FridrichMethod
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- ▌ Multipanel · fridrichmethodAssemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from already-rendered panels the user supplies (PNG/PDF). Ask the user to pick one of two approaches: (1) redraw every panel into one unified figure using independent, tightly packed `subfigures` (each sized to its own labels, so axes need NOT align), consistent style, correctly placed panel letters, and per-panel legends/colorbars; (2) composite already-rendered PNG/PDF panels onto a mosaic canvas and add panel letters (image compositing, not plotting). Both export vector PDF + high-DPI PNG. For a SINGLE plot from a data table, use the sibling `omics-plotting` skill instead.
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- ▌ Scikit Bio · fridrichmethod bundlePython library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination (PCoA, CCA, RDA), stats (PERMANOVA, ANOSIM, Mantel), file I/O (FASTA, FASTQ, Newick, BIOM). Use for microbiome, community ecology, or phylogenetics.
- ▌ Academic Paper Strategist · fridrichmethod bundleSystematic strategic planning framework for philosophy and interdisciplinary academic papers targeting preprint platforms (PhilArchive, arXiv, PhilSci-Archive). Use when users want to: (1) plan a paper on a specific topic, (2) identify research gaps and assess originality, (3) develop optimized paper outlines, (4) prepare for preprint submission, or (5) understand platform requirements and writing standards. Triggered by phrases like 'plan a paper on,' 'help me design a paper about,' 'identify research gaps in,' 'is this idea original,' or when users need structured research planning. The skill guides through three phases: Platform Analysis (identifying target venue and studying sample papers), Theoretical Framework (AI-driven literature search and gap identification), and Outline Optimization (structured design with reviewer-perspective self-assessment). Each phase includes quality evaluation standards and validation checkpoints.
- ▌ Umap Learn · fridrichmethod bundleUMAP dimensionality reduction for visualization, clustering prep, and feature engineering. Fast nonlinear manifold learning preserving local and global structure. Standard UMAP (fit/transform, sklearn-compatible), supervised/semi-supervised, Parametric UMAP (NN encoder/decoder, TensorFlow), DensMAP (density), AlignedUMAP (temporal/batch). 15+ distance metrics, custom Numba metrics, precomputed distances. For linear reduction use PCA; for neighborhood graphs use sklearn NearestNeighbors.
- ▌ Credentials · fridrichmethodInstructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.
- ▌ Bio Phasing Imputation Foundations · fridrichmethod bundleFrames the phasing/imputation pipeline before any tool runs: phasing and imputation are one Li-Stephens copying HMM (recombination is the transition, mutation the emission, the genetic map and Ne set the rates), imputation's honest output is a dosage with a self-estimated quality (INFO/R2/DR2) not a hard genotype, and the stages are ordered and each fails silently (QC, align build and strand to the panel, phase, impute per chromosome, filter by INFO/R2 plus a MAF floor, carry dosages to GWAS). Covers the strategy fork (array vs low-coverage WGS plus genotype-likelihood imputation), why the panel ancestry is the prior, and why a flipped strand or build mismatch destroys accuracy without an error. Use when deciding a genotyping strategy, sequencing the pipeline, choosing array vs low-coverage WGS, or diagnosing silently-wrong imputation. Mechanics route to reference-panels, haplotype-phasing, genotype-imputation, imputation-qc; read-backed phasing is long-read-sequencing/haplotype-phasing.
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- ▌ Paper 2 Web · fridrichmethod bundleThis 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.
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- ▌ Bio Geo Data · fridrichmethod bundleQuery NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.
- ▌ Bio Sra Data · fridrichmethod bundleDownload sequencing data from NCBI SRA using the SRA toolkit. Use when downloading FASTQ files from SRA accessions, prefetching large datasets, or validating SRA downloads.
- ▌ Embl Ebi Ols · fridrichmethod bundleQuery and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search for terms, retrieve details, navigate hierarchies (parents, children, ancestors), look up properties and individuals, get autocomplete suggestions, or access ontology metadata and statistics.
