This document provides guidelines for writing a Master's thesis in bioinformatics and computational biology at a particular university. It outlines the typical structure of a thesis, including sections like introduction, related work, methods, results, discussion and conclusion. It also discusses topics like choosing between a PhD versus Master's, publishing results, enabling replication of work, and style considerations for the scientific writing. The goal is to help students understand the expectations and best practices for writing a high-quality thesis.

1. Master's Theses in Bioinformatics
and Computational Biology
http://bbc.edu.ciencias.ulisboa.pt/
Francisco M. Couto
April, 2018

2. Outline
1) Substance
2) Structure
3) Style

3. Types of BBC Theses
● BIO:
– software as a tool to address a biological problem
– Example: new cancer treatment using text mining results
● BIOINF:
– new solution to address a bioinformatics problem
– Example: new sequence alignment tool
● INF:
– biology as a case study to validate new software
– Example: new text mining algorithm validated with cancer
literature

4. PhD vs. Master
● PhD
– Innovation on the methodology
– New results and knowledge
– More disruptive less incremental
● Master
– new results with a known methodology
– More incremental less disruptive

5. Think ahead
● Ask yourself what you would like to be doing in
3 or 5 years:
– Pharmaceutical Industry
– Health sector
– Biology laboratory
– Software industry
– or doing research

6. List of Topics
● Select some topics you like
– Email the supervisors
– Appoint a meeting
● Be open and let them know your future plans
● To better know their plans for you
– Check recent articles and previous thesis
● Not restricted to ones published in the spreadsheet
– Only restriction: one FCUL co-supervisor

7. Publish an article
● one of the best ways to validate your work and
improve its impact
● much more comfortable to discuss a work that
was already validated by other researchers
● Where should I publish?
– ask your supervisor, and check existing rankings
– Example:
http://www.scimagojr.com/journalsearch.php

8. Replication
● Enabling others to replicate your work is the basis of
science:
– It demonstrates that your theory is valid
– Otherwise is just faith
● The impact of your work depends on it
● Take notes of each step made
and about the data provenance
(data and source)
● Otherwise not even you
can replicate it :)
https://en.wikipedia.org/wiki/Medicine_Man_(film)

9. Outline
1) Substance
2) Structure
3) Style

10. Main Parts
● Introduction
● Related Work
● Work
● Results
● Discussion
● Conclusion
● Bibliography

11. Introduction
● One of the most import, since it gives an overview of
all your work
● Sections:
– Motivation
– Problem
– Objective
– Methodology
– Evaluation
– Contributions

12. Motivation
● Describes the impact of a possible solution
● Example:
– A research team in the lab is continuously reading
literature to identify new putative genetic markers.
– Automated tools could reduce the time spent
reading and avoid missing targets.

13. Problem
● Describes the complexity of the solution
● Example:
– There are no terminology and text mining software
available to automatically screen what is being
published
– Developing a terminology and software takes time
and expertise

14. Objective
● Describes the main idea for the proposed
solution
– Hypotheses or Scientific question
● Example:
– Reduce the time spent analyzing the literature using
text mining software

15. Methodology
● Describes the development process (main
steps) of the proposed solution
● Example:
– Search in Bioportal for related ontologies
– Create a new lexicon
– Adapt MER and DiShIn software to extract relevant
genetic markers

16. Evaluation
● Describes how the proposed solution validates
the proposed objectives
● Quantitative or qualitative results
● Example:
– Before the team spent 2 days per month screening the
literature, now only 1 day
– Describe examples where the tool was able to find new
genetic markers quicker
– Results in an international challenge

17. Contributions
● Describe the products that you created
● Examples:
– Software
– Database
– Terminology
– Scientific article
– Technical report

18. Evaluation
● Describes how the proposed solution validates
the proposed objectives
● Quantitative or qualitative results
● Example:
– Before the team spent 2 days per month screening the
literature, now only 1 day
– Describe examples where the tool was able to find
genetic markers quicker
– Results in an international challenge

19. Related Work
● Describe everything the reader needs to know
to understand your work
– Basic concepts
– State of the art
● Contrast it with your proposed solution
– External software used
● All except your work

20. Work
● Describe your work
– Try to follow a top-down approach
– Use examples and schemes
● May include Results and Discussion
– Or present them in a separate chapter

21. Conclusion
● Brief overview of the work done
– Contrast with the proposed objectives
● Summary of introduction in the "past"
● Future work
– Very important to access your knowledge about the
topic
– “Science never solves a problem without creating
ten more.” George Bernard Shaw

22. Bibliography
● Be careful with the references
– this is the contributions of other researchers
● Use Google Scholar (cite option), mendeley, …
● But manually check and complete missing
details:
– Year
– Journal name
– ...

23. Outline
1) Substance
2) Structure
3) Style

24. Number of pages???
● the number should be:
– the minimal size required to explain your work, so
others can understand and replicate
● avoid long thesis
– in the end will downgrade the importance of your
work to the reader
● Check previous thesis and your supervisor

25. Abstract
● Most future readers will decide to read your
thesis or not based on it
● Be very specific about:
– Problem addressed
– Proposed Solution
– Results and Contributions
● Do not present just an overview of the problem

26. Scientific Text
● It is all about scientific writing, not a novel
● Avoid ambiguity, adjectives, or long sentences
– Example:
“The proposed solution is really very good.“
● Make your work as clear as possible
● Present facts and know how to substantiate them
– Using references
– Express your opinions in the discussion and conclusion

27. Only one author
● The thesis document has only one author
– Avoid the usage of “we” without any other reference
– Example:
“We developed the solution”
– Suggestions:
“The team developed part of the solution...”
“This thesis developed part of the solution...”
“I developed part of the solution...”
● The jury wants to know your own contribution

28. Language
● English
– More readers, more impact
– No need to translate standard nomenclature
– Direct copy from your journal article
– Use a spelling consistently (US or British)
● Portuguese (mother language)
– Easier to express your ideas
– Less semantic errors

29. More Suggestions
Chandrasekhar, R.
"How to write a thesis: A working guide."
Crawley: The University of Western Australia.
2008
● The thesis will bear your name
as the single author forever
– So dedicate yourself to it!