CPT Galaxy and CPT Apollo
The Center for Phage Technology is one of a few phage labs in the country with a strong focus on creating bioinformatics tools for phage genomics research. All the tools developed by CPT are publically released to the scientific community via CPT Galaxy. CPT Galaxy is an instance of the Galaxy Project to provide a web interface for bioinformatics tools normally run on the command line. In addition, CPT Apollo is an instance of the GMOD Apollo project, a collaborative genome browser and annotation engine. CPT Apollo is bridged to accept and provide data into CPT Galaxy for analysis. CPT Apollo can be accessed via CPT Galaxy. Our research in phage genomics allows us to characterize and predict phage behavior, and also as an entry point to study phage biology.
See here for genomics workshops given by Dr. Jason Gill on DNA sequencing and using CPT Galaxy and WebApollo for phage whole genome annotation. Training videos on CPT phage annotation systems are also uploaded to YouTube.
Phage Genomics for Undergraduates
Phage Genomics for Undergraduates (PGU) is a signature pedagogical effort of the Center for Phage Technology. The key experience is simple in concept: an undergraduate student gets to do real creative research by doing the complete annotation of a novel phage genome and publishing this research in a real academic journal. This is done in the context of an upper-level 3 credit course, BICH464 Phage Genomics, where lectures give the student an intensive introduction into phage biology as well as in the bioinformatic techniques required for the de novo annotation and laboratory periods give hands-on experience with isolation, propagation, characterization and electron-microscopic imaging of phages from the environment. More information on PGU at the CPT is here.
Overviews of phage genome annotation using the CPT Galaxy/Apollo platforms, as well as the phage genomics course offered by the CPT are demonstrated in these presentations by Dr. Jolene Ramsey: