Difference between revisions of "CH391L 2013"
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* [http://www.marcottelab.org/users/CH391L/Handouts/BACsYACsCosmidsOhMy.pdf BACs, YACs, and cosmids, oh my!] | * [http://www.marcottelab.org/users/CH391L/Handouts/BACsYACsCosmidsOhMy.pdf BACs, YACs, and cosmids, oh my!] | ||
| − | Feb | + | Feb 21, 2013 - Gene finding |
* [http://www.marcottelab.org/users/CH391L/Handouts/GENSCAN.pdf The GENSCAN paper] | * [http://www.marcottelab.org/users/CH391L/Handouts/GENSCAN.pdf The GENSCAN paper] | ||
* Evaluating gene annotations: [http://www.marcottelab.org/users/CH391L/Handouts/GASP.pdf GASP], [http://www.marcottelab.org/users/CH391L/Handouts/EGASP.pdf EGASP], & [http://www.marcottelab.org/users/CH391L/Handouts/NGASP.pdf nGASP] | * Evaluating gene annotations: [http://www.marcottelab.org/users/CH391L/Handouts/GASP.pdf GASP], [http://www.marcottelab.org/users/CH391L/Handouts/EGASP.pdf EGASP], & [http://www.marcottelab.org/users/CH391L/Handouts/NGASP.pdf nGASP] | ||
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* [http://www.marcottelab.org/users/CH391L/ProblemSets/state_sequences-Tsegmenthistogram.pdf T segment histogram] | * [http://www.marcottelab.org/users/CH391L/ProblemSets/state_sequences-Tsegmenthistogram.pdf T segment histogram] | ||
| − | Feb | + | Feb 19, 2013 - HMMs and gene finding |
* [http://www.marcottelab.org/users/CH391L/Handouts/FlyCellMarkovChains.pdf Fly cell Markov chains] | * [http://www.marcottelab.org/users/CH391L/Handouts/FlyCellMarkovChains.pdf Fly cell Markov chains] | ||
| − | Feb | + | Feb 14, 2013 - HMMs |
* [http://www.marcottelab.org/users/CH391L/Handouts/nbt1004-1315-primer-whatareHMMs.pdf HMM primer] | * [http://www.marcottelab.org/users/CH391L/Handouts/nbt1004-1315-primer-whatareHMMs.pdf HMM primer] | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/ProblemSet2_2011.pdf Problem Set 2], due Feb. 24, 2011 |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/state_sequences State sequences] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/soluble_sequences Soluble sequences] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/transmembrane_sequences Transmembrane sequences] |
| − | Feb | + | Feb 12, 2013 - Profiles |
* [http://www.marcottelab.org/users/CH391L/Handouts/bioinformaticschallenges.2011.pdf A commentary] on computational challenges arising from DNA sequencing | * [http://www.marcottelab.org/users/CH391L/Handouts/bioinformaticschallenges.2011.pdf A commentary] on computational challenges arising from DNA sequencing | ||
* The remarkable growth of [http://www.ncbi.nlm.nih.gov/genbank/genbankstats.html Genbank], and similarly, [http://www.ebi.ac.uk/uniprot/TrEMBLstats/ UniProt] | * The remarkable growth of [http://www.ncbi.nlm.nih.gov/genbank/genbankstats.html Genbank], and similarly, [http://www.ebi.ac.uk/uniprot/TrEMBLstats/ UniProt] | ||
| − | Feb | + | Feb 7, 2013 - BLAST |
* [http://www.marcottelab.org/users/CH391L/Handouts/BLAST.pdf The original BLAST paper] | * [http://www.marcottelab.org/users/CH391L/Handouts/BLAST.pdf The original BLAST paper] | ||
* [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] | * [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] | ||
* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art. | * [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art. | ||
| − | Feb | + | Feb 5, 2013 - Sequence Alignment III |
* A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3] | * A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3] | ||
* Repeats in the human genome, tallied [http://www.biochem.arizona.edu/classes/bioc471/pages/Lecture7/a6GenomeRepeats.jpg here] | * Repeats in the human genome, tallied [http://www.biochem.arizona.edu/classes/bioc471/pages/Lecture7/a6GenomeRepeats.jpg here] | ||
| − | + | Jan 31, 2013 - Sequence Alignment II | |
* [http://www.marcottelab.org/users/CH391L/Handouts/GALPAS.xls An example of dynamic programming using Excel], created by [http://noble.gs.washington.edu/~mmh1/ Michael Hoffman] (a former CH391L student; you can read more about Michael [http://www.marcottelab.org/users/CH391L/Handouts/MichaelHoffman.pdf here]) | * [http://www.marcottelab.org/users/CH391L/Handouts/GALPAS.xls An example of dynamic programming using Excel], created by [http://noble.gs.washington.edu/~mmh1/ Michael Hoffman] (a former CH391L student; you can read more about Michael [http://www.marcottelab.org/users/CH391L/Handouts/MichaelHoffman.pdf here]) | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/CH391L_2013/Handouts/Lecture5-NBT-primer-dynamicprogramming.pdf Dynamic programming primer] |
