Research

Distill the current conversation into a structured note (decisions made, open questions, file pointers with line numbers, next 1–3 actions) and save to `quality_reports/session_logs/` before auto-compression. Differs from `/checkpoint` (explicit stop-point snapshot) and from auto-compaction (which truncates rather than distills). Use when context is approaching auto-compact threshold, when a long pipeline has accumulated many decisions, or when the user says "compress", "distil this session",...

Compile a Beamer LaTeX slide deck with XeLaTeX (3 passes + bibtex). Use when user says "compile", "build the slides", "rebuild the PDF", "run latex", "render the tex", or asks why a `.tex` file isn't producing a PDF. Operates on `Slides/*.tex`.

Stage, commit, push, open a PR, and merge to main. Use ONLY on explicit commit intent — user says "commit", "ship it", "push this", "open a PR", "merge to main", "let's commit this", or prefixes with `/commit`. Do NOT auto-invoke on vague end-of-task phrases ("we're done", "wrap up") — those require explicit confirmation first. Runs the standard commit-PR-merge cycle; never force-pushes or skips hooks.

Generate a co-author / collaborator handoff brief for a multi-author, multi-machine project — summarizing what changed since the last brief (git delta), the current state of each artifact (manuscript, analysis, slides), open questions, how to reproduce locally, and any restricted-data access steps. Use when user says "coauthor brief", "handoff brief", "bring my coauthor up to speed", "what changed since last week", "onboard a collaborator", "write a handoff for [name]", or before sending a co...

Save a structured state snapshot before stopping or handing off. Captures the active plan, recent decisions, file pointers (with line numbers), open questions, and the next 1–3 actions into a checkpoint file under `quality_reports/checkpoints/`. Optionally proposes `[LEARN]` entries to add to MEMORY.md. Use when user says "checkpoint", "save state", "snapshot before I stop", "where am I", "wrap up the session for handoff", or before a long break / model switch / collaborator handoff. Companio...

Snapshot the computational environment for a replication package — detects the analysis stack (R / Stata / Python) and emits the right lockfiles (renv.lock + sessionInfo.txt, requirements.txt / environment.yml / uv.lock, Stata version + ado package list), records seeds and RNG kind, optionally writes a pinning Dockerfile, and produces a paste-ready "Computational requirements" block. Use when user says "capture the environment", "snapshot my dependencies", "pin the versions", "make a renv.loc...

Enforce the replication-protocol.md rule by cross-checking numeric claims in a manuscript against the actual R / Stata / Python outputs. Report PASS/FAIL per claim against tolerance thresholds. Use before submission and before releasing a replication package.

Manage the research project's vault — the clean, visible, templated project folder (research/<project>/) where every file lives in a numbered lifecycle-stage place, plus the knowledge layer (canonical facts like sample size / IRB# / journal, one shared bibliography, decisions log, open questions, glossary, voice profile, entities — pseudonyms only, never PII). Initializes the folder from a template, shows a summary, ORGANIZES loose files into the right stage folders, AUDITS every artifact aga...

Turn a paper (or several, a thesis, a body of work) into an academic talk — outline, per-slide content, speaker notes, opening hook, single take-home message, backup slides for Q&A, rehearsal plan. Adapts to talk length (3-min lightning through 90-min defense), audience (specialists / general field / cross-disciplinary / clinical / public), format (contributed / lightning / invited / plenary / keynote / symposium / workshop / defense / job talk / public lecture / course lecture), and discipli...

Design rigorous surveys and questionnaires — question wording, response scales, ordering, validation, pilot testing, and translation. Spots leading questions, double-barreled items, social desirability traps, and acquiescence bias. Recommends validated instruments where they exist instead of inventing new ones. Trigger when: user says "design a survey", "survey questions", "questionnaire", "Likert scale", "question wording", "is this question biased", "validated scale for", "survey pilot", or...

Draft a rigorous, polite, point-by-point response to reviewer comments on a journal or conference submission (R1 / R2 / R3 letters), plus the corresponding manuscript revisions. Categorizes each comment as concession / pushback / clarification needed / minor fix, drafts the response and the revision for each, and assembles a cover letter. Composes with `peer-review` (consume comments from a review output) and `manuscript-drafter` (revise prose using the manuscript's voice profile and academic...

Generate, sharpen, and pressure-test research ideas — research questions, hypotheses, study angles, novel contributions, and contrarian framings. Pushes beyond obvious next steps to find what's actually worth studying. Useful at the start of a project or when stuck. Trigger when: user asks to "brainstorm research", "generate research ideas", "research questions", "hypothesis ideas", "what should I study", "I'm stuck on what to research", "thesis topic ideas", "novel angles", "what's interesti...

