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Lukecele/README.md
Luca Celebrano — Medicine, Computational Oncology & Bioinformatics

Luca Celebrano

Medical Student / MD Candidate at Università degli Studi di Napoli Federico II
Department of Clinical Medicine and Surgery · School of Medicine and Surgery · Naples, Italy
ORCID: 0009-0007-0931-3555 · LinkedIn · l.celebrano@studenti.unina.it

Computational Oncology · Biophysical Reaction-Diffusion Modeling · Spatial Multi-Omics · Digital Pathology AI


Open Flagship in Colab 60 FPS Simulator MedTerminal Cardio-Toracico Bioconda Hugging Face

Target: Nature Communications Research Square DOI Master Zenodo DOI Full Manuscript PDF PyPI Release bio.tools Registry nf-core Modules


⚡ Featured Flagship Systems (Try in 1-Click)

Project What It Solves & Why It Matters 1-Click Access & Verified Production
👑 Spatial Continuum Oncology Why do 68% of lung cancers relapse post-ADAURA?
Biophysical reaction-diffusion solver resolving why drug-sensitive persister cells survive in a 34.1 $\mu$m unperfused sanctuary cuff ($K_0$ Bessel decay).
Open in Colab
🎮 60 FPS Simulator · 🏥 Web App
Bioconda
🩺 MedTerminal Cardio-Toracico High-Yield Medical Exam Prep & Active Recall Engine
Piattaforma didattica interattiva per studenti di medicina che demolisce lo studio mnemonico noioso: modelli 3D WebGL (Three.js), monitor ECG dinamici per riconoscere aritmie e STEMI al volo, fonoteca Littmann reale e quiz d'esame commentati.
▶ Prova la Piattaforma Didattica ↗
React 19 · TypeScript · Three.js (Live Production)
👁️ InSituVision-AI Ultra-Low-Cost (< €5) Diagnostic AI
Deep learning Attention-MIL neural network predicting microvascular decoupling and relapse risk directly from routine H&E whole-slide images.
🌐 Live Vision Portal
Awesome AI4Path
PyTorch Attention-MIL
📐 Spatial Oncology Master Bessel $K_0$ Analytical Solver & MSKCC Validation ($N = 604$)
Cylindrical reaction-diffusion transport solver, Monte Carlo parameter sensitivity (10k draws), and stage-adjusted Cox modeling on real clinical cohorts.
Bioconda
🐳 Docker GHCR · 🌐 Web Portal
Springer Journal of Mathematical Biology

🔬 Scientific Research: Computational Oncology Program

Translational oncology and computational biophysics program investigating non-genetic targeted therapy resistance, reaction-diffusion drug transport, and low-cost diagnostic AI in EGFR-mutant non-small cell lung cancer (NSCLC). Affiliated with the Department of Clinical Medicine and Surgery, School of Medicine and Surgery, Università degli Studi di Napoli Federico II, Naples, Italy.

👑 Flagship Manuscript & Dissemination Dossiers

Conditions for Pharmacological Sanctuaries in Perivascular Tumour Cords: A Reaction–Diffusion Analysis, a Regrowth-Kinetics Identity, and a Descriptive Survival Analysis of Histologic Subtype in Resected Lung Adenocarcinoma
Target Journal: Nature Communications (Under Consideration, Tracking NCOMMS-26-091227)
Preprint DOI: 10.21203/rs.3.rs-11530312/v1 | Zenodo Master Archive: 10.5281/zenodo.23754999


🤗 Hugging Face Academic Organization: spatial-continuum-lab

Official clinical AI and computational biology laboratory of Università degli Studi di Napoli Federico II on Hugging Face:
🔗 huggingface.co/spatial-continuum-lab

