polymerase.nz is a free online suite for simulating nucleic acid polymerases -- mainly RNA polymerases. This software is open-source and free under the GNU license. Everything has been written in JavaScript and C++ and can be downloaded from GitHub, however >95% of the programs functionality can be executed here without the need to download.

An engine for visualising, simulating, and performing inference on the kinetics of nucleic acid polymerases. The copying of nucleic acids is a fundamental biological process studied by a range of people -- including students and molecular biologists.

SimPol is a sandbox for students and researchers alike to hone their understanding of transcription and other nucleic acid copying processes. This is achieved with the ability to manually apply a range of reactions to the polymerase, or by simulating the system as a Markov process. The kinetic and thermodynamic parameters which govern these processes can be modified and the effects can be displayed with a range of live-updating plots.

SimPol also comes with a Bayesian inference engine that can be used to fit these parameters to single-molecule data.

A predictor of transcriptional pause sites using thermodynamic and sequence information. RNA polymerases do not travel at homogeneous speeds along the template during transcription. While the average transcription elongation velocity is typically between 10-100 bp/s for prokaryotes and eukaryotes, there are sites in the template which take an average of seconds or even minutes to transcribe. These positions are known as pause sites and can play important regualtory roles in transcription.

Pauser uses SimPol to make pause site predictions on a series of user uploaded sequences, and then reports the evidence that any given site in the DNA template is a transcriptional pause site.

Probability density functions of standard distributions. A simple modular library for displaying simple animated pdf plots. The plots are easily embeddable using iframes and url parameters.