stanislavjiricek/phase-paper

phase-paper

The paper phase produces a reviewed and approved neuroscience manuscript. Every section draft is subjected to a brutal paper-writer → paper-critic loop before it is saved. Nothing reaches disk without critic approval or an explicit user decision to accept an unresolved draft.

Approach

• Read upstream phase flows (ideation, data-analyze, experiment) before drafting — pull facts from memory, not from recall
• Confirm target journal before writing any section; it determines structure, length, style, and the critic's review persona
• Draft section by section in logical order; write the abstract last
• Distinguish what the results show (Results) from what they mean (Discussion) — flag if they become conflated
• Every section draft is routed through the paper-critic agent using the full eight-area neuroflow:review-neuro methodology before saving
• Nothing is saved to output_path without a [STATUS: APPROVED] verdict or explicit user acceptance of an unresolved draft

Relevant skills

• neuroflow:neuroflow-core — read first; defines the command lifecycle and .neuroflow/ write rules
• neuroflow:worker-critic — defines the multi-agent revision loop protocol (max 3 iterations per section)
• neuroflow:review-neuro — the eight-area review methodology used by the paper-critic agent on every draft
• neuroflow:humanizer — run on every drafted section before the critic review; strips AI signatures, fixes rhythm, and calibrates register so the prose reads as genuinely human-authored
• neuroflow:notebooklm — use when the user wants a podcast, slide deck, or infographic generated from manuscript sections

Two-agent write→critique loop

The loop runs section by section, strictly following the neuroflow:worker-critic protocol:

1. paper-writer receives the task, upstream memory, journal target, and rubric — drafts the section
2. paper-critic receives the draft and rubric — applies the full six-area review-neuro methodology — returns [STATUS: APPROVED] or [STATUS: REJECTED] with specific actionable feedback
3. On REJECTED: paper-writer receives the draft and the critic's feedback — revises, addressing each bullet specifically
4. Loop repeats until APPROVED or three iterations are exhausted

On the third rejection the loop halts. The orchestrator presents draft v3 and the unresolved critique to the user, appends the critique to .neuroflow/paper/critic-log.md, and asks whether to continue with the next section.

After each section verdict (approved or halted), immediately — before moving to the next section:

• Append a one-liner to .neuroflow/sessions/YYYY-MM-DD.md recording the section name, outcome, and iteration count
• If any framing or scope decision was made, append it to .neuroflow/reasoning/paper.json

Write session and reasoning entries immediately after each section verdict — if the session is interrupted, the record must already reflect completed work.

Critic standards

The paper-critic agent applies the FULL eight-area neuroflow:review-neuro methodology to every draft — including partial section drafts. The eight areas are:

1. Language, Style & Terminology — spelling, grammar, notation, neuroscience terminology errors, causality language
2. Internal Consistency & Cross-Reference Integrity — figure/table references, value consistency across sections
3. Claim Support, Causality Language & Connectivity Interpretation — overclaims, causality creep, FC over-interpretation
4. Statistics, Network Inference & Multiple Comparisons — effect sizes, correction procedures, null models, estimator specification
5. Methods Reproducibility, Reporting Standards & Open Science — COBIDAS/ARRIVE compliance, data/code availability
6. Contribution, Novelty & Journal Fit — novelty assessment, prior work comparison, journal fit, referee recommendation
7. Literature Gap — whether key prior work is cited; uses Zotero or .neuroflow/ideation/papers/ as reference database
8. Figure Review — colormaps, font sizes, caption completeness, axis labels, figure–text consistency

A section is approved only if it would survive peer review at a top-tier neuroscience journal. The bar is not "acceptable draft" — it is "ready for submission".

Journal recommendation

If the user has not set a target journal and requests recommendations:

1. Read project_config.md for modality, research question, and tools.
2. Read .neuroflow/ideation/ if it exists for topic keywords and collected literature.
3. Use the scholar agent to search PubMed and bioRxiv for recent papers (past 3 years) in the same area. A journal is considered recurring if it appears in at least 3 of the top 20 results.
4. Rank 3–5 candidate journals using these criteria (in order of priority):
   • Scope alignment — does the journal publish this modality and methodology?
   • Paper type fit — empirical, methods, review, brief communication?
   • Open access — required, preferred, or irrelevant for this project?
   • Typical length — does the journal's word-count range suit the planned manuscript?
   • Prestige vs. speed — balance impact factor with typical time-to-decision
5. Present the shortlist in priority order. For each journal: name, publisher, one-sentence scope, why it fits this project, notable constraints (page limits, OA fees, data sharing policy).
6. Ask the user to pick or skip. If they pick, write target_journal: <name> to project_config.md — this is the authoritative location. Also write it to .neuroflow/paper/flow.md only if that file already exists — do not create the folder or file.

Output paths

| What | Where | |---|---| | Approved section drafts, final manuscript | output_path (default: manuscript/) — outside .neuroflow/ | | Phase memory, plans, critic logs | .neuroflow/paper/ | | Critic loop state per section | .neuroflow/paper/critic-log.md | | Scope and framing decisions | .neuroflow/reasoning/paper.json |

Log any framing or scope decisions that differ from the original research question in .neuroflow/reasoning/paper.json — ask before writing.

Slash command

/neuroflow:paper — runs this workflow as a slash command.