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  • San Francisco, CA

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Achievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Pull Sharkx3Achievement: Arctic Code Vault Contributor

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benjschiller/README.md

Benjamin Schiller

I build practical tools for scientific computing, automation, and developer workflows.

My public GitHub is a mix of maintained utilities and older bioinformatics work that I keep around for provenance. If you are trying to understand my current engineering taste, start with the actively maintained projects rather than the archaeology shelf.

Current Public Work

  • twobitreader: a Python package for reading UCSC .2bit genome files. This is the main public project here that appears to have real downstream use.
  • dotfiles: an old macOS / bash snapshot that I am reviving into a current personal setup.

Historical Archives

Several older repositories are intentionally archived, including grad-school-era bioinformatics tools and support forks:

  • seriesoftubes, checkmyclones, and scripter
  • samtools and tabix Windows-support forks
  • sphinx-minimal

They are public for context and provenance, not as current recommendations.

What I Tend To Care About

  • small tools that solve real workflow problems
  • reproducible scientific pipelines
  • clear maintenance state and boring operational details
  • interfaces that keep working after the novelty wears off

Popular repositories Loading

  1. twobitreader twobitreader Public

    A fast python class for reading 2-bit files (used by UCSC genome browser)

    Python 14 7

  2. seriesoftubes seriesoftubes Public archive

    Historical archive: Python 2.7-era UCSF ChIP-seq pipeline for Solexa data. Not maintained; kept for provenance.

    Python 2

  3. checkmyclones checkmyclones Public archive

    Historical archive: Python 2.7-era tool for checking Sanger sequencing results against references. Not maintained.

    Python 2

  4. tabix tabix Public archive

    Historical archive: old tabix fork for Windows support for pysam-era workflows. Not maintained; use upstream htslib.

    C 1

  5. scripter scripter Public archive

    Historical archive: Python 2.7-era helper for running functions over many files on multicore machines. Not maintained.

    Python 1

  6. samtools samtools Public archive

    Forked from lh3/samtools

    Historical archive: old samtools fork for Windows/MSVC support for pysam-era workflows. Not maintained; use upstream.

    C