3
"""
Slide image generation using Nano Banana Pro.
Generate presentation slides or visuals by describing them in natural language.
Nano Banana Pro handles everything automatically with smart iterative refinement.
Two modes:
- Default (full slide): Generate complete slides with title, content, vi... | 141 | 5,309 |
claude-code-templates | cli-tool/components/skills/scientific/exploratory-data-analysis/scripts/eda_analyzer.py | .py | #!/usr/bin/env python3
"""
Exploratory Data Analysis Analyzer
Analyzes scientific data files and generates comprehensive markdown reports
"""
import os
import sys
from pathlib import Path
from datetime import datetime
import json
def detect_file_type(filepath):
"""
Detect the file type based on extension and... | 548 | 21,318 |
claude-code-templates | cli-tool/components/skills/scientific/pytdc/scripts/load_and_split_data.py | .py | #!/usr/bin/env python3
"""
TDC Data Loading and Splitting Template
This script demonstrates how to load TDC datasets and apply different
splitting strategies for model training and evaluation.
Usage:
python load_and_split_data.py
"""
from tdc.single_pred import ADME
from tdc.multi_pred import DTI
from tdc import... | 215 | 6,350 |
claude-code-templates | cli-tool/components/skills/scientific/pytdc/scripts/molecular_generation.py | .py | #!/usr/bin/env python3
"""
TDC Molecular Generation with Oracles Template
This script demonstrates how to use TDC oracles for molecular generation
tasks including goal-directed generation and distribution learning.
Usage:
python molecular_generation.py
"""
from tdc.generation import MolGen
from tdc import Oracle... | 405 | 11,335 |
claude-code-templates | cli-tool/components/skills/scientific/pytdc/scripts/benchmark_evaluation.py | .py | #!/usr/bin/env python3
"""
TDC Benchmark Group Evaluation Template
This script demonstrates how to use TDC benchmark groups for systematic
model evaluation following the required 5-seed protocol.
Usage:
python benchmark_evaluation.py
"""
from tdc.benchmark_group import admet_group
from tdc import Evaluator
impor... | 328 | 9,238 |
claude-code-templates | cli-tool/components/skills/scientific/gget/scripts/gene_analysis.py | .py | #!/usr/bin/env python3
"""
Gene Analysis Script
Quick analysis of a gene: search, info, sequences, expression, and enrichment
"""
import argparse
import sys
import gget
def analyze_gene(gene_name, species="homo_sapiens", output_prefix=None):
"""
Perform comprehensive analysis of a gene.
Args:
ge... | 162 | 5,778 |
claude-code-templates | cli-tool/components/skills/scientific/gget/scripts/batch_sequence_analysis.py | .py | #!/usr/bin/env python3
"""
Batch Sequence Analysis Script
Analyze multiple sequences: BLAST, alignment, and structure prediction
"""
import argparse
import sys
from pathlib import Path
import gget
def read_fasta(fasta_file):
"""Read sequences from FASTA file."""
sequences = []
current_id = None
curre... | 192 | 5,978 |
claude-code-templates | cli-tool/components/skills/scientific/scikit-learn/scripts/classification_pipeline.py | .py | """
Complete classification pipeline example with preprocessing, model training,
hyperparameter tuning, and evaluation.
"""
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split, GridSearchCV, cross_val_score
from sklearn.preprocessing import StandardScaler, OneHotEncoder
from skl... | 258 | 8,044 |
claude-code-templates | cli-tool/components/skills/scientific/biorxiv-database/scripts/biorxiv_search.py | .py | #!/usr/bin/env python3
"""
bioRxiv Search Tool
A comprehensive Python tool for searching and retrieving preprints from bioRxiv.
Supports keyword search, author search, date filtering, category filtering, and more.
Note: This tool is focused exclusively on bioRxiv (life sciences preprints).
"""
import requests
import ... | 446 | 14,831 |
claude-code-templates | cli-tool/components/skills/scientific/medchem/scripts/filter_molecules.py | .py | #!/usr/bin/env python3
"""
Batch molecular filtering using medchem library.
This script provides a production-ready workflow for filtering compound libraries
using medchem rules, structural alerts, and custom constraints.
Usage:
python filter_molecules.py input.csv --rules rule_of_five,rule_of_cns --alerts nibr -... | 419 | 15,696 |
claude-code-templates | cli-tool/components/skills/scientific/pymoo/scripts/many_objective_example.py | .py | """
Many-objective optimization example using pymoo.
This script demonstrates many-objective optimization (4+ objectives)
using NSGA-III on the DTLZ2 benchmark problem.
"""
from pymoo.algorithms.moo.nsga3 import NSGA3
from pymoo.problems import get_problem
from pymoo.optimize import minimize
from pymoo.util.ref_dirs ... | 73 | 2,103 |
claude-code-templates | cli-tool/components/skills/scientific/market-research-reports/scripts/generate_market_visuals.py | .py | #!/usr/bin/env python3
"""
Market Research Report Visual Generator
Batch generates visuals for a market research report using
scientific-schematics and generate-image skills.
Default behavior: Generate 5-6 core visuals only
Use --all flag to generate all 28 extended visuals
Usage:
# Generate core 5-6 visuals (re... | 530 | 20,423 |
claude-code-templates | cli-tool/components/skills/scientific/clinpgx-database/scripts/query_clinpgx.py | .py | #!/usr/bin/env python3
"""
ClinPGx API Query Helper Script
Provides ready-to-use functions for querying the ClinPGx database API.
Includes rate limiting, error handling, and caching functionality.
ClinPGx API: https://api.clinpgx.org/
Rate limit: 2 requests per second
License: Creative Commons Attribution-ShareAlike ... | 519 | 14,295 |
claude-code-templates | cli-tool/components/skills/scientific/markitdown/scripts/convert_literature.py | .py | #!/usr/bin/env python3
"""
Convert scientific literature PDFs to Markdown for analysis and review.
This script is specifically designed for converting academic papers,
organizing them, and preparing them for literature review workflows.
"""
import argparse
import json
import re
import sys
from pathlib import Path
fro... | 284 | 8,915 |
claude-code-templates | cli-tool/components/skills/scientific/markitdown/scripts/convert_with_ai.py | .py | #!/usr/bin/env python3
"""
Convert documents to Markdown with AI-enhanced image descriptions.
This script demonstrates how to use MarkItDown with OpenRouter to generate
detailed descriptions of images in documents (PowerPoint, PDFs with images, etc.)
"""
import argparse
import os
import sys
from pathlib import Path
f... | 244 | 7,629 |
claude-code-templates | cli-tool/components/skills/scientific/markitdown/scripts/batch_convert.py | .py | #!/usr/bin/env python3
"""
Batch convert multiple files to Markdown using MarkItDown.
This script demonstrates how to efficiently convert multiple files
in a directory to Markdown format.
"""
import argparse
from pathlib import Path
from typing import List, Optional
from markitdown import MarkItDown
from concurrent.f... | 229 | 6,650 |
claude-code-templates | cli-tool/components/skills/scientific/perplexity-search/scripts/perplexity_search.py | .py | #!/usr/bin/env python3
"""
Perplexity Search via LitLLM and OpenRouter
This script performs AI-powered web searches using Perplexity models through
LiteLLM and OpenRouter. It provides real-time, grounded answers with source citations.
Usage:
python perplexity_search.py "search query" [options]
Requirements:
... | 278 | 8,068 |
claude-code-templates | cli-tool/components/skills/scientific/perplexity-search/scripts/setup_env.py | .py | #!/usr/bin/env python3
"""
Setup script for Perplexity Search environment configuration.
This script helps users configure their OpenRouter API key and validates the setup.
Usage:
python setup_env.py [--api-key YOUR_KEY] [--env-file .env]
Author: Scientific Skills
License: MIT
"""
import os
import sys
import ar... | 172 | 4,656 |
claude-code-templates | cli-tool/components/skills/scientific/arboreto/scripts/basic_grn_inference.py | .py | #!/usr/bin/env python3
"""
Basic GRN inference example using Arboreto.
This script demonstrates the standard workflow for inferring gene regulatory
networks from expression data using GRNBoost2.
Usage:
python basic_grn_inference.py <expression_file> <output_file> [--tf-file TF_FILE] [--seed SEED]
Arguments:
... | 98 | 2,969 |
claude-code-templates | cli-tool/components/skills/scientific/reactome-database/scripts/reactome_query.py | .py | #!/usr/bin/env python3
"""
Reactome Database Query Helper Script
This script provides convenient command-line access to common Reactome operations.
