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k-wavy/README.md

Howdy partner, welcome to my GitHub profile 👋

I am Seth Frazer, an evolutionary and computational biologist. I completed my Undergraduate degree in Biology and my Master's degree in Evolutionary Biology at the University of California, Santa Barbara (UCSB). Currently, I am a first-year PhD student in the Kreshuk Lab at EMBL in Heidelberg, Germany.

My work primarily sits at the intersection of evolutionary biology, sequence analysis, and machine learning, with a heavy focus on opsin phenotype prediction.

My Work

Much of my open-source work has centered around the VisualPhysiologyDB (VPOD), where I authored tools to predict and analyze opsin phenotypes from genomic data. Here are my featured repositories (all of which are still 'live' and updates will be on-going):

  • optics: An open-source Python tool that predicts the Opsin Phenotype (lambda max) from unaligned opsin amino-acid sequences.

  • visual-physiology-opsin-db: A database of opsin genotype-phenotype data and machine-learning models trained to predict opsin phenotypes.

  • mine_n_match: Python functions designed to mine and process sequence data directly from National Center for Biotechnology Information (NCBI) databases.

  • mutagenesis_tools: A repository for mutagenesis scripts, featuring a streamlined set of scripts for site-directed mutagenesis, chimera construction, and deep-mutational scanning.

Tech Stack & Tools

  • Languages: Python, R, HTML

  • Data Science: Jupyter Notebooks, Pandas, Scikit-learn, Torch

  • Domain Expertise: Computational Biology, Evolutionary Biology, Bioinformatics, Machine Learning

Pinned Loading

  1. VisualPhysiologyDB/visual-physiology-opsin-db VisualPhysiologyDB/visual-physiology-opsin-db Public

    A database of opsin genotype-phenotype data and machine-learning models trained to predict opsin phenotypes.

    Jupyter Notebook 9 2

  2. VisualPhysiologyDB/optics VisualPhysiologyDB/optics Public

    An open-source tool that predicts the Opsin Phenotype (λmax) from unaligned opsin amino-acid sequences.

    Python 4

  3. VisualPhysiologyDB/extra_optics_models VisualPhysiologyDB/extra_optics_models Public

    A repository for all the extra models that aren't part of the official VPOD releases. See the README for information about use.

    Python

  4. VisualPhysiologyDB/mine_n_match VisualPhysiologyDB/mine_n_match Public

    Python functions designed to mine and process sequence data from the National Center for Biotechnology Information (NCBI) databases.

    Pep8

  5. VisualPhysiologyDB/mutagenesis_tools VisualPhysiologyDB/mutagenesis_tools Public

    A repository for all mutagenesis scripts - separate from VPOD - for those who want a streamline set of scripts for site-directed mutagenesis, chimera construction, and deep-mutational scanning.

    Jupyter Notebook

  6. VisualPhysiologyDB/VisualPhysiologyDB.github.io VisualPhysiologyDB/VisualPhysiologyDB.github.io Public

    A repository for all html files and data needed to make configure our organization github.io pages :)

    HTML