- ▌ Hermes Tweet · fridrichmethod bundleInstall and operate Hermes Tweet, a Hermes Agent plugin for X/Twitter research, timeline reading, tweet analysis, and approval-gated private or state-changing operations. Use this skill when installing Hermes Tweet, researching X/Twitter accounts, monitoring launch signals, investigating mentions, auditing giveaways, or preparing gated X operations. Use proactively when a Hermes Agent workflow needs current X/Twitter context. Requires XQUIK_API_KEY for read and action tools.
- ▌ Ngs Analysis · fridrichmethodNext-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.
- ▌ Pdb Database · fridrichmethod bundleUse when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.
- ▌ Academy Guide · fridrichmethod bundleStop and check this skill before finishing any reply to a question about how to use Claude or a Claude product — it recommends matching courses, tutorials, and use cases from Claude Academy (academy.claude.com), Anthropic's learning hub. Trigger on: "how do I", "how can I", "getting started with", "what can Claude do", "teach me", "learn to use"; questions about artifacts, projects, skills, plugins, connectors, MCP; requests about rolling Claude out to a team, class, or organization; and any ask for training materials, onboarding content, or learning resources. Use it when the user is learning how to use a feature or product — not when they are mid-task and just want the task done. This skill composes with other skills: after consulting product documentation to answer how a Claude feature works, also check here for a matching course or tutorial — a docs-grounded answer and an Academy recommendation belong together. Only recommend on a strong match; never invent Academy content.
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- ▌ Gtex Database · fridrichmethod bundleUse when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.
- ▌ Nature Figure · fridrichmethod bundleCreate, revise, audit, and export submission-grade scientific figures for Nature-family and other high-impact venues in Python (matplotlib/seaborn) or R (ggplot2/patchwork/ComplexHeatmap), including multi-panel plots, figures4papers-style work, and journal-ready SVG/PDF/TIFF outputs. Use for paper or scientific plots, manuscript data visualization, 论文配图、学术写作配图、科研绘图、科研作图、画图、作图、出图、论文图表、可视化. Define the conclusion, evidence logic, data integrity, template compatibility, export needs, and reviewer risks before plotting; honor or persist the Python/R backend choice. Also use the separate OpenRouter GPT Image 2 route for explicit AI-generated graphical abstracts, mechanism diagrams, concept schematics, 论文示意图、机制示意图、图形摘要; this route skips backend choice and treats outputs as drafts. Do not use for interactive dashboards, statistics-only analysis, data cleaning, literature review, code debugging, pure photo editing, or Illustrator/Figma-first infographics without manuscript-figure intent.
- ▌ Session Guard · fridrichmethodUse when working on complex multi-step tasks, when a session is getting long (40+ tool calls), when the agent starts ignoring rules it followed earlier, when conventions drift, when output quality seems to degrade, or after any context compaction event. Prevents long-session corruption AND context compaction amnesia through behavioral self-enforcement.
- ▌ Spatial Agent · fridrichmethodAn agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.
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- ▌ Dbsnp Database · fridrichmethod bundleUse when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rsID, returns variant type, gene associations, clinical significance, allele frequencies, and genomic coordinates (GRCh38).
- ▌ Omics Plotting · fridrichmethodomics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not only when a plot is explicitly requested: whenever an analysis will produce a figure, load this first and follow its recipes. Covers volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA / UMAP / t-SNE scatter, Kaplan–Meier, Manhattan / QQ / forest. Supplies a shared journal-ready style and copy-paste recipes so every figure looks like one consistent system. To combine several plots into ONE multi-panel composite figure, use the sibling `multipanel` skill.
- ▌ Profile Report · fridrichmethod bundleUnified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
- ▌ Bio Codon Usage · fridrichmethod bundleAnalyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.
- ▌ Bio Entrez Link · fridrichmethod bundleFind cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, or discovering database relationships.
- ▌ Bio Local Blast · fridrichmethod bundleRun local BLAST searches using BLAST+ command-line tools. Use when running fast unlimited searches, building custom databases, performing large-scale analysis, or when NCBI servers are slow or unavailable.
- ▌ Bio Seq Objects · fridrichmethod bundleCreate and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records.
- ▌ Chembl Database · fridrichmethod bundleQuery the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.
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- ▌ Gnomad Database · fridrichmethod bundleQuery the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).