┌────────────────────────────────────────────────────────────────────────┐
│               🤗 spatial-continuum-lab (Federico II)                   │
├────────────────────────────────┬───────────────────────────────────────┤
│ 🩺 Bedside CRI Decision Engine │ Official bedside clinical risk web app│
│    (Interactive Space)         │ https://huggingface.co/spaces/        │
│                                │ spatial-continuum-lab/                │
│                                │ spatial-continuum-clinical-app        │
├────────────────────────────────┼───────────────────────────────────────┤
│ 🧬 Biophysical Digital Twin    │ 60 FPS perivascular reaction-diffusion│
│    (Simulator Space)           │ https://huggingface.co/spaces/        │
│                                │ spatial-continuum-lab/simulator       │
├────────────────────────────────┼───────────────────────────────────────┤
│ 📊 MSKCC LUAD Spatial Cohort   │ Curated multicenter cohort (N=1,274)  │
│    (Public Dataset)            │ https://huggingface.co/datasets/      │
│                                │ spatial-continuum-lab/                │
│                                │ mskcc-lung-adenocarcinoma-spatial-... │
└────────────────────────────────┴───────────────────────────────────────┘

🔬 Computational Oncology Program: Modular Research Suites

Research Repository Biophysical & Algorithmic Scope Clinical Cohort / Evidence Interactive Demos & Registries
👑 Spatial Continuum Oncology Grand Unified Theory: Full reaction-diffusion continuum, modified Bessel $K_0$, regrowth kinetics, Bedside CRI, and Phase III SG-ADAURA trial allocation. Multi-scale continuum • Zero third-party dependencies • Pure Python stdlib Grand Unified Portal
Bioconda
Reaction-Diffusion Solver Biophysical Transport: Perivascular cords, sanctuary sleeves ($\Delta r = r_{\text{ox}} - r_{\text{crit}}$), and multi-scale pharmacokinetics. MSKCC clinical survival validation ($N = 604$) • SciPy ODE solver Module 1: Bedside CRI
Bioconda
Study 4: InSituVision-AI Ultra-low-cost (< 5 €) diagnostic AI: Attention-MIL neural network predicting microvascular decoupling directly from routine H&E WSIs. $N = 570$ TCGA-LUAD cases • PyTorch Attention-MIL deep neural network Live Vision Portal
Awesome AI4Path
Study 3: Massive Validation Multi-cohort survival validation: Microvascular decoupling truncates median PFS from 78.6 to 24.0 mo ($p &lt; 10^{-15}$, $\text{HR} = 19.45$). $N = 854$ patients (TCGA-LUAD + GSE31210 + GSE301973) Module 5: Evidence
CI
Study 2: Spatial Architecture Subcellular transport limits: Microvascular decoupling in dense homotypic tumor sheets exceeding the $\lambda \approx 624,\mu\text{m}$ diffusion limit. 10x Visium HD ($211{,}104$ bins at $2,\mu\text{m}$ subcellular resolution) Module 2: Visium HD
CI
Study 1: InSituGame In situ evolutionary game assay: Infers tumor subclonal payoff matrices ($A$) and evolutionary adaptive therapy regimens from spatial transcriptomics. Pan-cancer ($20{,}093$ clinical spots) • Replicator dynamics solver Module 4: InSituGame
Bioconda

📦 Production Bioinformatics & Reproducibility Suite

All computational pipelines and CLI solvers are permanently packaged, versioned, and indexed in official public package managers:

# 1. Install the Grand Unified Spatial Continuum Framework (Flagship CLI)
conda install -c bioconda spatial-continuum

# 2. Or run via BioContainers Docker (Cloud / Cluster)
docker run --rm quay.io/biocontainers/spatial-continuum:1.0.2--pyhdfd78af_0 cri-calc --help

# 3. Or run via BioContainers Singularity (HPC / Hospital Clusters without root)
singularity exec https://depot.galaxyproject.org/singularity/spatial-continuum:1.0.2--pyhdfd78af_0 cri-calc --help

# 4. Install the In Situ Evolutionary Game Assay Engine
conda install -c bioconda insitugame

# 5. Install the Reaction-Diffusion Biophysical Sanctuary Solver
conda install -c bioconda spatial-sanctuary

🩺 Clinical Platforms & Medical Education

An interactive multimodal clinical simulation and educational platform developed for medical students at Università degli Studi di Napoli Federico II:

  • 3D Interactive WebGL Anatomy: Anatomical cardiac and thoracic models powered by Three.js.
  • Simulated Real-Time ECG Telemetry: Dynamic waveform rendering across normal sinus rhythm, conduction blocks, and acute STEMI/NSTEMI patterns.
  • Remastered Clinical Auscultation: High-fidelity audio syntheses of cardiac murmurs (AS, MR, AR) and respiratory lung sounds.
  • Active Recall Diagnostic Modules: Case-based clinical reasoning puzzles and bedside medical calculators.
  • Modern Web Stack: Built with React 19, TypeScript, Three.js, and Tailwind CSS v4.
    👉 Explore the live educational platform ↗

🌐 Verified Upstream Open-Source Contributions

A verified record of peer-reviewed and merged contributions across bioinformatics, computational oncology, and core software ecosystems:

🧬 Section A: Computational Biology, Omics & Registries

Ecosystem / Registry Pull Request & Contribution Scope Verification Status
Bioconda Recipes Official conda packaging: spatial-continuum v1.0.2 (#70930) Merged & Live
BioContainers Pre-built Docker (quay.io) & Singularity (.sif) images for spatial-continuum Live & Verified
Galaxy Project / IUC Official Galaxy tool wrapper for spatial-continuum (cri_calc) (#8838) PR Open (Under Review)
Snakemake Wrappers Official Snakemake pipeline wrapper for spatial-continuum (cri-calc) (#6233) PR Open (Under Review)
Bioconda Recipes Official conda packaging: insitugame v1.0.7 (#70893) Merged & Live
Bioconda Recipes Official conda packaging: spatial-sanctuary v2.2.2 (#70840) Merged & Live
nf-core / modules Nextflow DSL2 module: spatialcontinuum with Seqera Wave container (#13487) 100% CI Green
nf-core / modules Nextflow DSL2 module: insitugame with Seqera Wave container (#13471) 100% CI Green
nf-core / modules PostprocessGermlineCNVCalls output extension fix (#13080) Merged
nf-core / modules ABRA2 BAM index BAI snapshot pattern correction (#13039) Merged
Awesome-AI4DigitalPathology Digital pathology and spatial multi-omics additions (#28, #29) Merged
awesome-single-cell Spatial transcriptomics biophysics and continuum frameworks (#399, #404) Both Merged
awesome-healthcare Open-source clinical decision support and computational oncology indexing (#180) Under Review
Spatial Transcriptomics Tools Spatial pharmacokinetics and multi-scale biophysics catalog (#21) Under Review

💻 Section B: Core Systems & Developer Infrastructure

Ecosystem / Project Pull Request & Contribution Scope Verification Status
Angular Fix DevTools signal inspection buttons on host API support (#70986) Merged
viem Mainnet Plasma token definitions and Kortana EVM network support (#5108, #5136) Both Merged
Ethereum Lists Sonic mainnet RPC endpoint additions (#8730) Merged
DefiLlama Fee adapters, BSC telemetry, and yield protocol calibration (#9838, #9453) Both Merged

📬 Academic Credentials & Institutional Affiliation

Pinned Loading

  1. spatial-continuum-oncology spatial-continuum-oncology Public

    🔬 Why do 68% of lung cancers relapse post-ADAURA? Biophysical reaction-diffusion solver, 60 FPS simulator & 1-click Colab.

    HTML 1

  2. spatial-oncology-master spatial-oncology-master Public

    📐 Cylindrical Bessel K0 biophysical transport solver for perivascular tumour cords & pharmacological sanctuary sleeves.

    HTML 1

  3. spatial-architecture-osimertinib spatial-architecture-osimertinib Public

    🔬 10x Visium HD 2 µm subcellular spatial atlas uncovering perivascular transport limits (λ ≈ 624 µm) in EGFR-mutant NSCLC.

    Python 1

  4. spatial-game-assay spatial-game-assay Public

    🎮 In situ evolutionary game theory for spatial omics: inferring subclonal payoff matrices & Nash attractors in cancer.

    Python 1

  5. spatial-he-vision-study4 spatial-he-vision-study4 Public

    👁️ Ultra-low-cost (< €5) AI predicting lung cancer relapse from routine H&E biopsy slides via PyTorch Attention-MIL.

    Python 1

  6. spatial-massive-validation-study3 spatial-massive-validation-study3 Public

    📊 Multi-cohort clinical survival validation of microvascular decoupling across 854 lung adenocarcinoma patients (p < 10^-15).

    Python 1