While most of the papers that I have published have associated github repositories, this page is reserved for projects which I have contributed for that are intended to be used by anyone who wishes to.

rSNAPSIM (RNA Sequence to NAscent Protein SIMulator)

rsnapsim

This GUI is largely the work of Will Raymond and Luis Aguilera in Brian Munsky’s group at Colorado State. It is a software package which allows one to simulate dynamics of translating proteins using amino-acid specific elongation rates. For full details, see below. I contributed C++ codes to speed up Gillespie simulations as well as some of the original Python codes for simulating stochastic elongation of nascent proteins.

(Code,Publication)

MicroMator

micromator

This provides a software framework for reactive microscopy using Python. It provides an event system API to perform imaging and real-time image analysis, such as cell segmentation/tracking, and subsequently allow the microscope to react to new circumstances, for example by performing real-time control of protein production in individual yeast. Much of the core framework of the software was developed by Steven Fletcher at Institut Pasteur. I wrote the cell segmentation and tracking pipelines, as well as the single-cell control modules. See the manuscript for further details on the neat applications that this framework enables.

(Code)