Usage:
python reactome_query.py version
python reactome_query.py query <pathway_id>
python reactome_query.py analyze <gene_list_file>
python reactome_quer... | 287 | 9,254 |
claude-code-templates | cli-tool/components/skills/scientific/chembl-database/scripts/example_queries.py | .py | #!/usr/bin/env python3
"""
ChEMBL Database Query Examples
This script demonstrates common query patterns for the ChEMBL database
using the chembl_webresource_client Python library.
Requirements:
pip install chembl_webresource_client
pip install pandas (optional, for data manipulation)
"""
from chembl_webreso... | 279 | 7,160 |
claude-code-templates | cli-tool/components/skills/scientific/labarchive-integration/scripts/setup_config.py | .py | #!/usr/bin/env python3
"""
LabArchives Configuration Setup Script
This script helps create a config.yaml file with necessary credentials
for LabArchives API access.
"""
import yaml
import os
from pathlib import Path
def get_regional_endpoint():
"""Prompt user to select regional API endpoint"""
print("\nSele... | 206 | 6,412 |
claude-code-templates | cli-tool/components/skills/scientific/labarchive-integration/scripts/entry_operations.py | .py | #!/usr/bin/env python3
"""
LabArchives Entry Operations
Utilities for creating entries, uploading attachments, and managing notebook content.
"""
import argparse
import sys
import yaml
import os
from pathlib import Path
from datetime import datetime
def load_config(config_path='config.yaml'):
"""Load configurat... | 335 | 10,576 |
claude-code-templates | cli-tool/components/skills/scientific/labarchive-integration/scripts/notebook_operations.py | .py | #!/usr/bin/env python3
"""
LabArchives Notebook Operations
Utilities for listing, backing up, and managing LabArchives notebooks.
"""
import argparse
import sys
import yaml
from datetime import datetime
from pathlib import Path
def load_config(config_path='config.yaml'):
"""Load configuration from YAML file"""
... | 270 | 8,677 |
claude-code-templates | cli-tool/components/skills/scientific/pufferlib/scripts/train_template.py | .py | #!/usr/bin/env python3
"""
PufferLib Training Template
This template provides a complete training script for reinforcement learning
with PufferLib. Customize the environment, policy, and training configuration
as needed for your use case.
"""
import argparse
import torch
import torch.nn as nn
import pufferlib
from pu... | 240 | 8,027 |
claude-code-templates | cli-tool/components/skills/scientific/pufferlib/scripts/env_template.py | .py | #!/usr/bin/env python3
"""
PufferLib Environment Template
This template provides a starting point for creating custom PufferEnv environments.
Customize the observation space, action space, and environment logic for your task.
"""
import numpy as np
import pufferlib
from pufferlib import PufferEnv
class MyEnvironmen... | 341 | 10,157 |
claude-code-templates | cli-tool/components/skills/scientific/brenda-database/scripts/enzyme_pathway_builder.py | .py | """
Enzyme Pathway Builder for Retrosynthetic Analysis
This module provides tools for constructing enzymatic pathways and
retrosynthetic trees using BRENDA database information.
Key features:
- Find enzymatic pathways for target products
- Build retrosynthetic trees from products
- Suggest enzyme substitutions and al... | 1,053 | 44,863 |
claude-code-templates | cli-tool/components/skills/scientific/brenda-database/scripts/brenda_queries.py | .py | """
BRENDA Database Query Utilities
This module provides high-level functions for querying and analyzing
enzyme data from the BRENDA database using the SOAP API.
Key features:
- Parse BRENDA response data entries
- Search for enzymes by substrate/product
- Compare enzyme properties across organisms
- Retrieve kinetic... | 844 | 30,872 |
claude-code-templates | cli-tool/components/skills/scientific/brenda-database/scripts/brenda_visualization.py | .py | """
BRENDA Database Visualization Utilities
This module provides visualization functions for BRENDA enzyme data,
including kinetic parameters, environmental conditions, and pathway analysis.
Key features:
- Plot Km, kcat, and Vmax distributions
- Compare enzyme properties across organisms
- Visualize pH and temperatu... | 772 | 29,361 |
claude-code-templates | cli-tool/components/skills/scientific/neuropixels-analysis/scripts/compute_metrics.py | .py | #!/usr/bin/env python
"""
Compute quality metrics and curate units.