| − | Jan | + | Jan 24, 2013 - Sequence Alignment I |
* [http://www.marcottelab.org/users/CH391L/CH391L_SeqAlign1.pdf Taejoon's presentation file] | * [http://www.marcottelab.org/users/CH391L/CH391L_SeqAlign1.pdf Taejoon's presentation file] | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/CH391L_2013/Handouts/Lecture4-NBT-primer-BLOSUM.pdf BLOSUM primer] |
* [http://www.marcottelab.org/users/CH391L/Handouts/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!) | * [http://www.marcottelab.org/users/CH391L/Handouts/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!) | ||
| − | Jan | + | Jan 22, 2013 - Python primer |
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/ProblemSet1_Spring2013.pdf Problem Set 1], due Feb. 5, 2013 | * [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/ProblemSet1_Spring2013.pdf Problem Set 1], due Feb. 5, 2013 | ||
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Ecoli_genome.txt E. coli genome] | * [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Ecoli_genome.txt E. coli genome] | ||
Revision as of 18:21, 13 January 2013
Contents |
CH364C/CH391L Bioinformatics
Course unique #: 52716/52990
Lectures: Tuesday/Thursday 2:00 – 3:30 PM in WEL 3.260
Instructor: Edward Marcotte, marcotte@icmb.utexas.edu
- Office hours: Wednesdays 2:00 – 3:00 PM in MBB 3.148BA Phone: 471-5435
TA: John Woods, john.woods at marcottelab dot org
- TA Office hours: Tuesday/Friday 10:00 – 11:00 AM in MBB 3.128 Phone: 232-3919
Lectures & Handouts
Syllabus & course outline
An introduction to computational biology and bioinformatics. The course covers typical data, data analysis, and algorithms encountered in computational biology. Topics will include introductory probability and statistics, basics of programming, protein and nucleic acid sequence analysis, genome sequencing and assembly, synthetic biology, analysis of gene expression data, data clustering, biological pattern recognition, and biological networks.
Open to graduate students and upper division undergraduates in natural sciences and engineering.
Prerequisites: Basic familiarity with molecular biology, statistics & computing, but realistically, it is expected that students will have extremely varied backgrounds.
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.
Most of the lectures will be from research articles and handouts, with some material from the...
Recommended text (for sequence analysis): Biological sequence analysis, by R. Durbin, S. Eddy, A. Krogh, G. Mitchison (Cambridge University Press),
For non-molecular biologists, I highly recommend (really!) The Cartoon Guide to Genetics (Gonick/Wheelis)
For biologists rusty on their stats, The Cartoon Guide to Statistics (Gonick/Smith) is also very good.
Some online references:
An online bioinformatics course
Assorted bioinformatics resources on the web: #1, #2
Python coding for beginners
Online probability texts: #1, #2, #3
No exams will be given. Grades will be based on 4 problem sets (given every 2 weeks and counting 15% each towards the final grade) and a course project (40% of final grade), which can be individual or collaborative. If collaborative, cross-discipline collaborations are encouraged. The course project will consist of a research paper or project on a bioinformatics topic chosen by the student (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.
The final project is due on April 30, 2013.
Helpful links
- If you don't have a unix/linux account to do the homework and/or project, send email to 'john.woods at marcottelab dot org'.
- CH391L/Connecting_Server (If you don't know how to use the account info, this are the instructions.)
- If you are having trouble transferring files from your computer to server, here are some GUI programs that can help you:
- http://winscp.net/eng/index.php (WinSCP, Windows)
- http://cyberduck.ch/ (CyberDuck, Mac)
- http://filezilla-project.org/ (FileZilla, all platforms)
- How to make a web site for the final project
