*** Even more success: Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database. Published 26 June 2014! Read the paper here.***
Molecular data is cryptic, riddled with subtle patterns and there is a lot of it.
The Victorian Life Sciences Computation Initiative (VLSCI) needed a new approach and innovative way to deconstruct and reconstruct their data. They engaged the APR.Intern program to help with this challenge.
Working with VLSCI, APR.Intern Sori Kang, a Masters student at The University of Melbourne, was able to use her academic skills in a business setting to help in the design and implementation of software tools.
The new software — Annokey — takes a list of key words such as “DNA repair pathway” and searches the NCBI Gene Database for entries that contain those words. It also looks for those keywords in abstracts contained in the journal database PubMed. Annokey then returns a list of Genes that match the keywords, useful information about how often the match was found and relevant peer-reviewed journal articles.
Sori’s academic mentor, Dr Bernie Pope said: “Sori’s expertise helped turn concepts into working software tools. The new software saves researchers a lot of time because it allows them to sift through the rich sources of publicly available data with greater ease and efficiency.
“APR.Intern helps students to develop new skills in their chosen fields and be exposed to cutting edge research – human cancer genomics in Sori’s case.”
Dr Bernie Pope is a specialist programmer at VLSCI and an Honorary Fellow of the University of Melbourne’s Department of Computing and Information Systems.
“The APR.Intern program gave me valuable, practical, experience and a better understanding of what to expect in a career outside of academia,” Sori said. “I really recommend this program to ALL university students.”
EMBL Australia and BioPlatforms Australia are proud sponsors of the APR.Intern BioInfoSummer Internship program – supporting Australian BioInformatics research into the future.
If you are a company that has a research need, we have three internships on offer for 2014.
Sponsored by EMBL Australia and BioPlatforms Australia, APR.Intern offers industry partners research funding for these internships.
Industry partners only pay $3,000 per month for the duration (4-5 months) of the internship and all other costs are funded through the program.
Hear about the success of last years internships at the BioInfoSummer showcase 2013.