How to prepare for class in CPSC 545:

Preparing the background material:

The purpose of the background material is to give you a good understanding of the technical or biological setting of the original papers. The background material may, for example, involve a chapter of the "Biological sequence analysis" book or material from a biology book. It often corresponds to material that has been covered in greater detail in CPSC 445.

What you focus on when working through the background material very much depends on your background knowledge. You should remind yourself of some material and aim to fill any gaps in your technical or biological background so you can fully understand and appreciate the original papers.

I highly recommend preparing the reading material with one or more fellow students as you can then readily discuss your questions and test whether you can explain what you think you have understood.

• Read the original papers first and note down all your questions.
• Read the background material and try to clarify all questions.
• Now, work through the background material again in great detail in order to get a thorough understanding. By understanding I mean that you should be able to readily explain the contents to a colleague on a whiteboard with no or little written notes (for example, defining what hidden Markov models are and briefly explaining how the Viterbi algorithm works and what its key features are).
• Try to answer your remaining questions by consulting additional resources (books, paper, colleagues etc) and bring the list of your remaining questions to class. Having some remaining questions is ok, provided that these shown that you have made an effort to clarify them before class.

Preparing the original papers:

The original papers that we discuss either correspond to historical milestones or represent important ongoing research directions. As with many pieces of research, the context of the work needs to be understood to properly appreciate the work. This is what the background material is for, see above.

When preparing the original papers, start with the obvious questions before delving into the details.

Here are some questions to guide your preparation of the original papers:

• What are the authors trying to do ? Which question(s) do they address ? What is their motivation ?
• What was the state of art when the research was done (this is typically discussed in the introduction of the papers) ? What is novel, original or exciting about this work ? If any of the presented work fails to excite you, explain why this is. What has this paper to do with the papers that we discussed earlier ?
• What claims are the authors making and are all of these claims well supported by results ? If yes, explain by which results and in which way. If not, explain what is missing and suggest ways of how this could have been fixed.
• Of particular interest to us: Which computational techniques are the authors using, how do these work ? What is the input, the output, which type of predictions are being generated, which algorithms are being used, how do they work and what are their relelvant features ?
• Which biological data and features are being modeled ? How is this done ?
• Which implicit or explicit assumptions does this research make ? Are these justified ? Explain why or why not.
• Know what all the figures and tables show and what they mean.
• Finally, could this be done in a better way (technically or strategically) ? Or, could similar techniques or ideas be used to solve related, more exciting questions or to analyze new types of biological data ?

What to bring to class:

Please need to bring the following to every class:

• your own paper-copy of the paper(s) to be discussed on that day
• your own notes of the reading material and your remaining questions, i.e. documents you may want to refer in case you are selected to lead the discussion
• unless you are the speaker, please don't use your laptop during class