Open Source Projects
pyagadir
An open-source, Python implementation of Munoz & Serrano’s AGADIR model of α-helix formation. This model uses statistical mechanics and energy parameters trained on a database of over 400 peptides to predict the α-helical tendency (probability) per residue for a given peptide (see references in source).
pyfold
As part of the development effort for RBS Calculator v3.0, I am porting “kfold” (Fortran) to Cython to allow easier integration and updating of nearest neighbor energy parameters. Although this repo is public, this work is ongoing and this tool is currently unfinished. The README and this description will be updated when this project is finished.
ParseFold (email for source)
Code used to parse nucleic acid secondary structures represented in dot-parantheses format into usable structure graphs for efficient searching and processing of motifs of interest.
ELSA Calculator
This tool uses a genetic algorithm to assemble nonrepetitive genetic parts including promoters, sgRNA handles, terminators and spacers in the optimal configuration to maximize synthesis success and genetic stability of designed extra-long sgRNA arrays (ELSAs) for multiplex CRISPR applications (Reis et al., 2019).
SynBioMTS
This open source Model Test System includes a compiled database of thousands of 5’ UTR variants and a simple object-oriented interface to test and compare sequence-function models of gene expression (Reis & Salis, 2020). While we demonstrated use of the SynBioMTS on models of translation initiation rate, this code can be readily extended to other sequence-function models, for example, ones that predict promoter activity or transcription termination efficiency.
RBS Calculator
In 2009, Salis et al. published RBS Calculator v1.0, a thermodynamic equilibrium model of translation initiation rate in bacteria, for tunable protein expression control. Since then a number of minor improvements have been made to the model to increase its accuracy (to v2.1). I am actively developing a “v3.0” to account for non-equilibirium behavior of RNA folding dynamics at the ribosome binding site. More on this soon.
