> ## Documentation Index
> Fetch the complete documentation index at: https://hubify.com/docs/llms.txt
> Use this file to discover all available pages before exploring further.

# Publishing Papers

> End-to-end guide for taking experiment results through the paper pipeline to arXiv submission.

# Publishing Papers

This guide covers the full workflow from experiment results to a published paper on arXiv. Hubify Labs handles drafting, review, compilation, and submission packaging.

## Overview

```
Experiments → Claims Table → Outline → Draft → Review → Revise → Compile → Submit
```

The paper pipeline is agent-assisted at every step, but you maintain full editorial control.

## Step 1: Create a Paper

<Tabs>
  <Tab title="Web UI">
    1. Go to **Papers** in the sidebar
    2. Click **New Paper**
    3. Enter title, select template (`prd` for Physical Review D)
    4. The Paper Lead generates an initial outline based on your lab's completed experiments
  </Tab>

  <Tab title="CLI">
    ```bash theme={null}
    hubify paper create \
      --title "Observational Constraints on Bounce Cosmology" \
      --template prd
    ```
  </Tab>
</Tabs>

## Step 2: Build the Claims Table

The claims table is the backbone of your paper. Every scientific assertion must be backed by evidence.

```bash theme={null}
# View the claims table
hubify paper claims paper-1
```

| # | Claim                                    | Evidence            | Confidence | Status       |
| - | ---------------------------------------- | ------------------- | ---------- | ------------ |
| 1 | "Matter bounce predicts f\_NL = -4.375"  | EXP-031, Branch V   | High       | Verified     |
| 2 | "NANOGrav signal consistent with bounce" | EXP-042, gamma=3.0  | Medium     | Verified     |
| 3 | "Quintom-B favored at 2.3 sigma"         | EXP-048, w0-wa MCMC | Medium     | Under review |

```bash theme={null}
# Add a claim
hubify paper claim add paper-1 \
  --claim "SPHEREx can detect bounce f_NL at 4.7-12 sigma" \
  --evidence EXP-055 \
  --confidence high
```

## Step 3: Draft Sections

Agents draft sections in parallel. You can direct which experiments feed into which sections:

```bash theme={null}
# Have agents draft the full paper
hubify paper draft paper-1

# Or draft a specific section
hubify paper draft paper-1 --section results

# Review a section draft
hubify paper show paper-1 --section introduction
```

## Step 4: Cross-Model Peer Review

Run a structured peer review using multiple AI models:

```bash theme={null}
hubify paper review paper-1
```

The review checks:

* **Accuracy**, Are claims consistent with the data?
* **Completeness**, Are there missing analyses or citations?
* **Clarity**, Is the writing clear and well-structured?
* **Overclaiming**, Are conclusions justified by the evidence?
* **Novelty**, Does the paper clearly state what is new?

Review results appear as structured feedback with specific suggestions per section.

## Step 5: Revise

Apply review feedback:

```bash theme={null}
# Auto-apply review suggestions
hubify paper revise paper-1

# Apply specific suggestions
hubify paper revise paper-1 --apply "suggestion-3,suggestion-7"

# View revision history
hubify paper history paper-1
```

Each revision round is logged with a diff showing what changed and the rationale.

## Step 6: Compile to PDF

<Warning>
  LaTeX compilation requires `texlive-publishers` (for `revtex4-2`). This runs on a GPU pod, not locally.
</Warning>

```bash theme={null}
# Compile
hubify paper compile paper-1

# View the PDF
hubify paper open paper-1

# Check for issues
hubify paper compile paper-1 --check
```

The compiler verifies:

* Zero undefined references
* All figures embedded (PDF size should be 15-25 MB for a paper with 10+ figures)
* Correct page count
* Bibliography completeness

## Step 7: Package and Submit

```bash theme={null}
# Create arXiv submission package
hubify paper package paper-1 --output submission.tar.gz
```

The package includes:

* Compiled PDF
* LaTeX source (`.tex`)
* Figures (all PNGs)
* Bibliography (`.bib`)
* Supplementary data (if any)

Upload the package to [arxiv.org](https://arxiv.org) following their submission guidelines.

## Tracking Readiness

Monitor paper progress in the readiness dashboard:

```bash theme={null}
hubify paper status paper-1 --verbose
```

```
Paper: Observational Constraints on Bounce Cosmology
Status: In Review (Round 3)

Content:    ████████░░  80%  (6/7 sections drafted)
Figures:    ██████████  100% (11/11 placed)
Bibliography: █████████░  90%  (57/63 resolved)
Claims:     ██████████  100% (12/12 verified)
Compilation: ██████████  100% (0 errors)
Review:     ██████░░░░  60%  (3/5 rounds)

Overall Readiness: 88%
```

## Best Practices

* Lock claims **before** drafting, do not write sections around unverified claims
* Run reviews after **every** major revision, not just at the end
* Compile frequently to catch LaTeX issues early
* Use `revtex4-2`, not `aastex631`
* Keep figures in the same directory as the `.tex` file