FridrichMethod
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- ▌ Bone Marrow AI Agent · fridrichmethodAI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images.
- ▌ Cell Free Expression · fridrichmethodGuidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).
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- ▌ Ehr Fhir Integration · fridrichmethod bundleProvides comprehensive tools for working with Electronic Health Records (EHR) using the HL7 FHIR standard.
- ▌ Geopandas Geospatial · fridrichmethodGeospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric ops (buffer, simplify, centroid, affine), spatial analysis (joins, overlays, dissolve, clipping, distance), visualization (choropleth, interactive maps, basemaps). Use for spatial joins, overlays, CRS transforms, area/distance, maps.
- ▌ Bio Ml Docking Rescoring · fridrichmethod bundlePerforms ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.
- ▌ Opentargets Database · fridrichmethod bundleQuery Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
- ▌ Protein Sequence Msa · fridrichmethod bundlePerforms multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.
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- ▌ Statistical Analysis · fridrichmethod bundleGuided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for publication. Covers frequentist (t-test, ANOVA, chi-square, regression, correlation, survival, count, reliability) and Bayesian. Use statsmodels or pymc-bayesian-modeling to fit.
- ▌ Agentd Drug Discovery · fridrichmethod bundleUse the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks.
- ▌ Antibody Design Agent · fridrichmethod bundleAn advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).
- ▌ Bio Alignment Sorting · fridrichmethod bundleSort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
- ▌ Bio Bedgraph Handling · fridrichmethod bundleCreate, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.
- ▌ Bio Pileup Generation · fridrichmethod bundleGenerate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
- ▌ Bio Restriction Sites · fridrichmethod bundleFind restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or circular DNA. Use when finding restriction enzyme cut sites in sequences.
- ▌ Bio Splicing Pipeline · fridrichmethod bundleEnd-to-end alternative splicing analysis from FASTQ to differential splicing results. Aligns with STAR 2-pass mode, performs junction QC, runs rMATS-turbo for differential analysis, and generates sashimi visualizations. Use when performing comprehensive splicing analysis from raw RNA-seq data.
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- ▌ Encode Ccres Database · fridrichmethod bundleQuery the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.
- ▌ Bio Data Visualization Genome Browser Tracks · fridrichmethod bundleGenerate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures. Use when creating publication figures of genomic regions with multiple data tracks.
- ▌ Nk Cell Therapy Agent · fridrichmethodAI-powered NK cell therapy design for cancer immunotherapy including CAR-NK engineering, memory-like NK generation, and KIR/HLA matching optimization.
- ▌ Scientific Manuscript · fridrichmethodHigh-impact scientific manuscript preparation for journals like Nature, Blood, Cell. Use when writing abstracts, introductions, methods, results, discussions, or figure legends. Includes citation management, statistical reporting standards, ICMJE guidelines, and journal-specific formatting for hematology/oncology publications.
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- ▌ Visual Edit Precision · fridrichmethodUse when making UI/frontend changes guided by visual context, when the user selects elements visually, draws annotations, or provides screenshots alongside change requests. Also use when editing components where spatial context (element identity, DOM references, layout data) supplements text instructions.
- ▌ Bio Alignment Indexing · fridrichmethod bundleCreate and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
- ▌ Bio Duplicate Handling · fridrichmethod bundleMark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
- ▌ Bio Reverse Complement · fridrichmethod bundleGenerate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template and coding strands.
- ▌ Clinical Nlp Extractor · fridrichmethod bundleExtracts medical entities (Diseases, Medications, Procedures) from unstructured clinical text using regex and simple rules (or LLM wrappers).
