Alterlab Research Workflows

---
name: alterlab-research-workflows
description: "Runs AlterLab's packaged multi-agent academic workflows — citation audit, independent peer-review panel, claim stress-test, PRISMA dual-screening for systematic reviews, point-by-point rebuttal, grant mock panel, and literature map. In Claude Code they run as dynamic workflows (/alterlab-workflows:<name>) with genuinely independent agents, adversarial re-checks, and tallies computed in code; on claude.ai, the API, or anywhere without the Workflow runtime this skill runs the same stages as a staged playbook. Use when a research task needs many independent readers or a second, adversarial opinion at scale — auditing every citation in a manuscript, dual-screening hundreds of records, simulating a review panel or study section, drafting a response to reviewers, or mapping a field before a proposal. Part of the AlterLab Academic Skills suite."
license: MIT
allowed-tools: Read Write Edit Bash WebFetch WebSearch Task
compatibility: "Claude Code with dynamic workflows (paid plans or API access; v2.1.203+) runs the /alterlab-workflows:* commands; installing this plugin also installs alterlab-core, whose skills the workflows call. Other surfaces use the staged playbooks in references/. Database-backed stages use public scholarly APIs (Crossref, OpenAlex, PubMed, arXiv) and need network access."
metadata:
  skill-author: AlterLab
  version: "1.0.0"
  last_updated: "2026-09-23"
  depends_on: "alterlab-citation-verifier, alterlab-paper-reviewer, alterlab-deep-research (alterlab-core); optionally alterlab-openalex, alterlab-pubmed, alterlab-arxiv, alterlab-literature-review, alterlab-meta-analysis, alterlab-research-grants, alterlab-tubitak-proposal, alterlab-paper-writer"
---

# AlterLab Research Workflows

Seven academic jobs are too big or too judgment-sensitive for one pass of one model: checking
every citation in a 90-reference paper, dual-screening 800 abstracts, getting reviewers who
can't anchor on each other. This skill packages each as a **workflow** — a fixed orchestration
of many agents with the independence and adversarial checks the task needs, and with counts,
votes, and agreement statistics computed in code rather than estimated by a model.

In Claude Code each workflow is a saved dynamic-workflow script shipped by the
`alterlab-workflows` plugin. Everywhere else, follow the staged playbook for the same workflow
in `references/` — same stages, same acceptance rules, run sequentially.

## When to Use This Skill

- Audit **every** reference and cited claim in a manuscript, thesis, or grant before submission
- Get a **peer-review panel** whose reviewers work blind to each other, with each major concern checked against the text
- **Stress-test** a paper's headline claims against counter-evidence, citation support, and inferential logic
- **Screen records** for a systematic or scoping review with two independent screeners and adjudication (PRISMA 2020)
- Draft a **point-by-point response to reviewers** that is internally consistent and never invents results
- Run a **mock study section** for a grant on the funder's own criteria and scale (NIH, NSF, ERC, Horizon Europe, TÜBİTAK)
- **Map a literature**: themes, landmark works, methods, and research gaps that survive a search for existing answers

### Does NOT Trigger

| Scenario | Use Instead |
|----------|-------------|
| Checking a handful of references, or one bibliography file | `alterlab-citation-verifier` (the tool the audit calls) |
| A single-pass review report in one context | `alterlab-paper-reviewer` or `alterlab-peer-review` |
| The full research → write → review → revise pipeline for one paper | `alterlab-research-pipeline` |
| Designing a custom multi-agent workflow, or learning the orchestration patterns | `alterlab-workflow-orchestration` |
| An investigative, cited research report on an open question | `alterlab-deep-research` (or Claude Code's bundled `/deep-research`) |
| Full-text extraction, risk-of-bias, and pooling after screening | `alterlab-literature-review`, `alterlab-meta-analysis` |
| Writing the grant itself | `alterlab-research-grants`, `alterlab-tubitak-proposal` |

If the user doesn't know which skill fits, `alterlab-skill-finder` routes; it launches these
workflows in its orchestrate (`alterflow`) mode.

## The Workflows

| Command (Claude Code) | What it does | Input (`args`) | Agents, typical | Composes |
|---|---|---|---|---|
| `/alterlab-workflows:citation-audit` | Existence + metadata of every reference; support for every cited claim; each flag re-checked by two independent searchers before it is reported (TF/PAC/IH/PH/SH taxonomy) | path, or `{path, mailto?, out?}` | 10–40 | alterlab-citation-verifier |
| `/alterlab-workflows:review-panel` | 4–6 blind reviewers chosen for the paper's field and design; every major concern re-read against the manuscript; editor decision + revision roadmap | path, or `{path, venue?, field?, lenses?, out?}` | 8–20 | alterlab-paper-reviewer (field analysis) |
| `/alterlab-workflows:claim-stress-test` | 3 skeptics per headline claim (counter-evidence, citation support, inference); majority rating + calibrated rewrites | path, or `{path?, claims?, max_claims?, out?}` | 10–30 | alterlab-deep-research, alterlab-citation-verifier |
| `/alterlab-workflows:systematic-review-screening` | Codebook → optional database searches → de-duplication → two blinded screeners per batch → third-reviewer adjudication → PRISMA 2020 flow + Cohen's κ | `{question, records?, include?, exclude?, databases?, max_per_database?, batch?, out_dir?}` | 2 per batch of 25 records, plus adjudication | alterlab-pubmed, alterlab-openalex |
| `/alterlab-workflows:rebuttal` | Reviews split into atomic comments; one drafter per comment; a consistency pass across all drafts; response letter + change log + author action list | `{manuscript, reviews, out_dir?, tone?}` | 1 per comment + 3 | alterlab-paper-writer (revision) |
| `/alterlab-workflows:grant-mock-panel` | Funder criteria and scale → primary, secondary, tertiary reviewer + skeptic → major weaknesses checked → score spread computed → summary statement | `{path, funder, mechanism?, out?}` | 8–20 | alterlab-research-grants, alterlab-tubitak-proposal |
| `/alterlab-workflows:literature-map` | 4–6 search angles swept in parallel → merged in code → themes → each proposed gap searched for existing answers → field map | topic, or `{topic, seeds?, years?, out_dir?}` | 10–25 | alterlab-openalex, alterlab-pubmed, alterlab-arxiv, alterlab-citation-graph |

Each workflow writes its deliverable to a file in the working directory (the default name is in
its playbook) and returns a short summary plus the key numbers.

