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@Borealis-BioModeling

Borealis BioModeling

Open-source and custom tools for biomodeling, simulation, and data analysis.
README.md

Borealis BioModeling

From atoms to organisms: Multi-scale computational solutions for modeling biological systems and in silico drug discovery.

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Welcome

Welcome to the Borealis BioModeling GitHub Organization! I'm Blake A. Wilson, PhD, and this GitHub Organization is home to my work on open-source bio-modeling and analysis software. I aim to empower researchers and small drug discovery teams with adaptive open-source tools. I also offer custom solutions and expert consulting to help you meet your modeling and analysis needs.

If you're interested in the software tools I'm developing or want to explore potential collaborations, I'd love to hear from you! You can contact me at blakeawilson.phd@gmail.com or LinkedIn: linkedin/blakewilson3

Be sure to check out the Borealis BioModeling GitHub repositories to explore my latest projects.

A little bit about me

Profile Picture

Hi! I'm Blake Wilson. I have a PhD in Chemistry, specializing in theoretical and computational physical chemistry. I also have extensive postdoctoral research experience in systems biology and nano-bioengineering.

As a computational researcher, I've modeled biological systems across various scales, from the atomistic/molecular to the organismal scale. My expertise includes molecular simulations (classical molecular dynamics, Monte Carlo, free energy simulations) and differential equation-based modeling of biological systems and drug dynamics.

Check out my site, blakeaw.github.io, to learn more about me and my experience.

Supporting

I'm developing and maintaining these projects independently without external funding. If you find any of these tools or related work of value, please consider becoming a sponsor and contributing financially.

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  1. pysb-pkpd pysb-pkpd Public

    Forked from blakeaw/pysb-pkpd

    PySB add-on providing domain-specific macros and models for empirical and mechanistic PK/PD modeling.

    Jupyter Notebook

  2. pysb-units pysb-units Public

    PySB add-on providing utilities to add units to models and perform dimensional analysis.

    Python 1

Repositories

Showing 10 of 12 repositories
  • aurora-pkpd Public

    Open Python Web App for Pharmcological Modeling and Analysis

    Borealis-BioModeling/aurora-pkpd’s past year of commit activity
    Python 0 BSD-2-Clause 0 11 0 Updated Oct 25, 2024
  • radioligand-therapy-model Public

    Semi-mechanistic PK/PD model of radioligand therapy implemented in PySB with pysb-pkpd and pysb-units.

    Borealis-BioModeling/radioligand-therapy-model’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 17, 2024
  • pysb-pkpd Public Forked from blakeaw/pysb-pkpd

    PySB add-on providing domain-specific macros and models for empirical and mechanistic PK/PD modeling.

    Borealis-BioModeling/pysb-pkpd’s past year of commit activity
    Jupyter Notebook 0 BSD-2-Clause 4 0 0 Updated Sep 9, 2024
  • pysb-units Public

    PySB add-on providing utilities to add units to models and perform dimensional analysis.

    Borealis-BioModeling/pysb-units’s past year of commit activity
    Python 1 BSD-2-Clause 0 1 0 Updated Jul 29, 2024
  • GAlibrate Public Forked from blakeaw/GAlibrate

    Parameter estimation and model calibration using Genetic Algorithm optimization in Python.

    Borealis-BioModeling/GAlibrate’s past year of commit activity
    Jupyter Notebook 0 MIT 3 0 0 Updated Jul 25, 2024
  • pharmacodynamic-response-models Public Forked from NTBEL/pharmacodynamic-response-models

    Collection of pharmacodynamic response models, including dose-response, inhibitor-response, and various receptor-response models that can be fit to response data.

    Borealis-BioModeling/pharmacodynamic-response-models’s past year of commit activity
    Python 0 MIT 2 0 0 Updated Jul 22, 2024
  • .github Public
    Borealis-BioModeling/.github’s past year of commit activity
    0 0 0 0 Updated Jul 16, 2024
  • pyNCA Public

    Non-compartmental PK analysis in Python

    Borealis-BioModeling/pyNCA’s past year of commit activity
    0 BSD-2-Clause 0 0 0 Updated Jun 30, 2024
  • pysb-jlsimulator Public

    Julia-based simulator(s) for PySB models using tools like Catalyst.jl and PyJulia.

    Borealis-BioModeling/pysb-jlsimulator’s past year of commit activity
    0 BSD-2-Clause 0 0 0 Updated Jun 23, 2024
  • pysb-fit Public

    Tools to help automate PySB model calibration using a style similar to scikit-learn models.

    Borealis-BioModeling/pysb-fit’s past year of commit activity
    0 BSD-2-Clause 0 1 0 Updated Jun 23, 2024
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People

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