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Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: Pull Shark

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kchemorion/README.md

kchemorion

Knowledge Graph Engineer | Semantic Engineer | AI/ML | Data Science | Data Engineering

Building systems that bridge structured knowledge, biomedical data, and machine learning — from ontology embeddings and interaction networks to clinical data pipelines and publication-ready manuscript generation.

Featured

Project What it does
academic-manuscript-skill Claude Code skill for generating scientific manuscripts with real CrossRef references and Zotero field codes
PPIExtractor Automated protein-protein interaction network extraction pipeline
biomodelize Web app for simulating SBML models with RoadRunner — upload, run, visualize, download
ontoembed Ontology embedding methods for knowledge graph representation
slicerGUI Dockerized 3D Slicer with VNC/noVNC web interface for medical image visualization
eGBIM Extended graph-based interaction model
Mendoza Biochemical reaction network simulation using the Mendoza equation with SBML model generation

Domains

Knowledge Graphs & Semantics — ontology embeddings, interaction networks, graph neural networks, entity linking

Biomedical Computing — SBML simulation, spine parameter modeling, medical image processing (3D Slicer), protein interaction extraction

ML/AI — GNNs, tabular diffusion, missing data imputation, neural architecture search

Data Engineering — REDCap pipelines, Apache NiFi workflows, object storage hierarchies

Tech

Python TypeScript Vue C++ Docker Node.js Graph Neural Networks SBML OpenSim 3D Slicer

GitHub stats Top languages

@fkchemorion

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  1. slicerGUI slicerGUI Public

    Dockerized Slicer with Web Interface This repository provides a Dockerfile and associated files to containerize 3D Slicer, a popular open-source software platform for medical image informatics, ima…

    Dockerfile 4

  2. biomodelize biomodelize Public

    This is a web application for simulating Systems Biology Markup Language (SBML) models using the RoadRunner simulation engine. It allows users to upload SBML files, run simulations, visualize simul…

    JavaScript 1

  3. SwiftHierarchy SwiftHierarchy Public

    When working with object storage systems, organizing data into a hierarchical structure resembling traditional file systems is common. This script simplifies the creation of such a structure by app…

    Shell

  4. Mendoza Mendoza Public

    The Mendoza project involves simulating a network of biochemical reactions using the Mendoza equation to study the dynamics of a system of nodes under various activation and inhibition conditions. …

    Python