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    With modularity, interoperability, and openness as guiding principles, Next Generation Library Publishing (NGLP), is developing library publishing resources that combine the values alignment of open source software with the convenience of turnkey publishing and repository solutions. The project is simultaneously building interoperable software components tailored to the unique needs of library publishers and designing business and governance models, values-based assessment frameworks, and pilot implementations that will bring our code to life. This is a test instance undergoing active development.
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    Thaddeus Dillon Seher January 1, 2021

    This dissertation describes the work that I performed with a team to develop the AddTag method for genome editing. First, I introduce genome editing through CRISPR/Cas-induced homology-directed repair, and I introduce the Candida albicans biological system (Chapter 1). Next, I describe how AddTag editing utilizes CRISPR/Cas-induced homology-directed repair to edit the C. albicans genome, and then the process of validating the edits through phenotyping, sequencing, and PCR (Chapter 2). I introduce the ADDTAG software which assists with AddTag editing. First, I describe how ADDTAG identifies genome targets for RNA-guided nucleases (Chapter 3). Then I demonstrate how the software constructs artificial sequences for use as genome repair templates. Lastly, I explain a computational method for producing a set of verification PCR primers for determining if genome edits are successful (Chapter 4).

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