CMSC423-0101: Bioinformatic Algorithms, Databases, and Tools-Spring 2015 mpop
Computers have revolutionized modern biological research, by providing biologists with the means to manage and analyze the large amounts of data generated through high-throughput experiments. This course provides a practical introduction to the main algorithms, databases, and tools used in bioinformatics, at the same time providing insight into the biological problems being addressed.
Many of the techniques you learn in this course are applicable beyond the bioinformatics domain and are relevant to other data-driven fields of computer science.
No knowledge of biology is required for this course.
Logistics
Instructor: Mihai Pop
Links to an external site. (mpop@umiacs.umd.edu)
Instructor office: Biomolecular Sciences Building, Room 3120F; or AVW 3223 (by appointment only)
Instructor office hours: Mondays 10-11am, Tuesdays 11-12am in AVW 3223
TA: Rotem Katzir
TA office hours: Wednesdays 2-4pm in AVW 3223
Location: CSIC 1121
Days/time: Tue/Thu 12:30-1:45 pm
Textbook: http://bioinformaticsalgorithms.com/ Links to an external site. (available at University Bookstore - http://umcp.bncollege.com Links to an external site.)
Learning outcomes
- Translate a biological problem into an algorithm and a software implementation
- Learn algorithmic strategies for processing strings of letters (also relevant beyond computational biology)
- Learn about biomedical questions of current relevance
- Learn to work in teams
Resources
See: https://myelms.umd.edu/courses/1130480/pages/class-resources
Grading (see below for details)
- Quizzes/in class participation - 10%
- In-class teamwork - 5%
- Programming projects - 25%
- Two in-class midterms - 30% (15% each)
- In-class final - 30%
Late policy
- 1 day late - 10% off
- 2 days late - 20% off
- 3 days late - 0 points
Attendance policy
Please notify me in advance if you will miss any exam due to a University sanctioned excuse (medical absence, religious observance, etc.). In case of sudden illness that causes you to miss an exam you must provide me with a medical note documenting the illness, and clearly specifying the days/times that you were incapacitated due to illness.
Part of the class grade is participation/quizzes. Reasonable absences will be accommodated when grading - please inform me in advance if you will miss a class. For quizzes you can miss 4 without any penalty. See below for more details.
Religious observances
You must notify me within 2 weeks from the beginning of class if you will miss a class or exam due to a religious observance. Requests received after two weeks will not be accommodated.
NOTE: 2 weeks have passed. No further requests will be accommodated.
Accommodations for disabilities
You must notify me within 2 weeks from the beginning of class if you require special accommodations due to disabilities. All such requests must be accompanied by documentation from DSS Links to an external site.. Requests received after this deadline will not be accommodated.
NOTE: 2 weeks have passed. No further requests will be accommodated.
Communication is key
Please participate in Piazza discussions, interact with your colleagues, and contact me and the TA if you have questions or concerns. Please include "CMSC423" in the subject of emails so that they do not get lost. For general questions about class material you are better off using Piazza as you are more likely to receive a prompt response.
Academic honesty
Simply put: cheating will not be tolerated under any circumstance. While you are allowed to prepare for assignments together, you must complete all individual assignments by yourselves. Also, all exams are strictly individual.
Quizzes
Prior to each class you will have to complete a quiz that tests that you have prepared for the class (read material, watched videos, etc.) These quizzes will not test that you fully understand the material, just that you have done your due diligence in preparing. I anticipate there will be about 20 such quizzes. Grading of these quizzes will be all or nothing based on having a majority of answers correct. You may miss up to 4 quizzes and still receive full credit. For further missed quizzes grading will be proportionally reduced.
Class participation - Learners and Tutors
As part of each quiz you will have to come up with a question about the material - something that you did not understand while preparing the class. If you fill in this question you will be called a 'learner'. If you believe you have understood all the material and have no questions, you can leave this question empty, and will be called a 'tutor'. During class I will randomly select one or more learners and ask them to present their question to the rest of the class. I will also select one or more tutors and ask them to help answer the question. If either 'learner' or 'tutor' is not properly prepared, they will lose credit for the day's quiz.
Class participation - team assignments
I will assign you to teams of 4-5 students based on your responses to an initial class survey. The members of each team will be responsible for helping each other learn, and also for working together during in-class exercises. Each team will be randomly called upon during class - the credit received will depend on satisfactory performance in these assignments. Note that points will not be distributed evenly to all team members, rather they will be decided by 3 team peer-assessments, submitted at the time of the two midterms and at the end of the class.
Illness/emergency preparedness
See http://www.umd.edu/emergencypreparedness Links to an external site. for more information.
If you are sick, don't come to class - no need to get others sick.
Please report sickness on http://grades.cs.umd.edu
Links to an external site. and by email to me and the TA.
Course Summary:
Date | Details | Due |
---|---|---|
Tue Jan 27, 2015 | Calendar Event Introduction to class | 12:30pm to 1:45pm |
Wed Jan 28, 2015 | Quiz Getting to know you | due by 11:59pm |
Assignment Reading: introduction to biology | due by 11:59pm | |
Thu Jan 29, 2015 | Quiz Reading quiz: Introduction to biological sequences | due by 10am |
Calendar Event Introduction to Biology | 12:30pm to 1:45pm | |
Mon Feb 2, 2015 | Assignment Class expectations survey | due by 11:59pm |
Tue Feb 3, 2015 | Assignment Patterns in DNA - Chapter 1 in Compeau and Pevzner | due by 10am |
Quiz Reading quiz: DNA replication | due by 10am | |
Calendar Event Patterns in DNA - exact matching | 12:30pm to 1:45pm | |
Thu Feb 5, 2015 | Calendar Event Patterns in DNA - exact matching | 12:30pm to 1:45pm |
Tue Feb 10, 2015 | Quiz Reading Quiz: Z and KMP algorithms | due by 10am |
Assignment Reading: Z and KMP algorithms. | due by 10am | |
Calendar Event Exact matching - Z algorithm, KMP algorithm | 12:30pm to 1:45pm | |
Thu Feb 12, 2015 | Calendar Event Exact matching - Z algorithm, KMP algorithm | 12:30pm to 1:45pm |
Tue Feb 17, 2015 | Calendar Event Proteomics | 12:30pm to 1:45pm |
Assignment Exact matching with KMP and the Z algorithm | due by 11:59pm | |
Quiz Reading Quiz: Proteomics | due by 11:59pm | |
Assignment Reading: Proteomics - Chapter 2 in Compeau and Pevzner | due by 11:59pm | |
Thu Feb 19, 2015 | Calendar Event Proteomics | 12:30pm to 1:45pm |
Tue Feb 24, 2015 | Calendar Event Catch-up, exam prep | 12:30pm to 1:45pm |
Thu Feb 26, 2015 | Calendar Event Midterm 1 | 12:30pm to 1:45pm |
Tue Mar 3, 2015 | Quiz Reading quiz: Motifs in DNA | due by 10am |
Assignment Reading: Motif finding - Chapter 3 in Compeau and Pevzner | due by 10am | |
Calendar Event Motif finding | 12:30pm to 1:45pm | |
Assignment Expectation survey - Midterm 1 | due by 11:59pm | |
Quiz Rate your team-mates - midterm 1 | due by 11:59pm | |
Thu Mar 5, 2015 | Assignment Rosalind on proteomics | due by 11:59pm |
Tue Mar 10, 2015 | Calendar Event Motif finding | 12:30pm to 1:45pm |
Assignment Midterm 1 - team | due by 1:45pm | |
Quiz Exit ticket - motifs | due by 11:59pm | |
Assignment Rosalind: Motif finding | due by 11:59pm | |
Thu Mar 12, 2015 | Assignment Ethics readings | due by 10am |
