Writing your thesis
Congratulations! You are now at a stage where you are thinking about writing your thesis. Whether you are just commencing your degree or actively embarking on the writing phase, this compilation of ideas and resources is intended to assist you in this scholarly endeavor.
Models
Theses from the University of Ottawa can be accessed online via uO Research. It is highly recommended to review examples to gain a comprehensive understanding of the expected standards. Given that these expectations differ across disciplines, it is crucial to examine theses from your own program or from closely related fields.
For students who are applying machine learning techniques to the fields of bioinformatics or medicine, these examples serve as excellent models. My selection of these particular examples is informed by my experience as a member of those defense committees.
- Improving Protein Identification In Mass Spectrometry Imaging Using Machine Learning and Spatial Spectral Information by Soroush Shahryari Fard
- Clustering to Improve One-Class Classifier Performance in Data Streams by Richard Hugh Moulton
- RNA Sequence Classification Using Secondary Structure Fingerprints, Sequence-Based Features, and Deep Learning by Kevin Sutanto
- Surgical Workflow Anticipation by Kun Yuan
- Wide scale analysis of transcription factor biases and specificity by Aseel R. Awdeh
Tools
Scientific writing tools like LaTeX help maintaining consistency in document formatting, particularly in the organization and presentation of references. Both TeX, started in 1978, and LaTeX, released in 1984, are free and compatible with nearly all operating systems. They use text files with markup annotations, ensuring long-term editability and compilability. Unlike traditional word processors, LaTeX’s format enables continued access to documents decades later, for instance I can still edit and compile my PhD thesis from 1995.
Overleaf is a widely used online platform for creating and compiling LaTeX documents. It eliminates the need for local LaTeX installations by providing a cloud-based solution. The platform offers a free version with certain constraints, as well as a discounted subscription plan for students. A significant feature of Overleaf is its facilitation of collaborative work on documents, enabling multiple users to edit and review content simultaneously.
Refer to the following page to download and use LaTeX on Linux, macOS, Windows, and online platforms.
LaTeX provides numerous packages and styles, including specific thesis templates for the University of Ottawa.
- Unofficial uOttawa Thesis LaTeX Template maintained by Wail Gueaieb
- University of Ottawa Thesis Template authored by Nicholas Sorensen
- UOttawa LaTeX Thesis Template authored by Nicolas Bigaouette
Quarto and Typst are powerful tools for preparing documents, especially for incorporating mathematical equations and dynamic content with Python, R, Julia, and Observable. However, I hesitate to recommend them for thesis writing. They are not as established as LaTeX, which may lead to occasional frustration, and it is unclear if they will have the same longevity as LaTeX.
A common problem in thesis drafts is the handling of references, which are often incomplete, incorrect, or inconsistently formatted. LaTeX users can solve these issues by using BibTeX, which manages references and creates bibliographies. BibTeX keeps the bibliography in a separate file with a .bib extension, apart from the main LaTeX document. I personally use a single BibTeX file for all my projects, including academic papers, lecture notes, and my CV. Over 35 years, this file has grown to include over 10,000 references.
Please, please, please, and this is a golden rule: never enter references manually in your bibliography. Errors in entering bibliographic details, such as incorrect page ranges, volume numbers, or publication dates, are inevitable. To mitigate these errors, use a bibliography management tool that interfaces directly with databases like Scopus, Web of Science, Google Scholar, and PubMed. This allows for the seamless importation of references into your bibliography. As a macOS user, I prefer using BibDesk, although JabRef is a commendable alternative.
Copyright
You have dedicated significant effort to your research, possibly culminating in the publication of one or several papers—congratulations on this achievement. Naturally, you aspire for your work to be cited by others, as your primary objective is to contribute to the scholarly discourse. Similarly, it is essential to extend the same respect to the work of others. When referencing facts or ideas that are not your own, always seek out the primary source for citation. Avoid relying on reviews or secondary references, as you would prefer that others directly cite your original work rather than referencing it indirectly through third parties.
Despite good intentions, certain rules may still be inadvertently violated. A common example involves the reproduction of figures from published papers. Students frequently include such figures with a caption stating “reproduced from (citation).” However, this acknowledgment may be insufficient. It is imperative to consult the journal’s guidelines for each reproduced figure. Instructions are typically provided either at the top or bottom of the journal page. The permissions for figure reproduction can vary: in some instances, reproduction is prohibited; in others, it is allowed but requires written permission from the publisher or rights holder, and occasionally, a fee may be necessary. Notably, this process applies even to your own work; you might not automatically hold the rights to reuse a figure from your previous publications.
In the journal Bioinformatics, information regarding permissions is accessible via a link labeled “Permissions” at the top of the page. Here are two examples, without and with restrictions. Wang et al. (2024) is published under a Creative Commons license. You can click on the link to view the details. Conversely, Dobin et al. (2013) is fully reserved under Oxford University Press’s rights. You may follow the respective link to examine the specific permissions associated with this article.
To prevent any unforeseen issues, please review this concise document.