- ▌ Jaspar Database · fridrichmethod bundleQuery the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene symbols to JASPAR Matrix IDs, or getting TF metadata. Supports multiple output formats (MEME, TRANSFAC, PFM, JASPAR, YAML).
- ▌ Nature Citation · fridrichmethod bundleAdd strict Nature/CNS citations to manuscript text by splitting long passages into citable segments, searching only accepted flagship and subjournal titles from Nature Portfolio, the AAAS Science family, and Cell Press, filtering by publication time range, and exporting one reference-manager-ready output by default. Use this skill whenever the user asks to input text and automatically get references, add citations to a paragraph/manuscript, find Nature-series or CNS support for statements, create text-to-reference correspondence, "分段引用", "自动给出引用", "Nature系列引用", "CNS及子刊", "支撑文献", "补引用", "找引用", or export EndNote/RIS/ENW/Zotero RDF. Also trigger on general academic-writing citation needs even without the word "Nature", such as adding references while writing a paper, finding sources/literature for a claim, building a reference list, citation/referencing for academic writing, and Chinese phrasings like 学术写作引用、写论文加引用、写paper找文献、加参考文献、配文献、引用文献、文献支撑.
- ▌ Nature Response · fridrichmethod bundleDraft, audit, or revise Nature-style revision correspondence packages: point-by-point reviewer-separated response letters, rebuttal letters, revision cover letters, LaTeX cover/response templates, and red-marked revised-manuscript excerpts. Keep mutually blind reviewers isolated so no reviewer-facing response reveals another reviewer's comments, numbering, recommendation, or author response. Prevent reviewer-driven manuscript accretion by preferring replacement, compression, or SI relocation over appending non-central defense prose. Use for reviewer comments, editor decision letters, pasted editorial emails, response drafts, cover letters, response to reviewers, rebuttal, 修回信, 返修邮件, 编辑邮件, 返修 cover letter, 审稿意见回复, 逐点回复, 大修回复, 小修回复, 回复审稿人, 修改稿回复, 写rebuttal, 回应审稿意见, 标红修改, or LaTeX 模板.
- ▌ Nature Reviewer · fridrichmethod bundleSimulate Nature-style or general pre-submission peer review from the referee perspective, not an author rebuttal. Use for reviewer reports, mock peer review, manuscript critique, novelty/significance/technical-soundness assessment, 审稿人视角评估, 模拟审稿, 预审, 投稿前自审, 审稿意见模拟, or 帮我审一下论文. Produce evidence-grounded Major Concerns, Minor Comments, and blocking flags. For multiple reviewers, keep every reviewer mutually blind in a separate context, freeze all reports before comparison, and create any synthesis only afterward as a separate editor/author-facing artifact.
- ▌ Ontology Mapper · fridrichmethod bundleMap 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.
- ▌ Pubmed Database · fridrichmethod bundleSearch PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.
- ▌ Search Strategy · fridrichmethodQuery decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries into source-specific syntax, ranks results by relevance, and handles ambiguity and fallback strategies.
- ▌ String Database · fridrichmethod bundleQuery the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confidence scores, protein interaction partners, or pathway enrichments.
- ▌ Vaex Dataframes · fridrichmethod bundleOut-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10 GB–TB) for fast aggregation, filtering, virtual columns, and visualization without loading. Supports HDF5, Arrow, Parquet, CSV with cloud (S3, GCS, Azure). Built-in ML transformers (scaling, PCA, K-means). In-memory: polars; distributed: dask.
- ▌ AI Debt Detector · fridrichmethodUse after generating code, after accepting AI suggestions, or when reviewing AI-written modules. Also use when code works but feels brittle, when error handling seems thin, when orphaned resources or missing cleanup are suspected, or when the agent claims done but hidden debt may exist. Catches the specific failure patterns AI agents produce that humans would not.
- ▌ Bio Entrez Fetch · fridrichmethod bundleRetrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into Biopython objects.
- ▌ Bio Motif Search · fridrichmethod bundleFind patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme analysis, use the restriction-analysis skill.
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- ▌ Clinvar Database · fridrichmethod bundleUse when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.
