Bioinformatics Software Development

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We build high quality tools that make it easy for biological researchers to comprehend and interpret their data.

The Center for Phage Technology is looking for aspiring bioinformaticians to do 491 research! We’re one of the only phage labs in the country with a strong focus on creating novel tools for analysis of phages. In the past year alone we’ve added over 100 new tools to our arsenal, all of which have been publicly released for the benefit of the scientific community.

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We work with some exciting technologies and build systems which process and help researchers visualise huge amounts of data. Some of the technologies we work with include python’s numpy/scipy/scikit-learn, docker, and golang. We primarily focus on backend tool development, but we’ve been slowly expanding into building out our Javascript dynamic data visualization capabilities.

During this project you’ll become comfortable writing python through our feedback-intensive mentoring process. On the bioinformatics side, you’ll gain skills in command line bioinformatics tools, and all the basic linux commands you will need to succeed as a bioinformatician.

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One of our other primary focuses is building complex workflows to accomplish biological analyses and visualizations. The pictured workflow is one that was developed for the complete annotation of novel bacteriophage genomes; we leveraged a large number of external tools and used the Galaxy bioinformatics platform to mesh those with our own internal tools and generated a single coherent workflow that produce complete annotation sets for novel phages.

 

No prior programming experience is required, just the ability to think logically and desire to solve problems and puzzles. However, prior programming experience will let you attack larger and more complex problems which are more likely to be published in some form.

First semester projects for those new to programming often involves writing small utility scripts and integrating those with our pipelines. Second semester projects/more experienced programmers can move on to the more complex projects like adding large features to existing tools, development of novel tools, development of novel visualisations of datasets.

Contact Eric Rasche to get more information or apply. Please submit a résumé with your email.

Availability Every Semester
Spring 2017 Slots 0 Left
491W? Yes
Résumé/Relevant Coursework List? Required