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@NeuroBox3D @VRL-Studio @UG4

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stephanmg/README.md

About me

I'm a postdoctoral fellow in the lab of Jan Hasenauer where my research revolves around the interfaces of life sciences, mathematics and computer science. We develop mechanistic models (ODE/PDEs) and apply methods of parameter estimation (Julia/Python) for model calibration to shed light on the interplay and ramifications of dynamical biological processes in cells. Therefore also AI-tools, artificial neural networks/DL approaches and recent advances in bioinformatics are exploited. We develop pipelines for statistical data analysis and visualization (R/Python, Javascript/Typescript) of large-scale data sets, knowledge representation and reasoning on metadata using semantic web technologies (graph databases, SPARQL, ontologies) focusing on reusability and reproducibility in the life sciences.


Up to the 2020s I have been working in the field of computational neuroscience. I developed novel numerical methods and grid generation tools for modelling and simulation of spatially-resolved intracellular ion dynamics in neurons by PDEs/ODEs on HPC/HTC infrastructure. We made use of GPU programming on NVIDIA GPUs through CUDA/cg shader programming for interactively visualizing and numerical analysis of scientific data sets in the virtual reality framework Unity VR (C#). Major programming experience stems from C++/C and Lua, Java and Python. I developed prior to that also numerical models for multi-scale and hybrid-dimensional phenomena in molecular dynamics/computational neuroscience and mesh generation methods for the study of intracellular Calcium waves, neuronal plasticity and memory formation.

Contact

Contact information can be found on the left most panel - feel free to browse my recent and public projects.

For secure e-mailing find my GPG fingerprint as: F598 BCFF 445C C90F 3312 3C71 7D30 C7E5 7559 76A6.

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  1. NeuroBox3D/NeuGen NeuroBox3D/NeuGen Public

    NeuGen is made for generation of dendritic and axonal morphology of realistic neurons and networks in 3D

    Java 12 2

  2. c2m2/VRL-VRN-Generator c2m2/VRL-VRN-Generator Public

    VRL-Studio project for neuron mesh generation and containerizing to .vrn

    Java

  3. VRL-SWC-Density-Vis VRL-SWC-Density-Vis Public

    Density visualization plugin for neuronal morphologies

    Java 2

  4. c2m2/Neuro-VISOR c2m2/Neuro-VISOR Public

    A research tool based in virtual reality. Produced by the Center for Computational Mathematics and Modeling at Temple University

    C# 10 9

  5. NeuroBox3D/neuromorpho NeuroBox3D/neuromorpho Public

    Making use of the REST API (NeuroMorpho.org v7) to query the database

    Python 10 3

  6. NeuroBox3D/neuro_collection NeuroBox3D/neuro_collection Public

    UG4 plugin for unified neuro-related functionality

    C++ 1 1