PhD student at The Scripps Research Institute in the Yates Lab, developing Python tools for computational proteomics workflows. I maintain a suite of open-source packages and web applications for mass spectrometry data analysis. Currently setting up a server at Scripps to host production apps and services.

Active projects: MS1 feature finder, real-time mass spectrometry applications, machine learning modules for peptide property prediction, and MS1/MS2 search engines.

🔬 Streamlit Tools Homepage: https://proteomics-tools.streamlit.app/

Proteomics Analysis

• Peptacular - Proforma 2.1 compliant utility package for amino acid sequences (similar to pyteomics)
• FastaFrames - Convert between FASTA files and Pandas DataFrames
• MsDecon - Simple-ish MS deconvolution using rustworkx graph algorithms
• tdfpy - Parse Bruker timsTOF data with centroiding and noise filtering
• MsMsCompression - URL-compatible compression algorithms for mass spectra

Data Processing

• SagePeptideAmbiguityAnnotator - Annotate Sage output with missing fragments and unknown mass shifts
• msconvert-cli - Command-line wrapper for msconvert Docker image

• ProteinCleaverStreamlitApp - In silico protein digestion and enzyme site visualization
• PeptideFragmenterStreamlitApp - Interactive peptide fragment ion viewer
• StreamlitSpectrumViewer - Annotated mass spectrum visualization
• CSV_Viewer_Streamlit - Universal file viewer for common formats

• StreamlitThemes - Programmatic theme management
• Streamlit_Notify - Status notification queue system (part of Streamlit Extras)
• streamlit-permalink - Stateful widget URL parameters (forked)

Hopefully you'll never need these

• FilterFrames - Convert DTASelect-filter files to/from Pandas DataFrames
• serenipy - Utility package for IP2 file formats

Languages

"Scientific Computing"

Machine Learning

Visualization

Web

DevOps

I don't really use these, but feel free to follow anyway