Open access web portal for computational optogenetics tools

Optogenetics is a biotechnology that renders excitable cells light‐sensitive by inserting and expressing a single gene. It has become a key tool for neuroscience in exploring complex brain circuits, neurological and psychiatric illnesses such as epilepsy and Parkinson’s disease, and for creating new forms of optoelectronic prostheses to treat blindness and spinal cord injuries.

Designing and engineering optogenetic applications starts with effective models of the underlying molecular mechanisms and simulation of neurons and neural circuits. Dr Konstantin Nikolic’s BBSRC research grant created PyRhO to aid in this effort: an integrated suite of open-source, multi-scale computational tools to characterise opsins (light-sensitive ion channels), then rapidly develop and conduct virtual experiments with them. At completion it was available as a Virtual Machine file that required users to go through a VM installation process.

The BBSRC IAA fund was used to develop a web-based open access portal (Prometheus, Principal Designer: Dr Benjamin Evans - where researchers can access tools for computational optogenetics with no installation or configuration. To make PyRhO usable without any programming background, a Graphical User Interface (GUI) was also developed which runs in a browser-based notebook, making it easily accessible to an entire laboratory or classroom without requiring local installations on each machine. These combined achievements make the BBSRC-funded PyRhO quickly and easily accessible to a much broader audience than before, for both educational and research purposes.

The tool has generated sufficient interest in the open source market place that Imperial Innovations (the commercialisation arm of the College) have approached Dr Nikolic to include PyRhO on the Quicktech portal through which Innovations license and distributes materials and software.