Software

Computational Biology

Immune Dynamics

  1. scimmunity: scimmunity is a python tool for analyzing single-cell RNAseq data specifically for immune and cancer cells. It includes preprocessing, dimension reduction, clustering, annotation, visualization, differential expression testing, TCR analysis, and additional integration with existing single cell packages. co-authors: Rachel Ng.

  2. immunedynamics: immunedynamics is a tool to identify T and B cell repertoire dynamics, it a) identifies high frequency signals from noise and b) classifies high frequency dynamics using shape clustering techniques. co-authors: Rachel Ng, Natalie Dullerud.

  3. tcrconnect: tcrconnect is a tool to a) quantify the overlap metrics between TCR sequences from single cell RNAseq data and/or bulk TCR seq data and b) to calculate metrics associated to antigen specificity through GLIPH analysis. co-authors: Rachel Ng.

Viruses and antibodies

  1. fitnesslandscape: fitnesslandscape is a tool to a) compute fitness landscapes based on mutational scanning of molecular structures, b) run evolutionary dynamics simulations over quantifiable fitness landscapes using a hybrid stochastic/deterministic mathematical model.

  2. satlasso: satlasso is a tool that implements an extension of LASSO to account for saturated biological data. Applied to uncover virus/antibody binding locations and extract features on antibodies amenable to optimization or on viruses to uncover potential escape mutations. co-authors: Natalie Dullerud.

  3. abopt: abopt is a pipeline used to constrain antibody design based on neutralization and mutational scanning data. Also solves to optimal antibody cocktails to limit emergence of viral escape mutations. co-authors: Tea Freedman-Susskind, Natalie Dullerud.

Treatment Optimization

  1. treatmentopt: A suite of treatment optimization algorithms using techniques from dynamics and control. co-authors: Natalie Dullerud, Giulia Giordano.

Flight Software + Control Engineering

Aquarius Mission SAC-D Instrument, JPL/NASA

A new operating system for robotic space missions that reconfigures high level software in flight rather than through uplinking small sets of binary machine instructions to known locations in memory.

Paper. Code can be requested here.

co-authors: Mohammad Shahabuddin and Alexander Murray.

Mission Data Systems, JPL/NASA

A control systems and flight software architecture for robotic spacecraft missions.

Code can be requested here.