- ▌ Cnv Caller Agent · fridrichmethodAI-enhanced copy number variation calling and analysis from sequencing data for cancer genomics, constitutional CNV detection, and chromosomal aberration characterization.
- ▌ Ensembl Database · fridrichmethod bundleQuery the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.
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- ▌ Openfda Database · fridrichmethod bundleQuery, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data. Use for FDA adverse events, recalls, labeling, approvals, shortages, 510(k) clearances, NDC lookups, and any FDA safety or regulatory data query across all 28 API endpoints.
- ▌ Pubchem Database · fridrichmethod bundleQuery PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
- ▌ Quickgo Database · fridrichmethod bundleQuery the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find genes associated with a specific pathway/GO term, or explore the Gene Ontology hierarchy. Do not use for querying drug targets (use OpenTargets) or mechanistic signaling pathway diagrams (use KEGG).
- ▌ Unibind Database · fridrichmethod bundleQueries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.
- ▌ Uniprot Database · fridrichmethod bundleAccess protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or retrieving functional annotations and publications. Don't use for sequence alignment, protein folding, or sequence similarity search (use specialized skills for those tasks).
- ▌ Bio Entrez Search · fridrichmethod bundleSearch NCBI databases using Biopython Bio.Entrez. Use when finding records by keyword, building complex search queries, discovering database structure, or getting global query counts across databases.
- ▌ Bio Phylo Tree Io · fridrichmethod bundleRead, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees.
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- ▌ Discernment Nudge · fridrichmethod bundleAfter you give a substantive answer or draft that the user may act on — advice or recommendations, drafted artifacts such as goals, plans, pitches, proposals, or emails, estimates or projections, analysis or interpretation of data, factual claims they may rely on, or a multi-step argument — invoke this skill BEFORE finalizing your reply and then, if it applies, append 2-3 short follow-up questions, each tied to something specific in what you just produced, that help the user check key facts, probe the reasoning or assumptions, and notice missing context. Do this at most once per conversation. Skip it when the user asked a trivial how-to or simple lookup, wants a purely educational explanation, asked you only to format, convert, or assemble a file from content they provided, is writing code they will run, is doing creative writing or casual chat, or already asked you to double-check, cite, or review — the skill file explains these boundaries and the exact output format.
- ▌ Interpro Database · fridrichmethod bundleIdentify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significantly expands annotation and sequence coverage with deep learning. Includes domain architecture (IDA) search.
- ▌ Myeloma Mrd Agent · fridrichmethodAI-powered minimal residual disease (MRD) analysis for multiple myeloma using next-generation flow cytometry, NGS, and mass spectrometry approaches.
- ▌ Nature Statistics · fridrichmethod bundleAudit, revise, or draft manuscript statistical reporting for Nature / high-impact journal submissions. Use when the user asks to check statistical analysis sections, p values, confidence intervals, sample size, biological versus technical replicates, randomization, blinding, multiple-comparison correction, model assumptions, figure legends, Results statistics wording, reviewer comments about statistics, or Chinese academic drafts needing publication-ready Statistical analysis text. Also trigger on general paper-statistics requests such as 统计审查、统计分析小节、统计方法、p值、样本量、重复数、多重比较、置信区间、效应量、图注统计、审稿人统计意见.
- ▌ Ontology Explorer · fridrichmethod bundleParse, 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).
- ▌ Polars Dataframes · fridrichmethod bundleFast in-memory DataFrame with lazy evaluation, parallel execution, Arrow backend. Use for tabular data in RAM (1–100 GB) when pandas is too slow. Expression API: select, filter, group_by, joins, pivots, window. Lazy mode enables predicate/projection pushdown. Reads CSV, Parquet, JSON, Excel, DBs, cloud. Larger-than-RAM: Dask; GPU: cuDF.
- ▌ Predictingthepast · fridrichmethod bundleAncient text restoration, attribution, dating, contextualization, and embedding via Aeneas (Latin) / Ithaca (Ancient Greek). Use when asked to "restore", "attribute", "date", "contextualize", "find parallels", "where was it written", "when was it written", "embed", or "analyze" an ancient text, inscription, or epigraphic document, or when the user mentions "Aeneas", or "Ithaca".
