Difference between revisions of "BIO337 2014"
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Jan 16, 2014 - Intro to Python | Jan 16, 2014 - Intro to Python | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BIO337_2014/BIO337-Python_primer-Spring2014.pdf Python primer] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BIO337_2014/ProblemSet1_Spring2014.pdf Problem Set 1], due Feb. 5, 2013 |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BIO337_2014/Ecoli_genome.txt E. coli genome] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BIO337_2014/Tvolcanium_genome.txt T. volcanium genome] |
| − | * 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/ | + | * 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BIO337_2014/Mgene1 Mgene1], [http://www.marcottelab.org/users/BIO337_2014/Mgene2 Mgene2], [http://www.marcottelab.org/users/BIO337_2014/Mgene3 Mgene3] |
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Jan 14, 2014 - Introduction | Jan 14, 2014 - Introduction | ||
* Some warm-up videos to get you started on Python: [http://www.codecademy.com/tracks/python Python coding for beginners]<br> | * Some warm-up videos to get you started on Python: [http://www.codecademy.com/tracks/python Python coding for beginners]<br> | ||
| − | * We'll be conducting homework using the online environment [http://rosalind.info/faq/ Rosalind]. Go ahead and register on the site, and enroll specifically for BIO337 using [http://rosalind.info/classes/enroll/32e1671726/ ''this link'']. | + | * We'll be conducting homework using the online environment [http://rosalind.info/faq/ Rosalind]. Go ahead and register on the site, and enroll specifically for BIO337 using [http://rosalind.info/classes/enroll/32e1671726/ ''this link'']. Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is '''due by 11:59PM January 21'''. |
* A useful online resource if you get bogged down: [http://nematodes.org/martin/teaching/introduction-to-python-for-biologists/ Python for Biologists]. (& just a heads-up that some of their instructions for running code relate to a command line environment that's a bit different from the default one you install following the Rosalind instructions. It won't affect the programs, just the way they are run or how you specific where files are located.)<br> | * A useful online resource if you get bogged down: [http://nematodes.org/martin/teaching/introduction-to-python-for-biologists/ Python for Biologists]. (& just a heads-up that some of their instructions for running code relate to a command line environment that's a bit different from the default one you install following the Rosalind instructions. It won't affect the programs, just the way they are run or how you specific where files are located.)<br> | ||
* An oldie (by recent bioinformatics standards) but goodie: [http://www.marcottelab.org/users/BIO337_2014/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus] | * An oldie (by recent bioinformatics standards) but goodie: [http://www.marcottelab.org/users/BIO337_2014/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus] | ||
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'''No exams will be given. Grades will be based on online homework (counting 30% of the grade), 3 problem sets (given every 2-3 weeks and counting 15% each towards the final grade) and a course project (25% of final grade), which will be collaborative.''' Cross-discipline collaborations will be encouraged. The course project will consist of a research project on a bioinformatics topic chosen by the students (with approval by the instructor) containing an element of independent computational biology research (e.g. calculation, programming, database analysis, etc.). This will be turned in as a link to a web page.<br> | '''No exams will be given. Grades will be based on online homework (counting 30% of the grade), 3 problem sets (given every 2-3 weeks and counting 15% each towards the final grade) and a course project (25% of final grade), which will be collaborative.''' Cross-discipline collaborations will be encouraged. The course project will consist of a research project on a bioinformatics topic chosen by the students (with approval by the instructor) containing an element of independent computational biology research (e.g. calculation, programming, database analysis, etc.). This will be turned in as a link to a web page.<br> | ||
| − | Online homework will be assigned and evaluated using the free bioinformatics web resource [http://rosalind.info/faq/ Rosalind]. | + | Online homework will be assigned and evaluated using the free bioinformatics web resource [http://rosalind.info/faq/ Rosalind].<br> |
| + | |||
| + | All projects and homework will be turned in electronically and time-stamped. No makeup work will be given. Instead, all students have 5 days of free “late time” (for the '''entire semester''', NOT per project, and counting weekends/holidays). For projects turned in late, days will be deducted from the 5 day total (or what remains of it) by the number of days late (in 1 day increments, rounding up, i.e. 10 minutes late = 1 day deducted). Once the full 5 days have been used up, assignments will be penalized 10 percentage points per day late (rounding up), i.e., a 50 point assignment turned in 1.5 days late would be penalized 20%, or 10 points.<br> | ||
| + | |||
| + | Students are welcome to discuss ideas and problems with each other, but '''all programs, Rosalind homework, and written solutions should be performed independently''' (except the final collaborative project).<br> | ||
'''The final project is due by midnight April 28, 2014.''' | '''The final project is due by midnight April 28, 2014.''' | ||
Revision as of 16:41, 13 January 2014
BIO337 Systems Biology/Bioinformatics
Course unique #: 50524
Lectures: Tues/Thurs 11 – 12:30 PM in BUR 212
Instructor: Edward Marcotte, marcotte@icmb.utexas.edu
- Office hours: Wed 11 AM – 12 noon in MBB 3.148BA
TA: Dakota Derryberry, dakotaz@utexas.edu
- TA Office hours: Mon 4 - 5 PM/Fri 9 – 10 AM in MBB 3.304 Phone: 512-232-2459
Lectures & Handouts
Jan 14, 2014 - Introduction
- Some warm-up videos to get you started on Python: Python coding for beginners
- We'll be conducting homework using the online environment Rosalind. Go ahead and register on the site, and enroll specifically for BIO337 using this link. Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is due by 11:59PM January 21.
