Rsnapsim/ed – A computational Python package for analyzing and fitting mRNA nascent chain tracking experiments

mRNA translation is a crucial and heterogeneous process of decoding messenger-RNA polymers into functional proteins for cellular life. Within the recent history of studying translation, advanced microscopy techniques such as Nascent Chain Tracking (NCT) and fine-resolution transcriptomics such as scRNA-seq (single cell RNA-seq) have generated insights into the transcriptome like never before. To match these experimental techniques, we have developed an open source Python package to analyze, model, and predict a wide range of mRNA experiments, with a focus on simulating NCT experiments. RNA Sequence to Protein simulator (rSNAPsim) provides a general TASEP model builder for users to quickly design non-canonical mRNA models for their particular studied process. rSNAPsim also provides a wide range of analysis functions and model fitting capabilities. Its sister package, rSNAPed (ed for experimental design), takes models from rSNAPsim and visualizes them in simulated NCT experiments with a virtual microscope. Users can easily manage the microscopy parameters to match their real data for quick and efficient simulated data set creation, which can then be used to guide NCT experimental design or be used for ground truth testing for analytic methods.