Claude Skills by FreedomIntelligence

Comprehensive knowledge system for addiction recovery environments, supporting both residential and outpatient (IOP/PHP) patients. Expert in evidence-based treatment modalities (CBT, DBT, MI,

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

--> --- name: 'molecular-glue-discovery-agent' description: 'AI-powered molecular glue discovery for targeted protein degradation, enabling neo-substrate recruitment and undruggable target degradation through E3 ligase interface modulation.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Molecular Glue Discovery Agent** enables AI-driven discovery of molecular glue degraders that induce prot...

--> --- name: 'molecule-evolution-agent' description: 'Evolve Molecules' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Molecule Evolution Agent** acts as an autonomous medicinal chemist. It takes a starting molecule (or uses a default like Aspirin) and iteratively modifies its structure to optimize binding for a specific protein target.

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.

--> --- name: 'mpn-progression-monitor-agent' description: 'AI-powered myeloproliferative neoplasm monitoring for disease progression prediction, treatment response tracking, and transformation risk assessment in PV, ET, and myelofibrosis.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **MPN Progression Monitor Agent** provides comprehensive monitoring of myeloproliferative neoplasms (PV, ET,...

--> --- name: mpn-research-assistant description: "Myeloproliferative neoplasm (MPN) research expertise including JAK2/CALR/MPL mutations, myelofibrosis, polycythemia vera, essential thrombocythemia. Use for MPN literature search, driver mutation analysis, PPM1D pathway analysis, fibrosis markers, megakaryocyte biology, clinical trial data interpretation, and translational research." license: Proprietary ---

--> --- name: 'mrd-edge-detection-agent' description: 'Ultra-sensitive AI-powered molecular residual disease detection using MRD-EDGE deep learning for sub-0.001% VAF ctDNA detection and early relapse prediction.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **MRD-EDGE Detection Agent** implements the MRD-EDGE (Enhanced Detection of ctDNA through Genomic Error suppression) deep learning algo...

--> --- name: 'multi-ancestry-prs-agent' description: 'AI-powered multi-ancestry polygenic risk score calculation and optimization for equitable disease risk prediction across diverse global populations.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Multi-Ancestry PRS Agent** provides AI-optimized polygenic risk score calculation designed to work across diverse ancestral populations. It ad...

--> --- name: 'multimodal-medical-imaging' description: 'Analyzes medical images (X-ray, MRI, CT) using multimodal LLMs to identify anomalies and generate reports.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Multimodal Medical Imaging Analysis Skill** leverages state-of-the-art Vision-Language Models (VLMs) like Gemini 1.5 Pro and GPT-4o to interpret medical imagery alongside clinical text.

--> --- name: 'multimodal-radpath-fusion-agent' description: 'AI-powered multimodal diagnostic fusion integrating radiology imaging (CT/MRI/PET), digital pathology (WSI), genomics, and clinical data for comprehensive cancer diagnosis and treatment planning.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Multimodal Radpath Fusion Agent** integrates diverse clinical data sources including rad...

--> --- name: 'myeloma-mrd-agent' description: 'AI-powered minimal residual disease (MRD) analysis for multiple myeloma using next-generation flow cytometry, NGS, and mass spectrometry approaches.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Myeloma MRD Agent** provides comprehensive AI-driven minimal residual disease assessment for multiple myeloma. It integrates next-generation flow cyt...

Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.

Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

--> --- name: ngs-analysis description: "Next-generation sequencing data analysis pipelines including bulk RNA-seq, scRNA-seq preprocessing, variant calling, and quality control. Use when working with FASTQ files, alignment (STAR, BWA), quantification (featureCounts, Salmon), DESeq2/edgeR analysis, or building NGS pipelines. Supports GEO/SRA data retrieval." license: Proprietary ---

--> --- name: 'nicheformer-spatial-agent' description: 'Foundation model-powered spatial transcriptomics analysis leveraging 53M+ spatially resolved cells for cellular architecture modeling and tissue niche discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Nicheformer Spatial Agent** leverages the Nicheformer foundation model, trained on over 53 million spatially resolved cells, to ...

--> --- name: 'nk-cell-therapy-agent' description: 'AI-powered NK cell therapy design for cancer immunotherapy including CAR-NK engineering, memory-like NK generation, and KIR/HLA matching optimization.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **NK Cell Therapy Agent** provides AI-driven design and optimization of natural killer cell therapies for cancer treatment. It covers CAR-NK engi...

Select and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton methods, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration, diagnosing convergence issues, choosing line search vs trust region, and analyzing Jacobian quality.

Select and configure time integration methods for ODE/PDE simulations. Use when choosing explicit/implicit schemes, setting error tolerances, adapting time steps, diagnosing integration accuracy, planning IMEX splitting, or handling stiff/non-stiff coupled systems.

Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit schemes, diagnosing numerical blow-up, checking CFL/Fourier criteria, von Neumann analysis, matrix conditioning, or detecting stiffness in advection/diffusion/reaction problems.

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO, understanding class relationships, finding properties for a given class, or searching for ontology terms related to a materials science concept. Supports OWL/XML format from the OCDO ecosystem (CMSO, ASMO, CDCO, PODO, PLDO, LDO).

Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Supports any ontology registered in ontology_registry.json. Use when translating natural-language material descriptions to ontology terms, annotating simulation inputs with ontology metadata, or mapping crystal parameters (space group, Bravais lattice, lattice constants) to standardized ontology representations.

Validate material sample annotations and data structures against ontology constraints. Use when checking if CMSO annotations are correct, verifying that required properties are present, or validating that object property relationships have consistent domain and range. Catches unknown classes, unknown properties, domain mismatches, and missing required fields.

Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker podcasts from research, chatting with documents using context-aware AI, searching across materials with full-text and vector search, or running custom content transformations. Supports ...

Search Open Targets drug-disease associations with natural language queries. Target validation powered by Valyu semantic search.

--> --- name: 'opentrons-protocol-agent' description: 'Generates executable Python protocols for Opentrons OT-2 and Flex robots from natural language descriptions.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Opentrons Protocol Agent** bridges the gap between experimental design and physical execution by translating instructions into Opentrons Python API scripts.

--> --- name: 'organoid-drug-response-agent' description: 'AI-powered analysis of patient-derived organoid (PDO) drug screening for personalized oncology treatment selection and biomarker discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Organoid Drug Response Agent** provides AI-driven analysis of patient-derived organoid (PDO) drug screening data for personalized treatment selecti...

--> --- name: 'pan-cancer-multiomics-agent' description: 'AI-powered pan-cancer analysis integrating genomic, transcriptomic, proteomic, and epigenomic data for cancer subtyping, driver identification, and cross-cancer pattern discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Pan-Cancer Multi-Omics Agent** integrates multi-omics data across cancer types to identify shared oncogenic ...

This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection. Use for calibration, uncertainty studies, parameter sweeps, LHS sampling, Sobol analysis, surrogate modeling, or Bayesian optimization setup.

Search global patents with natural language queries. Prior art, patent landscapes, and innovation tracking via Valyu.

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

Patiently AI simplifies medical documents for patients. Takes doctor's letters, test results, prescriptions, discharge summaries, and clinical notes and explains them in clear, personalised language. Built by PharmaTools.AI.

Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.

Production-ready PDF processing with forms, tables, OCR, validation, and batch operations. Use when working with complex PDF workflows in production environments, processing large volumes of PDFs, or requiring robust error handling and validation.

Extract text and tables from PDF files, fill forms, merge documents. Use when working with PDF files or when the user mentions PDFs, forms, or document extraction.

--> --- name: 'pdx-model-analysis-agent' description: 'AI-powered analysis of patient-derived xenograft (PDX) models for drug response prediction, translational research, and personalized treatment selection.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **PDX Model Analysis Agent** provides AI-driven analysis of patient-derived xenograft models for preclinical drug testing, translational re...

Identify computational bottlenecks, analyze scaling behavior, estimate memory requirements, and receive optimization recommendations for any computational simulation. Use when simulations are slow, investigating parallel efficiency, planning resource allocation, or seeking performance improvements through timing analysis, scaling studies, memory profiling, or bottleneck detection.

--> --- name: 'pharmacogenomics-agent' description: 'AI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.' keywords: - pharmacogenomics - precision-dosing - cpic-guidelines - adverse-events - multi-omics measurable_outcome: 'Provides validated dosing recommendations for >50 drugs with 99% concordance to CPIC guidelines.' allowed-tools: - read_file - run_shell_command --- The **Pharmacogenomics Agent** integrates AI and multi-omics data t...

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.

Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.

--> --- name: 'popeve-variant-predictor-agent' description: 'AI-powered genetic variant pathogenicity prediction using PopEVE deep learning model for population-aware disease variant identification and rare disease diagnosis.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **PopEVE Variant Predictor Agent** leverages the PopEVE deep learning model from Harvard Medical School to predict pathoge...

Extract, analyze, and visualize simulation output data. Use for field extraction, time series analysis, line profiles, statistical summaries, derived quantity computation, result comparison to references, and automated report generation from simulation results.

Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.

--> --- name: precision-oncology-agent description: Fuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review. allowed-tools: - read_file - run_shell_command ---

--> --- name: 'prior-auth-coworker' description: 'Prior Auth Review' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill acts as an automated utilization management reviewer. It takes unstructured clinical notes and a procedure code, compares them against internal policy criteria (e.g., conservative therapy failure), and renders a decision.