Usage:
python compute_metrics.py sorting/ preprocessed/ --output metrics/
"""
import argparse
from pathlib import Path
import json
import pandas as pd
import spikeinterface.full as si
# Curation criteria presets
CURATION_CRITERIA = {
'alle... | 179 | 5,226 |
claude-code-templates | cli-tool/components/skills/scientific/neuropixels-analysis/scripts/neuropixels_pipeline.py | .py | #!/usr/bin/env python3
"""
Neuropixels Data Analysis Pipeline (Best Practices Version)
Based on SpikeInterface, Allen Institute, and IBL recommendations.
Usage:
python neuropixels_pipeline.py /path/to/spikeglx/data /path/to/output
References:
- https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_n... | 433 | 13,286 |
claude-code-templates | cli-tool/components/skills/scientific/neuropixels-analysis/scripts/preprocess_recording.py | .py | #!/usr/bin/env python
"""
Preprocess Neuropixels recording.
Usage:
python preprocess_recording.py /path/to/data --output preprocessed/ --format spikeglx
"""
import argparse
from pathlib import Path
import spikeinterface.full as si
def preprocess_recording(
input_path: str,
output_dir: str,
format: ... | 123 | 4,235 |
claude-code-templates | cli-tool/components/skills/scientific/neuropixels-analysis/scripts/explore_recording.py | .py | #!/usr/bin/env python3
"""
Quick exploration of Neuropixels recording.
Usage:
python explore_recording.py /path/to/spikeglx/data
"""
import argparse
import spikeinterface.full as si
import matplotlib.pyplot as plt
import numpy as np
def explore_recording(data_path: str, stream_id: str = 'imec0.ap'):
"""Expl... | 169 | 5,529 |
claude-code-templates | cli-tool/components/skills/scientific/neuropixels-analysis/assets/analysis_template.py | .py | #!/usr/bin/env python
"""
Neuropixels Analysis Template
Complete analysis workflow from raw data to curated units.
Copy and customize this template for your analysis.
Usage:
1. Copy this file to your analysis directory
2. Update the PARAMETERS section
3. Run: python analysis_template.py
"""
# ===========... | 272 | 9,014 |
claude-code-templates | cli-tool/components/skills/scientific/opentargets-database/scripts/query_opentargets.py | .py | #!/usr/bin/env python3
"""
Open Targets Platform GraphQL Query Helper
This script provides reusable functions for querying the Open Targets Platform
GraphQL API. Use these functions to retrieve target, disease, drug, and
association data.
Dependencies: requests (pip install requests)
"""
import requests
import json
... | 404 | 10,641 |
claude-code-templates | cli-tool/components/skills/scientific/research-lookup/research_lookup.py | .py | #!/usr/bin/env python3
"""
Research Information Lookup Tool
Uses Perplexity's Sonar Pro Search model through OpenRouter for academic research queries.
"""
import os
import json
import requests
import time
from datetime import datetime
from typing import Dict, List, Optional, Any
from urllib.parse import quote
class ... | 407 | 16,567 |
claude-code-templates | cli-tool/components/skills/scientific/research-lookup/lookup.py | .py | #!/usr/bin/env python3
"""
Research Lookup Tool for Claude Code
Performs research queries using Perplexity Sonar Pro Search via OpenRouter.
"""
import os
import sys
import json
from typing import Dict, List, Optional
# Import the main research lookup class
sys.path.append(os.path.join(os.path.dirname(os.path.abspath(... | 94 | 2,561 |
claude-code-templates | cli-tool/components/skills/scientific/research-lookup/examples.py | .py | #!/usr/bin/env python3
"""
Example usage of the Research Lookup skill with automatic model selection.
This script demonstrates:
1. Automatic model selection based on query complexity
2. Manual model override options
3. Batch query processing
4. Integration with scientific writing workflows
"""
import os
from research... | 175 | 5,672 |
claude-code-templates | cli-tool/components/skills/scientific/research-lookup/scripts/research_lookup.py | .py | #!/usr/bin/env python3
"""
Research Information Lookup Tool
Uses Perplexity's Sonar Pro Search model through OpenRouter for academic research queries.
