Research & Search

Run structured What-If scenario analysis with 4-6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use for speculative questions about uncertain futures, strategic forks, contingency planning, or stress-testing decisions.

Query documented public database APIs with explicit endpoints, filters, pagination, and provenance for reproducible retrieval of scientific, regulatory, or financial facts.

Discovers and uses scientific datasets, models, blog posts, and interactive demos from a curated catalog for AI/ML work in domains like biology, chemistry, physics, and genomics.

Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC with agency-specific formatting, review criteria, budget preparation, and compliance guidance.

Look up current research and scientific information across three backends: fast web search, deep multi-source synthesis, and scholarly paper searches. Automatically routes each query to the best backend and saves every result for reproducible citation.

Generate concise (3-4 page) medical treatment plans in LaTeX/PDF format across all clinical specialties, with SMART goals, evidence-based interventions, and HIPAA compliance.

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues, academic conferences, research posters, and grant proposals.

Generate comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports, clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries) with templates, regulatory compliance, and validation tools.

Submit and manage protocols on Ginkgo Bioworks Cloud Lab for autonomous lab execution, including protein expression, purification, quantification, RNA synthesis, and custom workflows via EstiMate.

Analyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions.

Conduct systematic literature reviews by searching multiple academic databases, synthesizing findings, and generating professionally formatted documents with verified citations.

Calculate sample sizes, minimum detectable effects, and power curves for study planning using closed-form formulas or Monte Carlo simulation.

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).

Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Covers over-representation analysis (ORA), Gene Set Enrichment Analysis (GSEA), and single-sample scoring using gseapy, g:Profiler, and Enrichr libraries.

Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.

Write scientific manuscripts in full paragraphs using IMRAD structure, with citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA) for research papers and journal submissions.

Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries.

Design experiments and studies before data collection — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable.

Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Access large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.

Guides statistical hypothesis testing with assumption checks, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting for research data.

Simulates a multi-perspective deliberation council to explore complex questions, decisions, or creative challenges from diverse thinking archetypes.

Formulate testable hypotheses from observations, design experiments, and generate predictions using a structured scientific method framework.

Create publication-quality scientific diagrams using AI generation with smart iterative refinement and quality review.

Access and manage LabArchives electronic lab notebooks programmatically via REST API. Create entries, upload attachments, backup notebooks, generate reports, and integrate with Protocols.io, Jupyter, REDCap, and other scientific tools.

Generate comprehensive, professional-grade market research reports (50+ pages) with LaTeX formatting, strategic frameworks, and data-driven visualizations.

Integrates with the protocols.io API v3 to search, create, update, and publish scientific protocols, manage steps and materials, handle discussions, organize workspaces, and upload files.

Generate novel research ideas through structured, conversational brainstorming that explores interdisciplinary connections, challenges assumptions, and identifies research gaps.

Generate professional clinical decision support documents for pharmaceutical and clinical research, including biomarker-stratified cohort analyses and evidence-based treatment recommendation reports with GRADE grading, statistical analysis, and publication-ready LaTeX/PDF output.

Automatically detect and analyze scientific data files across 200+ formats, generating detailed markdown reports with quality metrics and analysis recommendations.

Evaluate scientific claims and evidence quality by assessing experimental design, identifying biases and confounders, and applying evidence grading frameworks like GRADE and Cochrane Risk of Bias.

Develops comprehensive threat actor profiles for APT groups, criminal organizations, and hacktivist collectives by aggregating TTP documentation, historical campaign data, tooling fingerprints, and attribution indicators from multiple intelligence sources.

Detect and analyze heap spray attacks in memory dumps using Volatility3 plugins to identify NOP sled patterns, shellcode landing zones, and suspicious large allocations in process virtual address space.

Analyzes UEFI bootkit persistence mechanisms including firmware implants, ESP modifications, Secure Boot bypass techniques, and UEFI variable manipulation. Covers detection of known bootkit families, forensic inspection, and integrity verification.

Collects and synthesizes open-source intelligence (OSINT) about threat actors, malicious infrastructure, and attack campaigns using passive reconnaissance tools and public data sources.

Analyzes bootkit and rootkit malware that infects MBR, VBR, or UEFI firmware for pre-OS persistence, covering boot sector analysis, UEFI module inspection, and anti-rootkit detection.