Skip to main content

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

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

  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

​
Step 2: Build the Claims Table

The claims table is the backbone of your paper. Every scientific assertion must be backed by evidence. 
# View the claims table
hubify paper claims paper-1
#ClaimEvidenceConfidenceStatus
1”Matter bounce predicts f_NL = -4.375”EXP-031, Branch VHighVerified
2”NANOGrav signal consistent with bounce”EXP-042, gamma=3.0MediumVerified
3”Quintom-B favored at 2.3 sigma”EXP-048, w0-wa MCMCMediumUnder review
# 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: 
# 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: 
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: 
# 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

LaTeX compilation requires texlive-publishers (for revtex4-2). This runs on a GPU pod, not locally.
# 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

# 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 following their submission guidelines.

​
Tracking Readiness

Monitor paper progress in the readiness dashboard: 
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