"""
import os
import json
import requests
import time
from datetime import datetime
from typing import Dict, List, Optional, Any
from urllib.parse import quote
class ... | 407 | 16,530 |
claude-code-templates | cli-tool/components/skills/scientific/rdkit/scripts/substructure_filter.py | .py | #!/usr/bin/env python3
"""
Substructure Filter
Filter molecules based on substructure patterns using SMARTS.
Supports inclusion and exclusion filters, and custom pattern libraries.
Usage:
python substructure_filter.py molecules.smi --pattern "c1ccccc1" --output filtered.smi
python substructure_filter.py datab... | 387 | 12,351 |
claude-code-templates | cli-tool/components/skills/scientific/rdkit/scripts/similarity_search.py | .py | #!/usr/bin/env python3
"""
Molecular Similarity Search
Perform fingerprint-based similarity screening against a database of molecules.
Supports multiple fingerprint types and similarity metrics.
Usage:
python similarity_search.py "CCO" database.smi --threshold 0.7
python similarity_search.py query.smi databas... | 296 | 9,444 |
claude-code-templates | cli-tool/components/skills/scientific/rdkit/scripts/molecular_properties.py | .py | #!/usr/bin/env python3
"""
Molecular Properties Calculator
Calculate comprehensive molecular properties and descriptors for molecules.
Supports single molecules or batch processing from files.
Usage:
python molecular_properties.py "CCO"
python molecular_properties.py --file molecules.smi --output properties.c... | 244 | 7,361 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/extract_clinical_data.py | .py | #!/usr/bin/env python3
"""
Extract structured clinical data from reports.
Usage:
python extract_clinical_data.py <report_file>
"""
import argparse
import json
import re
def extract_vital_signs(content: str) -> dict:
"""Extract vital signs."""
vitals = {}
patterns = {
"temperature": r"(?i)tem... | 103 | 2,635 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/format_adverse_events.py | .py | #!/usr/bin/env python3
"""
Format adverse event data into tables for clinical trial reports.
Converts CSV or structured data into formatted AE summary tables.
Usage:
python format_adverse_events.py <ae_data.csv>
"""
import argparse
import csv
from collections import defaultdict
from pathlib import Path
def for... | 104 | 3,049 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/terminology_validator.py | .py | #!/usr/bin/env python3
"""
Validate medical terminology and coding in clinical reports.
Usage:
python terminology_validator.py <report_file>
"""
import argparse
import json
import re
# Common medical abbreviations that should be avoided (JCAHO "Do Not Use" list)
DO_NOT_USE = {
"U": "Unit",
"IU": "Intern... | 134 | 4,140 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/check_deidentification.py | .py | #!/usr/bin/env python3
"""
Check clinical reports for HIPAA identifiers that need removal.
Scans text for 18 HIPAA identifiers and flags potential privacy violations.
Usage:
python check_deidentification.py <input_file>
python check_deidentification.py <input_file> --output violations.json
"""
import argpars... | 347 | 10,710 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/compliance_checker.py | .py | #!/usr/bin/env python3
"""
Check clinical reports for regulatory compliance (HIPAA, GCP, FDA).
Usage:
python compliance_checker.py <report_file>
"""
import argparse
import json
import re
COMPLIANCE_CHECKS = {
"hipaa": {
"consent_statement": r"(?i)(informed\s+consent|written\s+consent).*obtained",
... | 79 | 2,176 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/validate_trial_report.py | .py | #!/usr/bin/env python3
"""
Validate clinical trial reports against ICH-E3 structure.
Checks Clinical Study Reports (CSR) for ICH-E3 compliance.
Usage:
python validate_trial_report.py <csr_file.md>
"""
import argparse
import json
import re
from pathlib import Path
ICH_E3_SECTIONS = {
"title_page": "Title Pa... | 90 | 2,871 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/generate_report_template.py | .py | #!/usr/bin/env python3
"""
Interactive template generator for clinical reports.
Helps users select and generate appropriate clinical report templates.
Usage:
python generate_report_template.py
python generate_report_template.py --type case_report --output my_case_report.md
"""
import argparse
import shutil
f... | 164 | 4,713 |
claude-code-templates | cli-tool/components/skills/scientific/clinical-reports/scripts/validate_case_report.py | .py | #!/usr/bin/env python3
"""
Validate case reports against CARE (CAse REport) guidelines.