- A useful online resource if you get bogged down: Python for Biologists. (& just a heads-up that some of their instructions for running code relate to a command line environment that's a bit different from the default one you install following the Rosalind instructions. It won't affect the programs, just the way they are run or how you specific where files are located.)
- An oldie (by recent bioinformatics standards) but goodie: Computers are from Mars, Organisms are from Venus
Syllabus & course outline
An introduction to systems biology and bioinformatics, emphasizing quantitative analysis of high-throughput biological data, and covering typical data, data analysis, and computer algorithms. Topics will include introductory probability and statistics, basics of Python programming, protein and nucleic acid sequence analysis, genome sequencing and assembly, proteomics, synthetic biology, analysis of large-scale gene expression data, data clustering, biological pattern recognition, and gene and protein networks.
Open to upper division undergraduates in natural sciences and engineering.
Prerequisites: Biochem I or equivalent (e.g. CH339J or CH339K/L), basic familiarity with molecular biology.
Note that this is not a course on practical sequence analysis or using web-based tools. Although we will use a number of these to help illustrate points, the focus of the course will be on learning the underlying algorithms and exploratory data analyses and their applications, esp. in high-throughput biology.
Most of the lectures will be from research articles and slides posted online, with some material from the...
Optional text (for sequence analysis): Biological sequence analysis, by R. Durbin, S. Eddy, A. Krogh, G. Mitchison (Cambridge University Press),
For biologists rusty on their stats, The Cartoon Guide to Statistics (Gonick/Smith) is very good. A reasonable online resource for beginners is Statistics Done Wrong.
Some online references:
An online bioinformatics course
Assorted bioinformatics resources on the web: Assorted links
Beginning Python for Bioinformatics
Online probability texts: #1, #2, #3
No exams will be given. Grades will be based on online homework (counting 30% of the grade), 3 problem sets (given every 2-3 weeks and counting 15% each towards the final grade) and a course project (25% of final grade), which will be collaborative. Cross-discipline collaborations will be encouraged. The course project will consist of a research project on a bioinformatics topic chosen by the students (with approval by the instructor) containing an element of independent computational biology research (e.g. calculation, programming, database analysis, etc.). This will be turned in as a link to a web page.
Online homework will be assigned and evaluated using the free bioinformatics web resource Rosalind.
All projects and homework will be turned in electronically and time-stamped. No makeup work will be given. Instead, all students have 5 days of free “late time” (for the entire semester, NOT per project, and counting weekends/holidays). For projects turned in late, days will be deducted from the 5 day total (or what remains of it) by the number of days late (in 1 day increments, rounding up, i.e. 10 minutes late = 1 day deducted). Once the full 5 days have been used up, assignments will be penalized 10 percentage points per day late (rounding up), i.e., a 50 point assignment turned in 1.5 days late would be penalized 20%, or 10 points.
Students are welcome to discuss ideas and problems with each other, but all programs, Rosalind homework, and written solutions should be performed independently (except the final collaborative project).
The final project is due by midnight April 28, 2014.
- How to make a web site for the final project