## Running a Workflow in Claude Code

1. **Install once**: `/plugin install alterlab-workflows@alterlab-academic-skills` (this also
   installs `alterlab-core`). Dynamic workflows need a paid plan or API access; on Pro, enable
   them under `/config` → Dynamic workflows.
2. **Launch** with the command and its input, or in plain words — Claude passes structured
   arguments for you:
   `/alterlab-workflows:citation-audit manuscript/paper.tex` ·
   `Run the AlterLab systematic-review-screening workflow on records.ris for the question "…" excluding non-English studies`.
3. **Approve** the run in the permission prompt (it lists the phases). Allow the tools the agents
   need (Bash for the verifier scripts, WebFetch/WebSearch for lookups) so a long run is not
   stopped by prompts.
4. **Watch** with `/workflows`; each phase shows agent counts and tokens. A stopped run resumes
   in the same session with completed agents cached.

**Before a large run, say what it will cost.** A workflow spawns many agents, so tell the user
the expected agent count from the table above and offer a small first slice — one chapter's
references, 100 records, three claims. See `references/running-workflows.md` for arguments,
permissions, cost control, resuming, and troubleshooting.

## Running Without the Workflow Runtime

On claude.ai, the API, or Claude Code with workflows disabled, run the same stages from the
workflow's playbook — `references/<workflow>.md`. The playbooks preserve what makes each
workflow trustworthy:

- **Independence.** Where a workflow uses separate agents (screeners, reviewers, skeptics), use
  separate subagents via the Task tool when the surface has one. Without subagents, complete each
  independent pass fully and record its output *before* starting the next, and never revise an
  earlier pass after reading a later one — the order-effect the separate agents exist to prevent.
- **Code for arithmetic.** Tallies, majority votes, agreement statistics, and score spreads are
  computed with a short script (the playbooks give the formulas), not estimated.
- **The same acceptance rules.** A citation flag stands only after two independent failed
  attempts to clear it; a major review concern stands only after the manuscript is re-read.

Scale the sequential run down to what one conversation can hold, and tell the user what was left
out (for example "references 1–40 of 112 audited").

## Choosing a Workflow

- The document is a **draft about to be submitted** → `citation-audit`, then `review-panel`.
- The user asks **"does my argument hold?"** → `claim-stress-test`.
- A **decision letter arrived** → `rebuttal` (then `citation-audit` on the revised draft).
- A **systematic or scoping review** is underway → `systematic-review-screening`, then
  `alterlab-literature-review` for full text and `alterlab-meta-analysis` for pooling.
- A **grant deadline** is weeks away → `grant-mock-panel`; an early-stage idea → `literature-map`.
- The request doesn't fit any of these → hand-design with `alterlab-workflow-orchestration`.

## Quality Standards

| Standard | What it means here |
|---|---|
| Evidence before verdicts | Every flag, concern, or gap carries a source (DOI/URL) and a verbatim quote, or the searches that came up empty. |
| No fabrication | Agents report only works they retrieved; results only the authors have become `[AUTHORS: …]` placeholders. |
| Lookup failure ≠ fabrication | A reference that could not be checked (network, rate limit) is `UNVERIFIED`, never `NOT_FOUND`. |
| No silent caps | When a workflow bounds coverage (claims, records, gaps), it logs what was left out and says so in the report. |
| Human sign-off | Screening decisions, integrity flags, and review decisions are drafts for the researcher to confirm. |
| AI disclosure | Every deliverable ends with an AI-assistance statement suitable for journal or funder policies. |

Measurable checks when reviewing a workflow's output: every row in an integrity table has
evidence; PRISMA numbers add up (identified − duplicates = screened; screened − excluded =
sought for retrieval); the κ and agreement values match the decision files; no reference in a
literature map lacks a DOI or URL.

## Edge Cases

- **No reference list / no claims / no records** — the workflow stops early and says so; nothing is invented to fill the gap.
- **Paywalled sources** — claim checks fall back to the abstract and mark `UNCHECKABLE` when that isn't enough.
- **Very large inputs** — citation-audit caps checked claims at 150 and screening at 2,000 records per run, and logs the remainder.
- **Non-English material** — agents work in the source language; reports follow the user's language.
- **Funder without published scoring** — the grant panel uses the funder's written criteria, notes the absence of a numeric scale, and scores on the scale it states.

## Resources

- `references/running-workflows.md` — install, arguments, permissions, cost, resume, troubleshooting
- `references/citation-audit.md` · `references/review-panel.md` · `references/claim-stress-test.md`
- `references/systematic-review-screening.md` · `references/rebuttal.md`
- `references/grant-mock-panel.md` · `references/literature-map.md`
- Workflow scripts: `../workflows/<name>.js` in this plugin (plain JavaScript you can read and adapt)

Part of the AlterLab Academic Skills suite.