The "How to Cite" Research Guide is an indispensable guide to citation manuals, citation management systems, avoiding plagiarism, and more
Assistance with Writing at UCSD Library
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There are various resources that can help you organize and format your thesis.
1. UCSD provides documentation for preparing graduate theses and dissertations which may help -- see especially Section III: Organization of Doctoral Dissertations and Master's Theses is probably most helpful, but this also provides very specific detail about specific sections (ie abstracts, acknowledgments, the use of images and statistics, etc.).
2. Looking at completed UCSD Theses and Dissertations can also be helpful: