Paper Editor Guide
Generate publication-ready manuscripts with inline statistics that link back to source data.
Overview
The Paper Editor is a block-based writing environment where every statistic is traceable—click any number to see exactly where it came from.
┌─────────────────────────────────────────────────────────────────┐
│ 📄 Paper Editor [Export ▾] │
├─────────────────────────────────────────────────────────────────┤
│ │
│ # Results │
│ │
│ A total of [1,247 patients]¹ were included in the analysis. │
│ The mean age was [64.2 ± 12.3 years]² and [58.4%]³ were male. │
│ │
│ In multivariable analysis, elevated HbA1c was associated │
│ with increased mortality ([HR 1.42, 95% CI 1.18-1.71]⁴). │
│ │
│ ──────────────────────────────────────────────────────────── │
│ ¹ Source: master_dataset.patient_count │
│ ² Source: analysis_run_3.demographics.age │
│ ³ Source: analysis_run_3.demographics.sex_male_pct │
│ ⁴ Source: analysis_run_3.cox_results.hba1c │
└─────────────────────────────────────────────────────────────────┘
Generating Sections
AI-Generated Sections
MedTWIN can draft entire sections based on your analysis results.
Available sections:
| Section | What AI Generates |
|---|---|
| Abstract | Structured summary (Background, Methods, Results, Conclusions) |
| Introduction | Literature context, research gap, objectives |
| Methods | Study design, population, statistical methods |
| Results | Narrative with inline statistics, table references |
| Discussion | Interpretation, limitations, conclusions |
Generate a Section
- Click + Add Section
- Select section type (e.g., "Results")
- Click Generate with AI
- Review and edit the draft
Generation Options
Generation Settings:
# Style
journal_style: "JAMA" # NEJM, Lancet, JAMA, BMJ, custom
voice: "passive" # active, passive
# Content
include_all_results: true
highlight_significant: true # p < 0.05
# References
auto_cite: true
citation_style: "Vancouver" # Vancouver, APA, Harvard
Block-Based Editing
Block Types
The editor uses blocks, like Notion:
| Block | Shortcut | Use |
|---|---|---|
| Paragraph | Just type | Regular text |
| Heading | # |
Section headers |
| Table | /table |
Data tables |
| Figure | /figure |
Charts, images |
| Equation | /equation |
LaTeX math |
| Citation | /cite |
Literature references |
| Statistic | /stat |
Linked statistics |
Keyboard Shortcuts
| Action | Mac | Windows |
|---|---|---|
| Bold | ⌘B |
Ctrl+B |
| Italic | ⌘I |
Ctrl+I |
| Link | ⌘K |
Ctrl+K |
| Command palette | ⌘/ |
Ctrl+/ |
| Insert citation | ⌘⇧C |
Ctrl+Shift+C |
| Insert statistic | ⌘⇧S |
Ctrl+Shift+S |
Inline Statistics
Inserting Statistics
Type /stat or press ⌘⇧S to open the statistics picker:
┌─────────────────────────────────────────────────┐
│ Insert Statistic [Search] │
├─────────────────────────────────────────────────┤
│ 📊 From: Analysis Run #3 │
│ │
│ Demographics │
│ ├── n = 1,247 │
│ ├── age: 64.2 ± 12.3 │
│ ├── male: 58.4% │
│ └── ... │
│ │
│ Cox Regression │
│ ├── hba1c: HR 1.42 (1.18-1.71), p<0.001 │
│ ├── age: HR 1.04 (1.02-1.06), p<0.001 │
│ └── ... │
│ │
│ [Insert Selected] │
└─────────────────────────────────────────────────┘
Statistic Properties
Each inserted statistic has:
- Display format: How it appears in text
- Source reference: Which analysis/variable
- Lock status: Whether it updates with new analyses
Formatting Options
Click a statistic to customize:
HR 1.42 (95% CI: 1.18-1.71)
│
├── Format: [HR with CI] ▾
│ HR only
│ HR with CI
│ HR with CI and p-value
│ Full (HR, CI, p, n)
│
├── Decimals: [2] ▾
│
└── Lock to run: [Run #3] ▾
Latest run
Run #3
Run #2
Tables
Auto-Generated Tables
Tables are generated from your analysis:
Table 1: Baseline Characteristics
| Overall (N=1,247) | Survived (N=935) | Died (N=312) | P-value | |
|---|---|---|---|---|
| Age, years | 64.2 ± 12.3 | 62.1 ± 11.8 | 70.5 ± 11.2 | <0.001 |
| Male, n (%) | 728 (58.4) | 534 (57.1) | 194 (62.2) | 0.12 |
| HbA1c, % | 7.8 ± 1.4 | 7.5 ± 1.2 | 8.6 ± 1.5 | <0.001 |
Editing Tables
- Add/remove columns: Right-click header
- Sort rows: Click column header
- Format cells: Select cells → format menu
- Add footnotes: Click cell → Add note
Table Traceability