This script checks a clinical case report for compliance with CARE guidelines
and provides a checklist of required elements.
Usage:
python validate_case_report.py <input_file.md|.txt>
python validate_case_report.py <input_... | 335 | 11,540 |
claude-code-templates | cli-tool/components/skills/scientific/scholar-evaluation/scripts/calculate_scores.py | .py | #!/usr/bin/env python3
"""
ScholarEval Score Calculator
Calculate aggregate evaluation scores from dimension-level ratings.
Supports weighted averaging, threshold analysis, and score visualization.
Usage:
python calculate_scores.py --scores <dimension_scores.json> --output <report.txt>
python calculate_scores... | 379 | 11,551 |
claude-code-templates | cli-tool/components/skills/scientific/citation-management/scripts/search_pubmed.py | .py | #!/usr/bin/env python3
"""
PubMed Search Tool
Search PubMed using E-utilities API and export results.
"""
import sys
import os
import requests
import argparse
import json
import time
import xml.etree.ElementTree as ET
from typing import List, Dict, Optional
from datetime import datetime
class PubMedSearcher:
"""S... | 399 | 12,832 |
claude-code-templates | cli-tool/components/skills/scientific/citation-management/scripts/format_bibtex.py | .py | #!/usr/bin/env python3
"""
BibTeX Formatter and Cleaner
Format, clean, sort, and deduplicate BibTeX files.
"""
import sys
import re
import argparse
from typing import List, Dict, Tuple
from collections import OrderedDict
class BibTeXFormatter:
"""Format and clean BibTeX entries."""
def __init__(self):
... | 350 | 11,444 |
claude-code-templates | cli-tool/components/skills/scientific/citation-management/scripts/extract_metadata.py | .py | #!/usr/bin/env python3
"""
Metadata Extraction Tool
Extract citation metadata from DOI, PMID, arXiv ID, or URL using various APIs.
"""
import sys
import os
import requests
import argparse
import time
import re
import json
import xml.etree.ElementTree as ET
from typing import Optional, Dict, List, Tuple
from urllib.par... | 570 | 20,794 |
claude-code-templates | cli-tool/components/skills/scientific/citation-management/scripts/validate_citations.py | .py | #!/usr/bin/env python3
"""
Citation Validation Tool
Validate BibTeX files for accuracy, completeness, and format compliance.
"""
import sys
import re
import requests
import argparse
import json
from typing import Dict, List, Tuple, Optional
from collections import defaultdict
class CitationValidator:
"""Validate ... | 498 | 17,482 |
claude-code-templates | cli-tool/components/skills/scientific/citation-management/scripts/search_google_scholar.py | .py | #!/usr/bin/env python3
"""
Google Scholar Search Tool
Search Google Scholar and export results.
Note: This script requires the 'scholarly' library.
Install with: pip install scholarly
"""
import sys
import argparse
import json
import time
import random
from typing import List, Dict, Optional
try:
from scholarly ... | 283 | 8,982 |
claude-code-templates | cli-tool/components/skills/scientific/uspto-database/scripts/peds_client.py | .py | #!/usr/bin/env python3
"""
USPTO Patent Examination Data System (PEDS) Helper
Provides functions for retrieving patent examination data using the
uspto-opendata-python library.
Requires:
- uspto-opendata-python: pip install uspto-opendata-python
Note: This script provides a simplified interface to PEDS data.
For... | 286 | 9,602 |
claude-code-templates | cli-tool/components/skills/scientific/uspto-database/scripts/patent_search.py | .py | #!/usr/bin/env python3
"""
USPTO PatentSearch API Helper
Provides functions for searching and retrieving patent data using the USPTO
PatentSearch API (ElasticSearch-based system, replaced legacy PatentsView in May 2025).
Requires:
- requests library: pip install requests
- USPTO API key from https://account.u... | 291 | 9,072 |
claude-code-templates | cli-tool/components/skills/scientific/uspto-database/scripts/trademark_client.py | .py | #!/usr/bin/env python3
"""
USPTO Trademark API Helper
Provides functions for searching and retrieving trademark data using USPTO
Trademark Status & Document Retrieval (TSDR) API.
