My Projects

My open-source software projects.

Active

These are the projects that are in active development.

  • mzspeclib-py PythonExecutableLibrary

    An implementation of the HUPO-PSI mzSpecLib format

  • chemical_elements RustLibrary

    Chemical compositions, formula parsing and isotopic pattern generation.

  • mzpeaks RustLibrary

    Representations of peaks and features for mass spectrometry data, and searchable collections there-of.

  • mzsignal RustLibrary

    Signal processing, peak picking, and feature extraction for mass spectrometry data.

  • mzdata RustLibrary

    Readers and writers for mass spectrometry data files and resources as well as spectrum and chromatogram structures.

  • mzdeisotope RustExecutableLibrary

    Deisotoping and charge state deconvolution for spectra and feature maps.

  • thermorawfilereader.rs RustC#Library

    FFI interface for reading Thermo RAW files from Rust via a self-hosted .NET runtime

  • mzdata-wasm RustTypeScriptLibraryDemo

    A demo of how to use WASM to run Rust code for mass spectrometry data processing in the browser. Demo is not mobile friendly

  • mass-fragment-index RustLibrary

    A generic framework for constructing in-memory or on-disk rapid search indices.

Maintenance

These projects are functionally complete or no longer being actively worked on. Some of them were superceded by other projects to work around language limitations or other technical issues.

  • glypy PythonCLibrary

    A library for representing and manipulating glycan structures and compositions. Also provides I/O interfaces with common formats and repositories of glycan structures.

  • glycopeptidepy PythonCLibrary

    An extension of glypy for modeling glycopeptides

  • brainpy PythonCLibrary

    A library to quickly generate isotopic patterns from elemental compositions.

  • ms_peak_picker PythonCLibrary

    A simple method adapted from Decon2LS for peak picking of mass spectra and cleaned up a little, with added signal processing filters

  • ms_deisotope PythonCExecutableLibrary

    Mass spectrum deisotoping and charge state deconvolution toolkit.

  • psims PythonLibrary

    A declarative writer for mzML, mzMLb and mzIdentML formats.

  • glycresoft PythonCJavaScriptExecutableLibrary

    A LC-MS/MS search engine for glycans and glycopeptides.

  • glycopeptide_feature_learning PythonCExecutableLibrary

    A plugin for glycresoft that includes a multinomial glycopeptide fragment intensity model and a "simple" Bayesian fragmentation modeling framework.