LitRadar 📡

Automated Literature Intelligence & Podcast Briefing Suite

An automated, dummy-friendly literature intelligence and podcast briefing suite targeting:

• Pillar 1: SHANK2 & Exon 24 Genetics (including ProSAP1 / CortBP1 synonyms & splice variants)
• Pillar 2: Anterior Cingulate Cortex (ACC) Synaptic Circuitry
• Pillar 3: Nanoscale Postsynaptic Density (Homer1, GluN1, GluA1, Scaffolding)
• Pillar 4: Pan-Expansion Microscopy (Pan-ExM) & Validated Antibodies
• Pillar 5: Synaptic Connectomics & 3D Circuit Reconstruction

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Tip

PRO-TIP FOR LAB MEMBERS & REPRODUCIBILITY: Back up your lab_config.env file to your personal cloud drive or secure password vault. When you switch computers, log into a shared microscope computer, or onboard a new workstation, simply drop your saved lab_config.env into this folder and all scripts are 100% configured instantly!

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Quickstart for New Users / Fresh Clones

Step 1: Clone the Repository

git clone https://github.com/allison714/LitRadar.git
cd LitRadar

Step 2: Run First-Time Setup (Takes ~60 seconds)

Double-click 00_First_Time_Setup.bat (or run python core/setup_wizard.py).

• The wizard automatically detects your Python/Anaconda environment, local Zotero database, and storage paths.
• Prompts for your name, recipient email (e.g., personal Gmail for weekly digests), and optional API keys.
• Tests your Zotero connection live and automatically installs missing Python packages.
• Generates your local lab_config.env (kept private by .gitignore).

Step 3: Run Any Launcher (Just Double-Click!)

The root directory contains 1-click batch launchers:

• 00_First_Time_Setup.bat: Interactive setup wizard (run whenever you need to update settings or onboard a new member).
• 01_Find_New_Papers.bat: Interactive paper finder. Search Europe PMC & PubMed with Boolean logic, filter by 4 journal scopes (All, Paywall/Top-Tier Flagships via Institutional VPN, Free/Open Access, Custom), deduplicate against Zotero, download PDFs to storage vault, and import directly to Zotero Cloud.
• 02_Retag_Zotero_Library.bat: Scans your entire 2,359+ Zotero library, filters out textbooks/books, detects matching literature, and uploads structured 4-tier tags to Zotero Cloud.
• 03_Run_Weekly_Surveillance.bat: Full autonomous weekly pipeline run (harvests all 5 pillars, deduplicates, classifies, downloads PDFs, generates Excel knowledge base, and compiles podcast dossiers).
• 04_Harvest_Foundational_Benchmarks.bat: Harvests the Top 20 all-time most-cited papers per pillar and generates 5 foundational "Master Class Intro" briefings for NotebookLM.
• 05_Export_NotebookLM_Bundle.bat: Date inspector & PDF packager for NotebookLM. Search your Zotero library by exact upload/arrival date, bundle all PDFs into an upload folder, and generate synthesis notes.
• Setup_Weekly_Scheduler.bat: Schedules Windows Task Scheduler to run surveillance autonomously every Sunday at 11:00 PM.
• Run_Diagnostic_Test.bat: Quick 30-day diagnostic dry run to verify all systems.

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Directory Architecture

LitRadar/
├── 00_First_Time_Setup.bat             <-- [FIRST STEP] Interactive questionnaire & environment validator
├── 01_Find_New_Papers.bat              <-- [DAILY SEARCH] Boolean discovery & Institutional VPN / OA filter
├── 02_Retag_Zotero_Library.bat         <-- [LIBRARY CLEANER] Scans 2,359+ items & syncs tags to cloud
├── 03_Run_Weekly_Surveillance.bat      <-- [SURVEILLANCE] Full 5-pillar weekly harvest & digest
├── 04_Harvest_Foundational_Benchmarks.bat <-- [PRIMERS] Harvests Top 20 landmark papers & intro podcasts
├── 05_Export_NotebookLM_Bundle.bat     <-- [NOTEBOOKLM] Filters Zotero by upload date & bundles PDFs
├── Setup_Weekly_Scheduler.bat          <-- Installs Sunday 11:00 PM background Windows Task
├── Run_Diagnostic_Test.bat             <-- 30-day diagnostic dry run
├── lab_config.env.example              <-- Clean template for new users & git tracking
├── lab_config.env                      <-- Member profile & credentials (ignored by git - private!)
├── .gitignore                          <-- Protects credentials, databases, and temporary caches
├── README.md                           <-- Visual manual & onboarding instructions
├── LitRadar_Code_and_Architecture_Guide.md <-- Educational code walkthrough & architecture guide
├── core/                               <-- Engine & Python modules (tucked away)
│   ├── config.py                       <-- Master settings loader & journal tiers
│   ├── find_new_papers.py              <-- Discovery engine
│   ├── retag_zotero_library.py         <-- Zotero library tagger
│   ├── zotero_sync.py                  <-- Zotero SQLite & Web API sync
│   ├── pdf_downloader.py               <-- Institutional PDF resolver (Institutional VPN)
│   ├── harvester.py                    <-- Multi-engine search APIs
│   ├── classifier.py                   <-- 4-tier AI tagging engine
│   ├── excel_generator.py              <-- Excel knowledge base manager
│   ├── podcast_prep.py                 <-- NotebookLM briefing dossier builder
│   ├── export_lm_bundle.py             <-- NotebookLM bundle exporter by date
│   ├── email_digest.py                 <-- HTML email generator & SMTP dispatcher
│   ├── harvest_foundational.py         <-- Top 20 cited paper harvester
│   ├── setup_wizard.py                 <-- Interactive onboarding logic
│   ├── main.py                         <-- Orchestrator CLI
│   └── requirements.txt                <-- Python dependencies
├── output/                             <-- Generated Excel files & HTML digests
└── podcast_briefings/                  <-- Markdown briefing packets for NotebookLM Audio Overviews