Every cell links to its source:
Cell: "64.2 ± 12.3"
├── Variable: age
├── Statistic: mean ± SD
├── Source: analysis_run_3.demographics
├── N: 1,247
└── [View computation details]
Figures
Insert Figures
Type /figure to insert:
- From Analysis: Charts generated by your analysis
- Upload Image: Your own figures
- Create Chart: Build a new visualization
Figure Types from Analysis
| Type | When Generated |
|---|---|
| Kaplan-Meier curves | Survival analysis |
| Forest plots | Regression results |
| ROC curves | Classification models |
| Box plots | Descriptive statistics |
| Bar charts | Categorical comparisons |
Figure Options
┌────────────────────────────────────────────┐
│ Figure Settings │
├────────────────────────────────────────────┤
│ Title: Kaplan-Meier Survival Curves │
│ Caption: [Auto-generated] ✓ │
│ Size: [Column width] ▾ │
│ Resolution: [300 DPI] ▾ │
│ Format: [PNG] ▾ │
│ │
│ Include in: │
│ ☑ Main text │
│ ☐ Supplementary │
│ │
│ [Update from Latest Analysis] │
└────────────────────────────────────────────┘
Citations
Add Citations
Type /cite or ⌘⇧C:
┌─────────────────────────────────────────────────┐
│ Insert Citation [Search] │
├─────────────────────────────────────────────────┤
│ 📚 Your Library (23 papers) │
│ │
│ Recently Added │
│ ├── Smith et al. (2023) - Diabetes outcomes │
│ ├── Jones et al. (2022) - HbA1c mortality │
│ └── ... │
│ │
│ 🔍 Search PubMed │
│ [ ] [Search]│
│ │
│ [Insert Selected] │
└─────────────────────────────────────────────────┘
Citation Styles
MedTWIN auto-formats citations:
| Style | Example |
|---|---|
| Vancouver | Smith et al.¹ |
| APA | (Smith et al., 2023) |
| Harvard | (Smith et al. 2023) |
| Numbered | [1] |
Smart Citations
AI suggests relevant citations as you write:
You typed: "Previous studies have shown that HbA1c is associated..."
💡 Suggested citations:
• Stratton IM et al. BMJ 2000 - HbA1c and complications
• Nathan DM et al. NEJM 2005 - Intensive glucose control
[Insert] [Dismiss]
Collaboration
Comments
Add comments to any block:
- Select text or block
- Click comment icon (or
⌘⇧M) - Type your comment
- Mention collaborators with
@
Track Changes
Enable track changes to see edits:
The mean age was [64.2]{+65.1+} ± 12.3 years
↑ deleted ↑ inserted
By: Dr. Smith | Jan 15, 2024
[Accept] [Reject]
Version History
Access previous versions:
- Click History in toolbar
- See all saved versions
- Preview any version
- Restore if needed
Export
Export Formats
| Format | Best For |
|---|---|
| Word (.docx) | Journal submission, editing |
| Sharing, final review | |
| LaTeX | Journals requiring LaTeX |
| Markdown | Version control, GitHub |
| HTML | Web publishing |
Journal Templates
Export with journal-specific formatting:
- JAMA
- NEJM
- Lancet
- BMJ
- PLOS ONE
- Nature Medicine
- Custom template
Export Options
Export Settings:
format: "docx"
template: "JAMA"
include:
title_page: true
abstract: true
main_text: true
references: true
tables: true # inline or end
figures: true # inline or end
supplementary: true
figures:
resolution: 300 # DPI
format: "TIFF" # PNG, TIFF, EPS
track_changes: false # include tracked changes
traceability:
include_source_notes: false # for internal review
Best Practices
Writing
- ✅ Let AI generate first draft, then edit
- ✅ Use inline statistics instead of typing numbers
- ✅ Add citations as you write, not after
- ✅ Use comments for collaboration
Statistics
- ✅ Lock statistics to specific analysis runs for submission
- ✅ Check that all statistics have valid sources
- ✅ Use consistent decimal places throughout
Before Submission
- ✅ Run Consistency Check to verify all stats match
- ✅ Export with journal template
- ✅ Download traceability report for your records
- ✅ Archive the analysis bundle
Troubleshooting
"Statistic not found"
The linked analysis may have been deleted. Options:
- Re-run the analysis
- Link to a different run
- Convert to plain text (loses traceability)
"Table won't format"
Tables must follow structure rules:
- First row = headers
- Consistent column count
- No merged cells (export handles merging)
"Export failed"
Check:
- All figures have valid sources
- No broken citation links
- File isn't too large (>50MB)