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教學大綱


本頁翻譯進度

燈號說明

審定:無
翻譯:張祐誠(簡介並寄信)
編輯:鄔書林(簡介並寄信)


修課條件

電腦程式的結構與詮釋 (6.001) 或演算法簡介(18.410J/6.046J)或得到任課教師的同意。預設沒有生物學的背景。必須熟悉某些適當的程式語言。

教科書

這本書將探討大部份的主題,但內容可能在某些領域較缺乏深度。

Jones, Neil C.與Pavel A. Pevzner 《生物資訊演算法簡介》(計算分子生物學),Bradford Books. Cambridge, MA: MIT Press,2004年8月1日。ISBN: 0262101068。

作業與計分

問題集

對於每個教學時程上的章節將會有一個問題集。由於某些章節比其他的章節短,某些問題集將會比其他的問題集要來得簡單。問題集將會在每個新章節開始的第一堂課公佈,並且在該章節最後一堂課的當週到期。問題集通常會需要於該公布課堂之後三堂課以內的時間繳交。

每個問題集會包含一些簡單的問題和少數具有挑戰性的問題(這些問題會被標註星號「*」)。如果問題集埵酗@個加分題,就表示我個人還沒有一個令人滿意的答案,而卻想知道你是否有辦法回答。除了需要解決那些簡單的問題,你也會希望能夠在那些具有挑戰性的問題上取得某些進展。若你對於加分題有令人滿意的答案且讓我十分欣賞,你的期末成績上就有可能得到加分。

小組工作

希望能夠兩人為一小組進行工作,尤其是具有不同背景(生物學或電腦科學)的學生。但每個學生仍需繳交自己的書面答案。如果有充份理由的話,期末專題可以由較大的小組完成。

筆記員與編輯者

除了問題集之外,每個學生都要負責一堂課的筆記和一堂課的編輯。如果你有興趣擔任某堂課的筆記,請用電子郵件告知我們,不然的話,在每堂課的開始時將會挑選自願者。感謝這些擔任筆記和編輯的自願者讓課堂講稿得以被放上網路。

期末專題

在期末專題得到好的成績對於每個學生都是必要的。此專題可以是對單一論文進行深入研讀、實作或延伸某個演算法、或是由學生選擇對某個問題提供理論上的結果。期末專題的主題應該由任課教師與學生在繳交期限之前共同訂定。


Prerequisites

Structure and Interpretation of Computer Programs (6.001) or Introduction to Algorithms (18.410J/6.046J) or permission of instructor. No biology background is assumed. Familiarity in some reasonable programming language is a must.

Textbook

This book will treat most of the topics, though it may lack depth in some areas.

Jones, Neil C., and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Bradford Books. Cambridge, MA: MIT Press, August 1, 2004. ISBN: 0262101068.

Homework and Grading

Problem Sets

There will be a problem set for each section on the calendar. Since some sections are shorter than others, some problem sets will be easier than others. Problem sets will be given out at the first lecture of a new section and will be due within a week of the last lecture of that section. Problem sets will be due no sooner than 3 classes after the class in which they are handed out.

Each problem set will contain several easy problems and a few challenging ones (which will be marked with a '*'). If a problem set contains an extra-credit question, then this means I do not have a good answer and I would like to know if you do. You are expected to solve the easy problems and make progress on the challenging ones. Good answers on the extra-credit will endear you to me and might put +'s on your final grade.

Group Work

Working in groups of two is encouraged, especially among students of different backgrounds (biology or computation). Each student will have to submit their own write-up of the solutions. Final projects can be done in larger groups if justified.

Scribes and Editors

In addition to the problem sets, each student is responsible for scribing one lecture and editing one lecture. If you are interested in scribing specific topics, let us know by email, otherwise, volunteers will be chosen at the beginning of each lecture. It is thanks to the scribe and editor volunteers that lecture notes are made available online.

Final Project

A final project is required of each student for them to get a good grade. The project can be studying a single paper in depth, implementing/extending an algorithm, or proving theoretical results on a problem of the student's choice. Topic for the final project should be set between the instructor and the student no later than drop date.


 
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