Requires:
- requests library: pip install requests
- USPTO API key from https://account.uspto.gov/api-manager/
Environment variabl... | 312 | 10,564 |
claude-code-templates | cli-tool/components/skills/scientific/deepchem/scripts/transfer_learning.py | .py | #!/usr/bin/env python3
"""
Transfer Learning Script for DeepChem
Use pretrained models (ChemBERTa, GROVER, MolFormer) for molecular property prediction
with transfer learning. Particularly useful for small datasets.
Usage:
python transfer_learning.py --model chemberta --data my_data.csv --target activity
pyth... | 376 | 11,353 |
claude-code-templates | cli-tool/components/skills/scientific/deepchem/scripts/predict_solubility.py | .py | #!/usr/bin/env python3
"""
Molecular Solubility Prediction Script
This script trains a model to predict aqueous solubility from SMILES strings
using the Delaney (ESOL) dataset as an example. Can be adapted for custom datasets.
Usage:
python predict_solubility.py --data custom_data.csv --smiles-col smiles --target... | 225 | 6,546 |
claude-code-templates | cli-tool/components/skills/scientific/deepchem/scripts/graph_neural_network.py | .py | #!/usr/bin/env python3
"""
Graph Neural Network Training Script
This script demonstrates training Graph Convolutional Networks (GCNs) and other
graph-based models for molecular property prediction.
Usage:
python graph_neural_network.py --dataset tox21 --model gcn
python graph_neural_network.py --dataset bbbp ... | 339 | 9,742 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-schematics/test_ai_generation.py | .py | #!/usr/bin/env python3
"""
Test script to verify AI generation implementation.
This script performs dry-run tests without making actual API calls.
It verifies:
1. Script structure and imports
2. Class initialization
3. Method signatures
4. Error handling
5. Command-line interface
Usage:
python test_ai_generation.... | 244 | 7,653 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-schematics/scripts/generate_schematic.py | .py | #!/usr/bin/env python3
"""
Scientific schematic generation using Nano Banana Pro.
Generate any scientific diagram by describing it in natural language.
Nano Banana Pro handles everything automatically with smart iterative refinement.
Smart iteration: Only regenerates if quality is below threshold for your document ty... | 140 | 5,016 |
claude-code-templates | cli-tool/components/skills/scientific/scientific-schematics/scripts/generate_schematic_ai.py | .py | #!/usr/bin/env python3
"""
AI-powered scientific schematic generation using Nano Banana Pro.
This script uses a smart iterative refinement approach:
1. Generate initial image with Nano Banana Pro
2. AI quality review using Gemini 3 Pro for scientific critique
3. Only regenerate if quality is below threshold for docume... | 839 | 33,173 |
claude-code-templates | cli-tool/components/skills/scientific/pubchem-database/scripts/bioactivity_query.py | .py | #!/usr/bin/env python3
"""
PubChem Bioactivity Data Retrieval
This script provides functions for retrieving biological activity data
from PubChem for compounds and assays.
"""
import sys
import json
import time
from typing import Dict, List, Optional
try:
import requests
except ImportError:
print("Error: req... | 368 | 9,845 |
claude-code-templates | cli-tool/components/skills/scientific/pubchem-database/scripts/compound_search.py | .py | #!/usr/bin/env python3
"""
PubChem Compound Search Utility
This script provides functions for searching and retrieving compound information
from PubChem using the PubChemPy library.
"""
import sys
import json
from typing import List, Dict, Optional, Union
try:
import pubchempy as pcp
except ImportError:
prin... | 298 | 8,302 |
claude-code-templates | cli-tool/components/skills/scientific/scanpy/scripts/qc_analysis.py | .py | #!/usr/bin/env python3
"""
Quality Control Analysis Script for Scanpy
Performs comprehensive quality control on single-cell RNA-seq data,
including calculating metrics, generating QC plots, and filtering cells.
Usage:
python qc_analysis.py <input_file> [--output <output_file>]
"""
import argparse
import scanpy a... | 201 | 6,706 |
claude-code-templates | cli-tool/components/skills/scientific/scanpy/assets/analysis_template.py | .py | #!/usr/bin/env python3
"""
Complete Single-Cell Analysis Template
This template provides a complete workflow for single-cell RNA-seq analysis
using scanpy, from data loading through clustering and cell type annotation.
Customize the parameters and sections as needed for your specific dataset.
"""
import scanpy as sc... | 296 | 9,515 |
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