Results for “sam”

Perform constraint-based metabolic modeling with COBRApy: run FBA, FVA, gene knockouts, flux sampling, and manage SBML models for systems biology and metabolic engineering.

Design prospective clinical studies by selecting and classifying endpoints, estimating sample size and power for two-arm designs, and scoring study plans for feasibility with phase-gate decisions.

Plan and synthesize product/user research with method rigor: select the right method for the goal, compute defensible sample sizes with confidence labels, and cluster coded observations into insights while flagging single-source anecdotes.

Search SAM.gov for contract opportunities and registered entities, and query USASpending.gov for federal award data.

Orchestrates structured experiments end-to-end: initialize, plan, run, and evolve with reproducibility tracking and hypothesis validation.

Parses external reviews, enforces coverage and grounding, and drafts a text-only rebuttal under venue limits, managing follow-up rounds.

Conducts multi-source web research on any topic, cross-referencing claims and delivering a structured report with sources and recommendations.

Iteratively improves a compiled LaTeX paper through two rounds of external LLM review, fix implementation, and recompilation.

Produces decision-oriented market research, competitive analysis, investor due diligence, and industry intelligence with source attribution.

Design surveys that collect reliable, unbiased quantitative data to validate hypotheses and measure user attitudes at scale.

Manages a persistent hypothesis tree in markdown, tracking falsifiable claims with linked evidence, timestamps, and next experiments for multi-step research investigations.

Runs Stanford's STORM pipeline to produce Wikipedia-quality research articles with citations, using Claude models and a search engine API.

Query the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.

Read, write, and manipulate genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.

Interrogates research plans before evals or published claims, forcing explicit null hypotheses, confound checks, and data verification across four review waves.

Runs a multi-agent academic research pipeline covering systematic review, LaTeX paper writing, peer review, and end-to-end orchestration with integrity gates.

Analyzes evaluation results by requiring a stated hypothesis before examining data, then compares expectations to actual result files to prevent post-hoc rationalization.

Conducts autonomous multi-source research using a planner/executor architecture and an MCP server, with tools for deep research, quick search, report writing, and source retrieval.

Embody Carl Sagan's voice and perspective to communicate science with wonder, rigor, and accessibility.

Embody the voice and methodology of Adam Smith for systematic, observational analysis of markets, ethics, and policy.

Simulates a NeurIPS/SC/ICSE-style peer review with five reviewer personas (HPC, ML, Stats, Reproducibility, Devil's Advocate) that verify every claim against actual result data before submission.

Verifies every bibliographic entry in a paper for existence, metadata accuracy, and contextual support using web/DBLP/arXiv lookups, flagging hallucinated authors, wrong years, fabricated venues, and misattributed citations.

Audits a paper draft by tracing every numeric claim and assertion back to result files on disk, flagging untraced, mismatched, stale, uncited, and phantom references.

Compress the entire current conversation into a clean, structured handoff document that lets a new chat session, a colleague, or future-you resume the work without losing decisions, constraints, or progress. Use this skill whenever the user says "handoff", asks to summarize the thread to continue elsewhere, mentions hitting context limits or the chat getting too long, wants to brief a teammate on this conversation, or asks to export or save where things stand. ALSO offer it proactively when a long working thread is clearly winding down or the user says they'll "pick this up later". Do NOT use for summarizing external documents or meetings; this skill summarizes the conversation itself.

Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Professional LaTeX formatting, strategic analysis frameworks (Porter's Five Forces, PESTLE, SWOT, TAM/SAM/SOM, BCG Matrix), and deep research integration.

Generate and rank theory-first or proof-oriented research ideas. Use when the user wants non-experimental research ideas, theoretical methods, proof programs, theorem candidates, impossibility results, convergence/sample-complexity analyses, or "analysis" variants of idea creation.

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.

Verifies that every number, comparison, and scope claim in a research paper matches raw result files, using a fresh cross-model reviewer with no prior context to prevent confirmation bias.

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.

Provides nine skills for Nature-journal-family academic publishing, covering figure creation, prose polishing, manuscript writing, citation formatting, data availability statements, paper reading, reviewer responses, paper-to-PPT conversion, and academic search via an MCP server.