Paper Submission Manager

Overview

Guide the full handoff from manuscript finalization to journal submission, keeping files organized, requirements satisfied, and acceptance odds improved through a structured, quality-first workflow.

Workflow Decision Tree

Choose the shortest path that matches the request:

1. New submission target: run Intake -> Plan -> Package -> QA.
2. Existing submission folder: jump to QA -> Package -> Tracking.
3. Single artifact update (cover letter/figures/forms): update the artifact, then run QA.

Step 1: Intake & Target Selection

Identify the target journal and the most current submission bundle:

• Prefer the newest dated folder (e.g., 20260210_CSBJ/) if it matches the target.
• If no folder exists, plan to create a new dated folder like YYYYMMDD_Journal/.
• Locate journal instructions inside the target folder if present (e.g., Instructions for Authors.md).

Step 2: Build the Submission Plan

Create a checklist that maps requirements to files:

• Manuscript: manuscript-full.docx and/or Somatic Mechanotherapy Activates a Spatiotemporally Synchronized CPTC.md
• Figures: figs/ or figs_for_cellreports/
• Cover letter and forms: in the target folder (e.g., 01_Cover_Letter_*.md)
• Suggested reviewers, declarations, questionnaires: target folder

Use references/submission-checklist.md as the baseline checklist, then customize.

Step 3: Prepare & Normalize Files

Ensure consistent naming and content alignment:

• Keep figure filenames consistent with manuscript references (e.g., Fig.1.pdf, Supplementary Figure 1.ai).
• Keep cover letters aligned with the target journal name and submission type.
• When duplicating bundles, copy from the latest folder and update dates and journal-specific sections.

Step 4: Quality Assurance

Run a short QA pass before submission:

• Manuscript: title, abstract, keywords, references, and figure callouts match.
• Figures: resolution, labeling, and legend consistency; check for missing panels.
• Forms: conflicts-of-interest, funding statements, author info, and required checkboxes.

Step 5: Submission Package & Tracking

Assemble the final package in the target folder and log submission metadata:

• Include a brief submission summary (date, journal, version tag).
• Record any confirmations or submission IDs in a short note file.

References

Use the reference files when needed:

• references/submission-checklist.md: baseline checklist and QA items.
• references/journal-intake.md: intake questions and bundle naming rules.