Design a direct, conceptual, or generalization replication of a published study. Walks through identifying the target effect, extracting the original design with enough fidelity to replicate it, deciding what to hold equivalent vs. what to update, calculating sample size for adequate replication power (typically ~2.5x the original under reasonable assumptions), pre-registering the replication on OSF / AsPredicted, multi-site logistics if applicable, and statistically assessing replication suc...

Code qualitative data — interview transcripts, open-ended survey responses, field notes, documents, social media — using inductive, deductive, or hybrid approaches. Generates and refines codebooks, applies codes consistently, identifies themes, and supports inter-rater reliability checks. Includes NLP-assisted techniques (sentiment, topic modeling, embeddings) for exploring large corpora. Trigger when: user mentions "thematic analysis", "code transcripts", "qualitative coding", "codebook", "t...

Rigorous academic peer review in the voice of a seasoned professor. Two verdict modes (paper, homework), five alternative workflows (committee panel, fact-check audit, plagiarism-check, draft thinking-partner, presentation feedback), plus iterate mode for post-review dialogue. Auto-detects Hebrew or English and the work's academic domain (any field) and applies rigor criteria for that field. Annotates source documents at the relevant text / shape / page locations and returns a reviewed file: ...

Advise on quantitative and qualitative research methodology — design, sampling, validity, reliability, measurement, ethics, analysis plan, and — mandatory in every methodology output — creative AI / ML / Big Data extensions tailored to the specific research question. The creative-extensions section is not optional: it forces researchers to consider non-conventional, modern methods before settling on a design. Trigger when: user asks about "study design", "research design", "methodology", "wha...

Draft long-form manuscript sections — abstract, introduction, related work, methods, results, discussion, limitations, conclusion — from a methodology document and an analysis report. Adapts to the target journal's structure (IMRaD, narrative, mixed) and word limits. Preserves the existing manuscript's voice, enforces hard per-section word budgets, holds to an academic register (no colloquialisms, no conversational openers, no vague quantifiers), and grounds every new idea in the user's bibli...

Conduct rigorous, fact-checked academic literature reviews. Synthesizes sources, traces citation chains, flags weak claims, and produces structured outputs (narrative, systematic, scoping, or thematic). Trigger when: user asks for a "literature review", "lit review", "background research", "state of the field", "what does the research say about…", "summarize the literature on…", "find sources on…", or runs /lit-review. Works from sources the user provides (PDFs, links, citations) AND from web...

Draft sections of a grant proposal — specific aims / lay summary / significance / innovation / approach / broader impacts / budget justification / data management plan / biosketch — adapted to the funder's format and review criteria. Supports NSF, NIH (R01, R21, R03, F31, F32, K-series), ERC (Starting, Consolidator, Advanced), Wellcome, Horizon Europe, NSF GRFP, foundation grants, and other major schemes. Works from research-brainstorm and methodology-advisor outputs, plus the funder's publis...

Act as a research ethics committee — stress-test a protocol the way an IRB / REC / HREC would. Reviews informed consent, risk-benefit balance, vulnerable populations, data privacy, deception, debriefing, payment, dual-use risks, AI/LLM use in research, and equity in recruitment. Produces a committee-style decision letter with required revisions, recommended changes, and approval pathway. Useful before IRB submission, when responding to IRB feedback, when drafting ethics sections of a paper or...

End-to-end quantitative data work — cleaning, exploration, statistical testing, modeling, visualization, and reproducible scripting in Python or R. Handles messy CSVs, survey data, time series, panel data, and small-to-medium datasets. Produces analysis scripts and a written interpretation. Trigger when: user mentions "clean this data", "analyze", "statistics", "regression", "EDA", "explore the data", "fit a model", "visualize", "summary stats", "hypothesis test", "ANOVA", "t-test", "correlat...

Format citations and bibliographies in any major academic style — APA 7, MLA 9, Chicago (notes-bibliography and author-date), Harvard, Vancouver, IEEE, AMA, and discipline-specific journal styles. Converts between formats, builds reference lists from raw input, validates DOIs, and generates BibTeX/RIS exports. Trigger when: user asks to "format this citation", "convert to APA", "bibliography in Chicago", "reference list", "BibTeX", "fix my references", "is this APA correct", or runs /cite.

Podcast knowledge workflows powered by Podwise CLI: search podcasts and episodes by keyword, monitor followed shows for new releases, find popular episodes, ask questions and extract insights from transcript content, process Podwise episode URLs, YouTube videos, Xiaoyuzhou links, and local audio or video files to retrieve transcripts, summaries, chapters, Q&A, mind maps, highlights, and keywords — plus catch up on your backlog, refine your listening taste, generate weekly recaps, export episo...

End-to-end research brainstorming and first-paper construction workflow from raw idea or materials to research spine, study design, evidence bank, first draft, and audit.