- ▌ Bio Pathway Enrichment Foundations · fridrichmethod bundleChooses the enrichment generation before any tool runs, mapping the input shape to a method class - a pre-selected gene list plus a background to over-representation analysis (ORA, hypergeometric), a ranked statistic for all genes to gene set enrichment (GSEA), a signed signaling topology to pathway-topology (SPIA) - then making the null explicit (competitive vs self-contained, gene vs subject sampling) and running a trustworthiness checklist (testable-gene universe, FDR, redundancy collapse, leading-edge check, version reporting). Covers why every clusterProfiler GSEA is the inter-gene-correlation-uncorrected competitive null, why the background not the gene list decides ORA significance, and why no method is universally best. Use when deciding ORA vs GSEA vs topology, which gene-set DB, whether a result is trustworthy, or which null a tool computes. For ORA see go-enrichment, GSEA see gsea, databases kegg-pathways/reactome-pathways/wikipathways; the ranking comes from differential-expression/de-results.
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- ▌ Labarchive Integration · fridrichmethod bundleSecurely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint selection, signed-request construction, user authorization and UID flows, local LA container validation, and verified LabArchives integration workflows.
- ▌ Medical Imaging Review · fridrichmethod bundleWrite comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses on topics like segmentation, detection, classification in CT, MRI, X-ray, ultrasound, or pathology imaging. Triggers on requests for "review paper", "survey", "literature review", "综述", "systematic review", or mentions of writing academic reviews on deep learning for medical imaging.
- ▌ Mpn Research Assistant · fridrichmethodMyeloproliferative 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.
- ▌ Nature Academic Search · fridrichmethod bundleMulti-source literature search, citation verification, strict independent other-citation audits, article-level citation metric tables, influential citer profiling with citation-context extraction, MeSH search strategy, citation file management (.nbib/.ris/.bib conversion), and reference management (BibTeX, related articles, ID conversion) via MCP tools (PubMed, CrossRef, arXiv, Scopus, ScienceDirect). Use for coordinated literature workflows beyond one MCP call, including 文献检索、 查文献、找文献、文献综述检索、查论文、引文核对、参考文献管理、文献去重、 严格他引、他引判定、排除自引、谁引用了我的文章、引用我的文章的人有没有大牛、 院士引用、校长引用、院长引用、杰青引用、长江学者引用、Fellow引用、文章引用表、 指定文章引用数、严格他引数、整理成表格.
- ▌ Researchwrite · fridrichmethod bundleProposal-first scientific writing pipeline, installed under the compatibility trigger researchwrite and the repository package name nature-proposal-writer. Use for composing, revising, or auditing research proposals, opening reports, research plans, and evidence-grounded scientific writing. Three modes (compose/revise/hybrid) with a four-layer QA pipeline. Enforces evidence-before-prose, argument-before-sections, and contracts-before-paragraphs.
- ▌ Pharmacogenomics Agent · fridrichmethodAI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.
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- ▌ Workflow Skill Creator · fridrichmethod bundleDistills a completed user workflow or interaction into a reusable agent skill. Use when the user asks to turn their workflow, interaction, or multi-step process into a skill, or when they say "make this a skill", "create a skill from what we just did", "package this workflow" or similar. Do not use for creating skills from scratch without an existing workflow (use a generic skill-creator for that).
- ▌ Aav Vector Design Agent · fridrichmethodAI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
- ▌ Bio Alignment Filtering · fridrichmethod bundleFilter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
- ▌ Bio Restriction Mapping · fridrichmethod bundleCreate restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps. Use when creating or analyzing restriction maps.
- ▌ Bio Sequence Properties · fridrichmethod bundleCalculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.
- ▌ Cancer Metabolism Agent · fridrichmethodAI-powered analysis of cancer metabolic reprogramming including Warburg effect, glutamine addiction, lipid metabolism, and metabolic vulnerabilities for therapeutic targeting.
- ▌ Chemcrow Drug Discovery · fridrichmethod bundleAn LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design.
- ▌ Datamol Cheminformatics · fridrichmethodPythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns native rdkit.Chem.Mol. Prefer datamol for standard workflows; use RDKit directly for advanced control.
- ▌ Gene Panel Design Agent · fridrichmethodAI-powered design of targeted gene panels for clinical and research applications including cancer diagnostics, pharmacogenomics, and rare disease testing.
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- ▌ Literature Search Arxiv · fridrichmethod bundleSearch for scientific papers, preprints, and publications on arXiv. Extract metadata, abstracts, and download full-text PDFs or HTML versions of papers. Use when the user asks to find research papers, literature, or specific arXiv IDs.
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- ▌ Microbiome Cancer Agent · fridrichmethodAI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targeted therapeutic opportunities.
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- ▌ Bio Data Visualization Specialized Omics Plots · fridrichmethod bundleReusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.
- ▌ Trial Eligibility Agent · fridrichmethod bundleParse trial protocols and patient data to produce criterion-level MET/NOT/UNKNOWN determinations with evidence and gaps for clinical trial screening tasks.
- ▌ Wearable Analysis Agent · fridrichmethod bundleAnalyzes longitudinal wearable sensor data (heart rate, activity, sleep) to detect anomalies and provide personalized health insights.
- ▌ Binding Characterization · fridrichmethodGuidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.
- ▌ Bio Alignment Validation · fridrichmethod bundleValidate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
- ▌ Bio Reference Operations · fridrichmethod bundleGenerate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
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- ▌ Chemical Property Lookup · fridrichmethod bundleCompute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools.
- ▌ Clinical Trials Database · fridrichmethod bundleQuery ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching.
- ▌ Ctdna Dynamics Mrd Agent · fridrichmethodAI-powered circulating tumor DNA dynamics analysis for molecular residual disease detection, treatment response monitoring, and early relapse prediction using liquid biopsy.
- ▌ Drug Interaction Checker · fridrichmethod bundleChecks for potential drug-drug interactions (DDIs) between a list of medications.
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- ▌ Mrd Edge Detection Agent · fridrichmethodUltra-sensitive AI-powered molecular residual disease detection using MRD-EDGE deep learning for sub-0.001% VAF ctDNA detection and early relapse prediction.
- ▌ Multi Ancestry Prs Agent · fridrichmethodAI-powered multi-ancestry polygenic risk score calculation and optimization for equitable disease risk prediction across diverse global populations.
- ▌ Opentrons Protocol Agent · fridrichmethod bundleGenerates executable Python protocols for Opentrons OT-2 and Flex robots from natural language descriptions.
- ▌ Pdx Model Analysis Agent · fridrichmethodAI-powered analysis of patient-derived xenograft (PDX) models for drug response prediction, translational research, and personalized treatment selection.
- ▌ Precision Oncology Agent · fridrichmethod bundleFuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review.
- ▌ Scfoundation Model Agent · fridrichmethodUnified agent for leveraging single-cell foundation models (scGPT, scBERT, Geneformer, scFoundation) for cross-species annotation, perturbation prediction, and gene network inference.
- ▌ Tooluniverse Single Cell · fridrichmethod bundleProduction-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering, differential expression (Wilcoxon, t-test, DESeq2), cell type annotation, per-cell-type statistical analysis, gene-expression correlation, batch correction (Harmony), trajectory inference, and cell-cell communication analysis. NEW: Analyzes ligand-receptor interactions between cell types using OmniPath (CellPhoneDB, CellChatDB), scores communication strength, identifies signaling cascades, and handles multi-subunit receptor complexes. Integrates with ToolUniverse gene annotation tools (HPA, Ensembl, MyGene, UniProt) and enrichment tools (gseapy, PANTHER, STRING). Supports h5ad, 10X, CSV/TSV count matrices, and pre-annotated datasets.
- ▌ Alphafold Database Access · fridrichmethod bundleAccess AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
- ▌ Armored Cart Design Agent · fridrichmethodAI-powered design of armored CAR-T cells with cytokine/chemokine expression for enhanced solid tumor efficacy, including IL-12, IL-15, IL-18, and IL-7 armoring strategies.
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- ▌ Bioinformatics Singlecell · fridrichmethod bundleAdvanced single-cell multi-omics analysis including scRNA-seq, scCITE-seq, scATAC-seq, and TARGET-seq. Use when analyzing single-cell data, cell type identification, trajectory analysis, differential expression, UMAP/clustering, integrating protein and RNA modalities (TotalVI), or working with Scanpy, Seurat, scvi-tools. Includes workflows for MPN, hematologic malignancies, megakaryocyte biology.
- ▌ Cellular Senescence Agent · fridrichmethodAI-powered analysis of cellular senescence for aging research, cancer therapy response, and senolytic drug development.
- ▌ Data Visualization Expert · fridrichmethodGenerate insightful, publication-quality visualizations from complex datasets.
- ▌ Exosome Ev Analysis Agent · fridrichmethodAI-powered extracellular vesicle and exosome analysis for cancer biomarker discovery, liquid biopsy applications, and intercellular communication profiling.
- ▌ Uv · fridrichmethodChecks whether the uv Python package manager is installed and installs it if missing. Ensures uv is on PATH. Use when another skill requires uv as a prerequisite.
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- ▌ Exploratory Data Analysis · fridrichmethod bundleMethodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence, image, spectral, structural, omics), quality assessment, report generation, format detection across 200+ formats. Use when given a data file for initial exploration or to pick an analysis before a pipeline.
- ▌ Literature Search Biorxiv · fridrichmethod bundleBrowse, filter, and download life sciences, biology, and medical preprints from bioRxiv and medRxiv. Supports fetching paper metadata by DOI, and browsing by date range with category and keyword filters. Keyword filtering is local, so date ranges MUST be narrow (1-4 weeks) with a category to prevent timeouts.
- ▌ Nicheformer Spatial Agent · fridrichmethodFoundation model-powered spatial transcriptomics analysis leveraging 53M+ spatially resolved cells for cellular architecture modeling and tissue niche discovery.
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- ▌ Shap Model Explainability · fridrichmethod bundleModel interpretability via SHAP (Shapley values from game theory). Covers explainer choice (Tree, Deep, Linear, Kernel, Gradient, Permutation), feature attribution, and plots (waterfall, beeswarm, bar, scatter, force, heatmap). Use to explain ML predictions, rank features, debug models, audit fairness, or compare models. Works with tree, deep, linear, and black-box models.
- ▌ Spatial Epigenomics Agent · fridrichmethodAI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.
- ▌ Tcr Pmhc Prediction Agent · fridrichmethodAI-powered TCR-peptide-MHC interaction prediction using AlphaFold3 and deep learning for therapeutic TCR discovery, neoantigen validation, and T cell immunogenicity assessment.
- ▌ Tpd Ternary Complex Agent · fridrichmethodAI-powered ternary complex prediction for targeted protein degradation, modeling POI-degrader-E3 ligase assemblies to optimize PROTAC and molecular glue efficacy.
- ▌ Tumor Heterogeneity Agent · fridrichmethodAI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and longitudinal sequencing.
- ▌ Bio Liquid Biopsy Pipeline · fridrichmethod bundleCell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring.
- ▌ Bio Workflows Hic Pipeline · fridrichmethod bundleEnd-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization. Use when processing Hi-C data to compartments and TADs.
- ▌ Bio Workflows Imc Pipeline · fridrichmethod bundleEnd-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics. Use when analyzing imaging mass cytometry data end-to-end.
- ▌ Bio Workflows Rnaseq To De · fridrichmethod bundleEnd-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization. Use when running RNA-seq from FASTQ to DE results.
- ▌ Bio Workflows Tcr Pipeline · fridrichmethod bundleEnd-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.
- ▌ Bioservices Multi Database · fridrichmethod bundleUnified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.
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- ▌ Context Driven Development · fridrichmethod bundleCreates and maintains project context artifacts (product.md, tech-stack.md, workflow.md, tracks.md) in a `conductor/` directory. Scaffolds new projects from scratch, extracts context from existing codebases, validates artifact consistency before implementation, and synchronizes documents as the project evolves. Use when setting up a project, creating or updating product docs, managing a tech stack file, defining development workflows, tracking work units, onboarding to an existing codebase, or running project scaffolding.
- ▌ Crispr Offtarget Predictor · fridrichmethod bundlePredicts potential off-target sites for a given sgRNA sequence using mismatch analysis.
- ▌ Foldseek Structural Search · fridrichmethod bundlePerforms 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.