CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

This is the personal academic website for Aditya Pratapa, a computational biologist and postdoctoral researcher at Duke University. The site is built using Quarto and is based on the Quarto Academic Website Template.

The repository is intended for deployment at adyprat.github.io.

About the Owner

Aditya Pratapa works at the intersection of computational biology, machine learning, and spatial biology. Key research areas include: - Multimodal spatial omics integration (SAME method) - Foundation models for biological imaging (USHER framework) - Gene regulatory network inference (BEELINE benchmark, published in Nature Methods) - Mathematical optimization for biological discovery (Fast-SL, CrossPlan)

Current position: Postdoctoral Associate, Duke University (Cell Biology, with Rohit Singh and Purushothama Rao Tata)

Education: PhD in Computer Science from Virginia Tech, MS from IIT Madras

Build Commands

# Preview site locally
quarto preview

# Render site (outputs to docs/)
quarto render

# Install Quarto extensions if needed
quarto add quarto-ext/fontawesome
quarto add schochastics/academicons

Repository Structure

  • _quarto.yml - Main site configuration (title, navbar, footer, theme)
  • index.qmd - Homepage with bio, links, and recent posts
  • publications.qmd - Publications list with citation badges
  • teaching.qmd - Teaching information
  • projects.qmd / projects.yml - Research projects
  • people.qmd / people/ - Team/collaborators
  • posts/ - Blog posts, news, events (categorized)
  • files/ - PDFs, images, includes
  • docs/ - Rendered output for GitHub Pages (publish from this directory)
  • _extensions/ - Quarto extensions (fontawesome, academicons)

Key Files to Customize

  1. _quarto.yml: Update site title, description, navbar links, footer, Google Analytics ID
  2. index.qmd: Replace bio, image path, social links, experience/education
  3. publications.qmd: Add publications with Dimensions/Altmetric badges
  4. files/nsf-biosketch.pdf: Replace with actual CV

Reference Materials

Owner’s research statement and CV source files are in: - demo/AP_res/ - Research statement (main.tex) - demo/AP_CV/ - CV source (cv.tex, all_publications_merged.tex)

Portrait image: imgs/AP_portait.jpg

Deployment

GitHub Pages should be configured to publish from the docs/ directory (not root). After running quarto render, commit the docs/ folder and push to deploy.