SURVEY PROJECT (Cpt S 580, Spring 2009)

FORMAT

- Talk: The total duration for each presentation is 35 minutes (30 mins talk + 5 mins questions). The presentation should be in powerpoint and should be emailed to me by the morning (8am) of the day of the presentation. This way I can pre-load the talk on to my laptop and there will be no overhead in switching over from one talk to the next. Be creative in the way you organize your slides but ensure that the contents address all the guidelines listed below.

- Written Report: The manuscript should not exceed 5 single-space 11-point pages. This includes space for the main text, figures and acknowledgements (if any). For the bibliography (alphabetically listed), use up to an extra 2 pages. The manuscript should contain the following sections: Introduction and Biological Background, Problem Definition(s), Survey of Algorithms, Availability of Software and Tools, and Current and Future Trends.

SCHEDULES

- Talks will be held in two classes on 4/28 and 4/30.  The presenter schedule will be decided in class.

- Written reports are due by Email by May 7th, 5pm.

Grading: Out of the total 20% points for the survey project, 12% will be allocated to the presentation, and 8% for the written report.

General Guidelines for contents of both the talk and report:

- The contents should be understandable to a lay audience with a CS background. All required biological basics should be covered up-front.

- Less text, more figures & tables in slides

- The problem definition should contain all the following information:

• (i) what is the biological interpretation of the problem?
• (ii) how will solving the problem impact the underlying biological science?
• (iii) since when has the problem been in focus?
• (iv) what is the problem statement of the computational aspect of the problem? - ie., how does the biological question translate into a computational problem with specific input and output ? If there are several ways to model/formulate the problem they need to be explained, with a comparative account of why and when would one pick one formulation over the other.

- The algorithmic survey part should address the following issues:

• (i) what is a brute-force way of solving the problem,
• (ii) then explain the different approaches to solve the problem. This puts the methods in perspective of how effective they are and what they achieve.
• (iii) In the interest of time, do not explain each and every method to depth. Instead first say what are the main computational challenges in designing a solution, and then outline the different "approach ideas" developed so far to address them. Eg., say here is approach 1,  here is why it makes sense, here are the underlying assumptions and limitations, and here are the following methods/algorithms that use this approach/idea. Then move on to approach 2, and so on. While explaining each approach, mention the algorithmic techniques and data structure it uses. Make a table of some sorts that captures the key differences and similarities among these different approaches, their strengths, and their weaknesses.

- Comment on the software availability of the methods you discuss and if they are practically used in real-world projects

- Give a broad perspective of what's going on today in the context of this problem, and what are the future trends. If you do not find any particular reference that gives this perspective, then give your own assessment.

- Extra tips for the talk: Do not crowd slides with texts. Figures (w/ animations) and tables are generally preferred over text. If you have a lot to say, then just "say" it and use the slides to only guide what you want to say.  Reading out directly from the slides should be avoided as much as possible. Highlight important parts of the text using colored fonts, bold face or italics. Complete the talk in time. Rehearsing helps!