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Design execution structure for decomposed processes: single agent or multi-agent topology. Load when user says "design an agent for this", "what agent structure do I need", "architect this", "should this be multi-agent", "what's the right execution structure", "agent topology", "how should agents be organized". Takes process-decomposer output as primary input. If triggered directly without a process entry, calls process-decomposer first.

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Automate Cloudinary media management including folder organization, upload presets, asset lookup, transformations, and usage monitoring through natural language commands

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Automate Capsule CRM operations -- manage contacts (parties), run structured filter queries, track tasks and projects, log entries, and handle organizations -- using natural language through the Composio MCP integration.

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Automate Anthropic Admin tasks via Rube MCP (Composio): API keys, usage, workspaces, and organization management. Always search tools first for current schemas.

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Automate Apollo.io lead generation -- search organizations, discover contacts, enrich prospect data, manage contact stages, and build targeted outreach lists -- using natural language through the Composio MCP integration.

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Automate SEO research with Ahrefs -- analyze backlink profiles, research keywords, track domain metrics history, audit organic rankings, and perform batch URL analysis through the Composio Ahrefs integration.

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Automate Calendly scheduling, event management, invitee tracking, availability checks, and organization administration via Rube MCP (Composio). Always search tools first for current schemas.

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Automate Basecamp project management, to-dos, messages, people, and to-do list organization via Rube MCP (Composio). Always search tools first for current schemas.

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Azure API Center Management SDK for Python. Use for managing API inventory, metadata, and governance across your organization.

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Manage MongoDB Atlas Organizations as Azure ARM resources with unified billing through Azure Marketplace.

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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.

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Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity data-driven thresholds, flowClust model-based gates), organized as a hierarchical GatingSet (flowWorkspace) and round-tripped with FlowJo via CytoML. Covers the canonical gate order (time -> debris -> singlets -> live -> lineage), FMO-vs-isotype boundary setting, gate-order dependence and recompute semantics, rare-event/MRD gating, and per-population statistics. Use when building a gating strategy, automating a manual FlowJo scheme across samples, choosing manual vs data-driven gates, or extracting population frequencies.

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Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.

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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.

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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, HLA-LA, T1K, Polysolver, HLA-HD, arcasHLA, StarPhase, or HIBAG imputation. Use when typing for HSCT, solid-organ transplant, neoantigen prediction, PGx screening (B*57:01, B*15:02, etc.), or disease-association studies, with reconciliation across tools and IPD-IMGT/HLA version mismatch handling.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Use this skill to respond to an FMCSA audit document request efficiently. Covers organization, file labeling, secure transmission.

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Troubleshoot Coval OpenTelemetry trace ingestion, missing trace UI, sparse traces, bad simulation or conversation correlation, auth/org errors, oversized payloads, duplicate spans, and production debugging with Trace Search.

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Delegate a read-only Coval evaluation, simulation, monitoring, product-how-to, or troubleshooting subtask to Sofia through the official Coval MCP consult_sofia tool. Use when the user needs Coval-specific FDE judgment, analysis of organization data, metric or test-set recommendations, or a diagnosis grounded in Coval runs and conversations.

日本語の概要は準備中です。原文の説明を表示しています。