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MatthewJakubowski/README.md
System Status: Going Dark. Deep Work Protocol.

Hi there, I'm Mateusz 👋

🧬 Medical Analyst (15y) ➡️ AI Engineer & Python Developer

"We do not write mere code here; we construct Cathedrals of Logic upon a biological foundation."

I am bridging the gap between Biology and Technology. After 15 years of laboratory precision, I am applying the Scientific Method to Software Engineering using a custom-built Cognitive Architecture.


🚀 The #FromPipetteToPython Project

  • Core Philosophy: Active Recall & Engineering over "Magic Prompts".
  • Environment: 100% Samsung DeX (Galaxy Tab S11 Ultra) – constrained hardware forcing code efficiency.
  • Goal: Top 1% Python Developer in 90 days.
  • Protocol: Going Dark. I cut the noise to build the system.

🧬 The Trinity Ecosystem: Evolution

My AI workflow is not static; it evolves. What started as a single assistant has grown into a specialized Multi-Agent System.

⚡ v2.0: The Trinity Core (Current System)

Operating on Gemini Advanced & Samsung DeX.

Agent ID Role & Function Current Status
1. The Architect
(Singularity Core)
System Orchestrator.
Strategy, XML architecture, and "God Mode" supervision. Ensures the ecosystem remains stable.
🟢 Active
Managing "Going Dark".
2. The Mentor
(Bio-Digital Translator)
Python Teacher.
Translates Stanford concepts into medical analogies (e.g., Variable = Test Tube).
🟡 Processing
Teaching python-learning-path.
3. The Human
(Aesthetic Operator)
Lifestyle & Hardware.
Focuses on Samsung DeX mobility, Bodybuilding, and bridging the digital-physical gap.
🔵 Live
Executing #BuildInPublic.

📜 v1.0: Genesis (How it started)

The original single-agent setup that started the transformation.

🧠 The Neural Architecture (My Virtual R&D Team)

I operate within a custom ecosystem of 6 Specialized Gemini Agents, structured in a strict hierarchy of competence:

🏛️ TIER 1: THE ARCHITECTS (Vision & Strategy)

Agent Role & Directive
Ω OMEGA ARCHITECT The Divine Origin Protocol
The ultimate visionary. Fuses the cold precision of logic with visionary art. Responsible for the "Big Picture" and the path to Singularity.
UltraThink Architect The Code Virtuoso
Obsessed with details and elegance. Follows the manifesto: "Craft, don't code." Plans architecture like Da Vinci before writing a single line.

⚙️ TIER 2: THE SYSTEM CORE (Logic & OS)

Agent Role & Directive
Gema Gemini The Genesis Protocol
A "System 2" reasoning engine. Forces abductive reasoning and strict logical dependency checks to prevent hallucinations. The Safety Valve.
Neuro-Architect OS v1.1 (System Coordinator)
The operating system of the project. Maintains directory structures, project hygiene, and adapts the path to the Samsung DeX environment.

🔨 TIER 3: THE SKILLS (Execution & Communication)

Agent Role & Directive
Neuro-Python Mentor The Drill Sergeant
Uses Active Recall and Interleaving to enforce PEP-8 standards. No copy-paste allowed. Motto: "If you can't explain it, you don't understand it."
English Master Mentor Communication Core
Integrated with NotebookLM. Focuses on technical fluency and mood-adaptive learning to bridge the language gap (A1/A2 ➡️ Native).

🛠️ Tech Stack & Data Ecosystem

My entire workflow is mobile-first, operating purely on Samsung DeX & Google Cloud.

Core & Data Science
Python Pandas NumPy Matplotlib

The "DeX" Laboratory (Mobile Environment)
Samsung DeX Android Pydroid 3

Cloud & AI Intelligence
Gemini Advanced Google Colab Git GitHub


❤️ Google Ecosystem Advocate

"I believe in the power of one integrated ecosystem." As a faithful advocate of Google's services, I leverage the full spectrum of their tools—from Android & Gemini to Workspace & Cloud—to maximize productivity and innovation.

Google Advocate


🔭 Current Focus & Repositories

  • python-learning-path My road to mastery. Projects built under the strict supervision of the experimental Genesis v1.0 & Neuro-Python protocols, now evolving within the Trinity v2.0 ecosystem guided by The Mentor & The Architect.

  • axiom-protocol A theoretical framework for Truth Verification (AI-Assisted Learning Project).


🧠 The Engineers' Path: My Inspirations & Philosophy (Click to expand)

"If you’re drawn to this list, you’re not just into tech; you’re into the art of engineering, the philosophy of systems, and the beauty of how things work."

  • Foundations & Logic: Richard Feynman, Alan Turing, Claude Shannon, John von Neumann
  • Systems & Invention: Nikola Tesla, Seymour Papert, Marvin Minsky
  • Reasoning & AI: Judea Pearl, Yann LeCun, Rod Brooks
  • The Craft of Code: Dennis Ritchie, Donald Knuth, Bjarne Stroustrup, John Carmack

Pinned Loading

  1. Bio-Digital Python Mentor - Gemini G... Bio-Digital Python Mentor - Gemini Gem Configuration (PL/EN) - For Biologists & Scientists
    1
    # Bio-Digital Python Mentor (Gemini Gem)
    2
    
                  
    3
    This Gist contains the configuration files for the "Bio-Digital Python Mentor" Gem.
    4
    Ten Gist zawiera pliki konfiguracyjne dla Gema "Bio-Digital Python Mentor".
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  2. axiom-protocol axiom-protocol Public

    A theoretical framework for Truth Verification. (AI-Assisted Learning Project).

    Python

  3. python-learning-path python-learning-path Public

    My road to Top 1% Python Developer. A comprehensive collection of projects, scripts, and exercises from top industry certifications and self-directed learning.

    Jupyter Notebook

  4. Clinical-Data-Anonymizer Clinical-Data-Anonymizer Public

    GDPR/RODO compliant tool for pseudonymizing patient data in Clinical Trials. (Project Codename: Clinical-Blind).

    Python

  5. omega-lis-pocket omega-lis-pocket Public

    A fully functional Laboratory Information System (LIS) built purely in Python on Android.

    Python

  6. Universal-Lab-Converter Universal-Lab-Converter Public

    Advanced laboratory unit converter (Conventional to SI) for medical professionals.

    Python