Mirscan runs on Linux and uses the Python interpreter. It is compatible with Python 2.3.4 and will likely work with most versions of Python; however, because the Python programming language is not developed with a strong "do-no-harm" philosophy, it is possible that previous or future versions of Python will be incompatible with mirscan as implemented here.

The core scripts of the mirscan system can be downloaded here. These scripts should be placed into one directory, and all mirscan jobs should be executed with that directory as the current working directory.

The current implementation of mirscanModule.py requires that RNAfold from the Vienna RNA package be installed on the host computer and be callable from the command line. That software is available here. Alternatively, the implementation of the get_folds function in mirscanModule.py can be altered to use some other tool to determine the mfe secondary structures for a set of nucleic acid sequences.