Calendar Event Biomedical ethics | 12:30pm to 1:45pm | |
Tue Mar 17, 2015 | Calendar Event SPRING BREAK | 12:30pm to 1:45pm |
Thu Mar 19, 2015 | Calendar Event SPRING BREAK | 12:30pm to 1:45pm |
Tue Mar 24, 2015 | Quiz Reading quiz: Assembly part 1 | due by 10am |
Assignment Reading: Genome assembly part1 | due by 10am | |
Calendar Event Genome assembly | 12:30pm to 1:45pm | |
Quiz Exit ticket - Genome Assembly | due by 10pm | |
Thu Mar 26, 2015 | Assignment Reading: Genome assembly part 2 | due by 10am |
Calendar Event Genome Assembly | 12:30pm to 1:45pm | |
Tue Mar 31, 2015 | Quiz Reading quiz: sequence alignment | due by 10am |
Assignment Reading: Sequence Alignment (Chapter 5) | due by 10am | |
Calendar Event Inexact alignment - dynamic programming | 12:30pm to 1:45pm | |
Quiz Exit ticket: Sequence Alignment | due by 10pm | |
Assignment Rosalind: Overlap Graph Problem | due by 11:59pm | |
Thu Apr 2, 2015 | Calendar Event Inexact alignment dynamic programming | 12:30pm to 1:45pm |
Tue Apr 7, 2015 | Calendar Event Catch-up, exam prep | 12:30pm to 1:45pm |
Thu Apr 9, 2015 | Calendar Event Midterm 2 | 12:30pm to 1:45pm |
Tue Apr 14, 2015 | Quiz Reading quiz: Genome rearrangements | due by 10am |
Assignment Reading: Genome rearrangements | due by 10am | |
Calendar Event Genomic rearrangements | 12:30pm to 1:45pm | |
Quiz Exit ticket - Genome rearrangements | due by 10pm | |
Assignment Rosalind: Fitting Alignment Problem | due by 11:59pm | |
Thu Apr 16, 2015 | Calendar Event Genomic rearrangements | 12:30pm to 1:45pm |
Assignment Midterm 2 - team | due by 1:45pm | |
Assignment Expectation survey - Midterm 2 | due by 11:59pm | |
Quiz Rate your team-mates - midterm 2 | due by 11:59pm | |
Tue Apr 21, 2015 | Quiz Reading quiz: String indexing | due by 10am |
Assignment Reading: String indexing - Chapter 7 | due by 10am | |
Calendar Event String indexing - suffix trees, Burrows Wheeler transform | 12:30pm to 1:45pm | |
Quiz Exit ticket - Genome indexing | due by 10pm | |
Thu Apr 23, 2015 | Calendar Event String indexing - suffix trees, burrows wheeler transform | 12:30pm to 1:45pm |
Assignment Perception survey | due by 11:59pm | |
Assignment Rosalind: Greedy reversal sorting | due by 11:59pm | |
Tue Apr 28, 2015 | Quiz Reading quiz: clustering | due by 10am |
Assignment Reading: clustering | due by 10am | |
Calendar Event Tentative: clustering | 12:30pm to 1:45pm | |
Wed Apr 29, 2015 | Quiz Exit ticket: clustering | due by 10pm |
Thu Apr 30, 2015 | Calendar Event Tentative: clustering | 12:30pm to 1:45pm |
Assignment Rosalind: Inverse Burrows-Wheeler Transform Problem | due by 11:59pm | |
Tue May 5, 2015 | Calendar Event Genome assembly validation and variant discovery | 12:30pm to 1:45pm |
Thu May 7, 2015 | Calendar Event Metagenomics/dealing with populations | 12:30pm to 1:45pm |
Tue May 12, 2015 | Calendar Event Parting thoughts | 12:30pm to 1:45pm |
Tue May 19, 2015 | Calendar Event FINAL EXAM | 1:30pm to 3:30pm |
Assignment Class policies | ||
Assignment Final exam | ||
Assignment First set of Rosalind exercises | ||
Assignment Midterm 1 - in class | ||
Assignment Midterm 2 in class | ||
Assignment Peer evaluation midterm 1 | ||
Assignment Peer evaluation midterm 2 |
