Software
We are proud to develop and contribute the following open-source tools to the broader polymer community. For each tool, we include a brief description, relevant publication, and link to the source code for installation. Please visit our GitHub page for more information.
Polymer rate insights and sequence modeling: Enabling reconstruction and analysis of synthetic polymer sequences. Prism includes modules to estimate monomer reactivity ratios from kinetics data of RAFT polymerization from two- and three-monomer systems, a kinetic stochastic simulation strategy to reconstruct these sequences, and a variety of metrics to enable visualization and quantification of chemical patterning.
PRISM
Extracting population data from electron and atomic force microscopy data is challenging and time intensive. Particle-Counting automates the initial stages of microscopy data processing by identifying all spherical particles in a given acquisition and measures them. This tool interfaces with the free ImageJ software (https://imagej.net/ij/).
Particle-Counting
PeptoidSeq
Peptidomimetics remain challenging to sequence due to noncanonical monomers and linkages. PeptoidSeq facilitates rapid sequencing of peptoid (N-substituted glycines) by reading a MALDI TOF-TOF spectrum and outputting a candidate sequence. This tool also supports user input to resolve ambiguous assignments. PeptoidSeq was developed and validated on a binary monomer peptoid system consisting of glycine and N-butylglycine.
ColorClassify
One-bead one-compound (OBOC) libraries are high-throughput strategies for synthesis and characterization of macromolecules. ColorClassify quantifies images of OBOC libraries stained for a colorimetric assay. It consists of two parts: (1) an image quantification code that returns RGB values of selected beads in an image, and (2) a machine-learning classification algorithm that will classify lists of RGB values into groups based on pre-classified test data.
MotifFold
MotifFold is an implementation of a data-driven strategy towards elucidating sequence-structure relationships for synthetic macromolecules. It uses a language-inspired "motif" strategy, where sequences are separated into motif features and then regressed against a conformation descriptor. MotifFold was developed to describe sequence-dependent folding in peptoids as quantified by a colorimetric screen.
Synthetic polymers are stochastic objects with dispersities in sequence and length. CopolymerSequenceGeneration is a tool to generate an ensemble of polymer sequences given the reactivity ratios of the composite monomers. Using a Kinetic Monte Carlo strategy, it simulates the chain growth and monomer incorporation process, and comparisons between various ensembles can be performed through calculation of Jensen-Shannon divergence.