CMSC 423 Bioinformatics Fall 2010 Course objectives Study interesting algorithms and methods for the analysis of biological data We will cover string matching algorithms string searching string pattern finding e g gene finding discovery of protein binding sites genome assembly phylogenetics protein structure prediction and several topics of current research interest in bioinformatics Professor Carl Kingsford Office CBCB 3113 Email carlkcs umd edu Office hours Mondays 2 303 30 If you cannot attend office hours at this time email me about scheduling a different time Web page http www cs umd edu class fall2010 cmsc423 Grades will be posted on http grades cs umd edu Class time Tue Thr 9 30am 10 45pm in CSIC 2107 Textbook An Introduction to Bioinformatics Algorithms by Neil C Jones and Pavel A Pevzner The MIT Press 2004 ISBN 0 262 10106 8 Unfortunately because bioinformatics is a broad new and raplidly changing field there is no great textbook The material in the textbook will be supplemented by lecture slides and handouts Course work There will be 5 homework sets of 3 5 problems each There will be 2 in class exams each non cumulative and a comprehensive final There will be a multi part group project Approximate grading weight 10 for homeworks 20 for each exam 30 for the final and 20 for the project The class will be graded on a curve Homework policies Written problem sets are due at the start of class No late homework will be accepted turn in what you have completed If you will miss class turn in the homework early Answers to homework problems should be written concisely and clearly Messy or poorly written homeworks will not be graded Typesetting homeworks with LaTeX is encouraged but not required Homework problems that ask for an algorithm should present a clear English description or pseudocode of the algorithm a convincing argument for why the algorithm is correct and an estimate of the running time Graded homeworks should be picked up in class if you miss the class when the homework is returned please pick it up during office hours Regrade requests should be made in writing within 1 week of the homework being returned You may discuss the problems with classmates You must list the names of the class members with whom you worked at the top of your homework You must write up your own solution independently Exam policies Exams and the final will be closed book closed note The midterms will be held in class on September 30 2010 and November 11 2010 The final exam will be in class at the time set by the official university exam schedule Project policies Projects will be completed in small groups and will involve programming You may NOT copy or give code to other groups Providing code and using code from other groups are both academic integrity violations that generally receive the same punishment You cannot incorporate code from the internet into your projects Submitted projects may be checked automatically for inappropriate code use More details about the projects will be available in a few weeks 1 The maximum possible score of a project will be reduced by 10 for every day it is late After 5 late days the project will no longer be accepted Excused absences Students claiming an excused absence must apply in writing and furnish documentary support such as from a health care professional who treated the student for any assertion that the absence qualifies as an excused absence The support should explicitly indicate the dates or times the student was incapacitated due to illness Self documentation of illness is not sufficient to excuse the absence Absences for religious observances must be submitted in writing to the instructor within two weeks of the start of the semester The instructor is not under obligation to offer a substitute assignment or to give a student a make up assessment unless the failure to perform was due to an excused absence An excused absence for an individual typically does not translate into an extension for team deliverables on a project Academic accommodations Any student eligible for and requesting reasonable academic accommodations due to a disability is requested to provide to the instructor in office hours a letter of accommodation from the Office of Disability Support Services DSS within the first two weeks of the semester Course evaluations At the end of the semester please fill out a course evaluation at http www courseevalum umd edu Course evaluations are read and taken seriously Academic honesty All class work should be done independently unless explicitly indicated on the assignment handout You may discuss homework problems with classmates but must write your solution by yourself If you do discuss assignments with other classmates you must supply their names at the top of your homework Projects may be completed in teams as specified on the project handout No excuses will be accepted for copying others work from the current or past semesters and violations will be dealt with harshly Every year many CS students are referred to the honor board which is an unpleasant experience for everyone and can seriously impact plans for graduate school graduation etc Getting a bad grade is much preferable to cheating To quote the honor council The University of Maryland College Park has a nationally recognized Code of Academic Integrity administered by the Student Honor Council This Code sets standards for academic integrity at Maryland for all undergraduate and graduate students As a student you are responsible for upholding these standards for this course It is very important for you to be aware of the consequences of cheating fabrication facilitation and plagiarism For more information on the Code of Academic Integrity or the Student Honor Council please visit http www shc umd edu To further exhibit your commitment to academic integrity remember to sign the Honor Pledge on all examinations and assignments I pledge on my honor that I have not given or received any unauthorized assistance on this examination assignment 2 Tentative Schedule Sequence Comparison Dynamic Programming 3 weeks Dynamic programming Longest common subsequence Sequence alignment local global semiglobal Space efficient sequence alignment Multiple sequence alignment RNA folding Sequence Search String Data Structures 1 5 weeks Suffix trees Suffix arrays Burrows Wheeler transform Pattern Finding with Hidden Markov Models EM Gibbs Sampling 2 weeks Hidden Markov models HMMs for gene finding HMMs for