February 2, 2016
A student researcher from the Westmead Institute has developed a program which makes tracing genetic pathways easier and has the potential to assist in the development of new drug therapies for glaucoma.
Designed by Linda Feng from the Institute’s Centre for Vision Research, the ‘Genebunny’ app can search large volumes of publications sourced from public databases and, via an algorithm, links the genetic influences. It then displays the links in a tree-like diagram on any smart device or personal computer.
Linda, who has an undergraduate degree in biomedical engineering, says the program is easy to use and provides researchers from across disciplines with all-platform access to gene pathways, essentially speeding up genetic research.
“Tracing genetic pathways can be difficult and time consuming,” says Linda. “With the information explosion of the last decade or so, the literature you need to trawl through to make these connections can be massive. To jump from what seems like one unrelated thing to another completely different thing and then finally down to something that you want to link to the previous idea - that's a big undertaking.
“Genebunny accelerates this process by mapping out genetic pathways quickly. Users simply define a start point and end point, which gives the program a sense of directionality. The program then goes through the interactions and forms links.”
Genebunny is highly customisable, and allows the user to choose the number of documents to be searched and the number of jumps or “hops” they want displayed.
“For example," says Linda, "If there are certain genes that you don’t want to see, you can ‘blacklist’ them, which enables you to ‘trim the tree down’ until you get a rough area of what you want to see or the pathology or drug cascade that you are interested in."
According to Linda’s supervisor, Dr Andrew White, the program is useful for generating ideas for future projects, and even has a role to play in developing drug therapies for glaucoma.
“It has helped us to define the most efficient pathways to test as we move towards developing a new drug therapy for glaucoma based on the personalised medicine model. Because Genebunny is so user friendly and intuitive, it assists us to better understand the genetic process behind this disease.
“Furthermore, it can be mounted on any smartphone and is handy tool to take to conferences," says Dr White. "I have used it to show people genetic linkage in real time. It speeds up discussions considerably and gives me a flight of ideas for new projects.”
While there are other gene-mapping programs that can provide more detailed and robust results, Linda says they are often difficult to use and can be very expensive.
Genebunny – named after the programs ability to “hop” between points – may be easy to use but Linda says the program’s flexibility has a downside.
“It comes with a warning: If you are not careful, you could just keep going and disappear down a rabbit hole.”