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Midnighter/README.md

About Me

I currently work at Unseen Bio where I build technology to provide deeper insights into your personal gut microbiome. That means, I want to predict how you can best adjust your diet to favour communities of bacteria that are beneficial to your health.

As a bioinformatician, one of my guiding questions is, "How can I use my knowledge of biological research and software development for the good of humanity?"

This question leads me to the following topics that I am very passionate about:

  • Thinking in systems, both biological networks and software architecture.
  • Designing automated solutions for and with human beings.
  • Access to and transparency of knowledge as embodied by, for example, the open science movement or the Open Knowledge Foundation and Wikipedia to name but a few.

Contact

You can also find me on the following platforms:

Pinned

  1. Retrieve and print Python package dependencies.

    Python 4 3

  2. Parse and process information from MetaNetX for MIRIAM compatibility using the Identifiers.org registries.

    Python 4

  3. A Python 3 port of Simon Brown's Structurizr diagrams-as-code architecture description tool.

    Python 54 13

  4. A base Docker image for microservices using FastAPI. The Docker image environment is based on Alpine Linux or Debian.

    Dockerfile 8 2

  5. COBRApy is a package for constraint-based modeling of metabolic networks.

    Jupyter Notebook 359 193

  6. memote – the genome-scale metabolic model test suite

    HTML 95 23

Contribution activity

September 2022

Created 1 repository

Created a pull request in nf-core/test-datasets that received 3 comments

feat: add minimal SARS-CoV-2 kraken2/Bracken database

I suggest to add a kraken2/Bracken database. This one comes from the modules test data and is based on the SARS-CoV-2 genome. So it's probably not …

+1 −0 3 comments

Created an issue in nextflow-io/nextflow that received 3 comments

Joining channels using maps as the key to join by can fail on resume

Bug report Expected behavior and actual behavior When joining two channels, for example, on the first element which is often a map with sample meta…

3 comments

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