- ▌ Reactome Database · fridrichmethod bundleQuery the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.
- ▌ Social Publishing · fridrichmethodSchedule and publish social media posts across 13 platforms (X, LinkedIn, Instagram, Facebook Pages, TikTok, Discord, Telegram, YouTube, Reddit, WordPress, Pinterest) via the SocialClaw API. Use when the user wants to publish, schedule, or manage social media content programmatically. Requires SOCIALCLAW_API_KEY.
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- ▌ Virtual Lab Agent · fridrichmethodAI-powered virtual laboratory orchestrating multi-agent scientific research teams for autonomous hypothesis generation, experimental design, and validation in biomedical research.
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- ▌ Bio Blast Searches · fridrichmethod bundleRun remote BLAST searches against NCBI databases using Biopython Bio.Blast. Use when identifying unknown sequences, finding homologs, or searching for sequence similarity against NCBI's nr/nt databases.
- ▌ Bio Sam Bam Basics · fridrichmethod bundleView, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
- ▌ Bio Uniprot Access · fridrichmethod bundleAccess UniProt protein database for sequences, annotations, and functional information. Use when retrieving protein data, GO terms, domain annotations, or protein-protein interactions.
- ▌ Cellfree Rna Agent · fridrichmethodAI-powered cell-free RNA analysis from liquid biopsy for cancer detection, tissue-of-origin identification, and non-invasive transcriptomic profiling.
- ▌ Hrd Analysis Agent · fridrichmethodAI-powered homologous recombination deficiency (HRD) analysis for PARP inhibitor response prediction using genomic scarring signatures and BRCA pathway assessment.
- ▌ Ontology Validator · fridrichmethod bundleValidate 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.
- ▌ Regulatory Drafter · fridrichmethod bundleAutomates the drafting of regulatory documents (e.g., FDA CTD sections) with citation management and audit trails.
- ▌ Rna Velocity Agent · fridrichmethodAI-powered RNA velocity analysis for predicting cellular state transitions, differentiation trajectories, and dynamic gene regulation from single-cell RNA sequencing data.
- ▌ Bio Batch Downloads · fridrichmethod bundleDownload large datasets from NCBI efficiently using history server, batching, and rate limiting. Use when performing bulk sequence downloads, handling large query results, or production-scale data retrieval.
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- ▌ Knowledge Synthesis · fridrichmethodCombines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on freshness and authority, and summarizes large result sets effectively.
- ▌ Nature Ref Verifier · fridrichmethod bundle对学术文献逐条执行多源交叉验证，逐字段对比作者、标题、年份、卷期、页码， 标记卷年/DOI年冲突、作者顺序异常、页码偏差等问题，输出结构化验证报告。 可批量处理整篇论文/开题报告的参考文献列表，也可单条校验，支持与 Zotero 同步修正。
- ▌ Ncbi Sequence Fetch · fridrichmethod bundleRetrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.
- ▌ Poster Presentation · fridrichmethod bundleCreate scientific conference posters as native, editable .pptx files using python-pptx. Handles A0/A1 layouts, section placement, figure insertion, and academic color schemes. Exports editable .pptx and PDF. Use when the user wants a directly editable PowerPoint poster; for HTML/CSS-based posters exported to PDF/PPTX use pptx-posters, and for standard LaTeX posters use latex-posters.
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- ▌ Protac Design Agent · fridrichmethodAI-powered PROTAC (Proteolysis Targeting Chimera) design for targeted protein degradation, integrating ternary complex prediction, linker optimization, and ADMET modeling.
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- ▌ Scienceskillscommon · fridrichmethod bundleShared Python package for Science Skills, currently containing http_client -- a unified HTTP client with rate limiting, retries, and exponential backoff. Not a standalone agent skill. Do not invoke directly.
- ▌ Bio Sequence Similarity · fridrichmethod bundleFind homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis. Use when identifying orthologs, distant homologs, or protein family members where standard BLAST is not sensitive enough.
- ▌ Bio Sequence Slicing · fridrichmethod bundleSlice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.
- ▌ Biomni General Agent · fridrichmethod bundleUse the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.