Use on procedure terminal step, explicit customer close, session end, or pending-state submit-now branch.
Using BDD to validate architectural hypotheses in TMNL. Covers H1/H2/H3 hypothesis patterns from testbeds, connecting specs to acceptance criteria, and damage reports for…
Create Beamer-style academic PPTX presentations using python-pptx. Produces publication-quality .pptx files with navy-blue Metropolis theme (16:9, frame title bars, progress bar)…
BeatLab JSON contract for 16-step (0-15) pianoSequence & drumSequence. Use when generating or editing beats.
Deterministic BeatLab pipeline utilities (validate, render grid, export MIDI/WAV). Use for running scripts instead of reasoning about validation/rendering.
Extracts structured citation data from academic repositories using BeautifulSoup4 with lxml parser. Parses DOI metadata, author affiliations, and reference lists from PubMed,…
Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features.
Plaited behavioral programming patterns for event-driven coordination and symbolic reasoning. Use when implementing behavioral programs with behavioral()/useBehavioral, designing…
Biological foundations of behavior and mental processes. Covers brain structure and function (cerebral cortex, limbic system, brainstem, cerebellum, lateralization),…
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data m — from…
Score deep research agents on benchmark tasks using factual verification, report-quality scoring, and process evaluation before model or workflow changes ship.
[METHODOLOGY] Industry benchmark research — reverse-engineer how the fastest-growing companies in a given industry actually scaled (source harvest → company synthesis →…
Audit government benefits and entitlement systems for fraud prevention, detection, and recovery capabilities.
Get started with the BERIL Research Observatory. Use when a user is new, wants orientation, or asks what they can do.
Use this agent when you need to research external best practices, documentation, and examples for any technology or development practice.
Optimal posting time analysis — research platform-specific engagement patterns for the user's niche and audience, recommend best times to post on note, X, and Instagram.
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.
Evidence-based medical knowledge and research mentor grounded in the Bian Que tradition. Covers clinical reasoning, diagnostic thinking (望闻问切), pharmacology, pathology,…
Use before any research activity or significant decision. Reviews cognitive biases relevant to the current stage.
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC — from…
Use when you need to run a binary, trace execution, or observe runtime behavior. Runtime analysis via QEMU emulation, GDB debugging, and Frida hooking - syscall tracing ( — from…
Use when analyzing binary structure, disassembling code, or decompiling functions. Deep static analysis via radare2 (r2) and Ghidra headless - function enumeration, cross — from…
Use when ready to document findings, generate a report, or summarize binary analysis results. Compiles analysis findings into structured reports - correlates facts from t — from…
Use when reverse engineering tools are missing, not working, or need configuration. Installation guides for radare2 (r2), Ghidra, GDB, QEMU, Frida, binutils, and cross-co — from…
Use when first encountering an unknown binary, ELF file, executable, or firmware blob. Fast fingerprinting via rabin2 - architecture detection (ARM, x86, MIPS), ABI ident — from…
Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting…
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics.
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics.
Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program…
Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro).
Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate,…
Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-fa — from…
Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes.
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package.
Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or…
Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR.
Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments.
Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data.
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples.
Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or…
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions.
Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective…
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discove — from…
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks.
Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R…
Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cu — from…
Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data bo — from…
Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated…
Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE)…
Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood,…
Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional estimand reporting per FDA 2023 covariate adjustment guidance,…
Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-based multiple imputation (J2R,…
Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, mixed), Hochberg/Hommel/Holm with…
Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2 — from…
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RER — from…
Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing…
Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA 2023 covariate adjustment guidance.
Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF.
Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.