BCH391L 2015
BCH364C/391L Systems Biology/Bioinformatics
Course unique #: 54995/55095
Lectures: Tues/Thurs 11 – 12:30 PM in BUR 212
Instructor: Edward Marcotte, marcotte@icmb.utexas.edu
- Office hours: Wed 4 PM – 5 PM in MBB 3.148BA
TA: Joe Taft, taft@utexas.edu
- NOTE THE CHANGE IN OFFICE HOUR TIMES & LOCATIONS
- TA Office hours: Mon/Fri 10 AM - 11 AM in MBB 2.456/3.204 Phone: listed on the syllabus
Lectures & Handouts
April 23, 2015 - Networks II
- We're finishing up the slides from Apr. 21.
April 21, 2015 - Networks
- Today's slides
- Metabolic networks: The wall chart (it's interactive, e.g. here's enolase), the current state of the human metabolic reaction network, and older but still relevant review of transcriptional networks (with the current record holder in this regard held by ENCODE), and an early review of protein interaction extent and quality whose lessons still hold.
- Useful gene network resources include:
- FunctionalNet, which links to human, worm, Arabidopsis, mouse and yeast gene networks. Not the prettiest web site, but useful, and helped my own group find genes for a wide variety of biological processes. Try searching HumanNet for the myelin regulatory factor MYRF (Entrez gene ID 745) and predicting its function, which is now known but wasn't when the network was made.
- STRING is available for many organisms, including large numbers of prokaryotes. Try searching on the E. coli enolase (Eno) as an example.
- GeneMania, which aggregates many individual gene networks.
- MouseFunc, a collection of network and classifier-based predictions of gene function from an open contest to predict gene function in the mouse.
- The best interactive tool for network visualization is Cytoscape. You can download and install it locally on your computer, then visualize and annotated any gene network, such as are output by the network tools linked above. There is also a web-based network viewer that can be incorporated into your own pages (e.g., as used in YeastNet).
Reading:
- Functional networks
- Review of predicting gene function and phenotype from protein networks
- Primer on visualizing networks
Apr 16, 2015 - Genome Engineering
- Guest speaker: Dr. Chris Yellman
Apr 14, 2015 - Principal Component Analysis (& the curious case of European genotypes)
- Today's slides
- European men, their genomes, and their geography
- Relevant to today's discussion for his eponymous distance measure: Mahalanobis
A smattering of links on PCA:
- NBT Primer on PCA
- A PCA overview (.docx format) & the original post
- Science Signaling (more specifically, Neil R. Clark and Avi Ma’ayan!) had a nice introduction to PCA that I've reposted here (with slides)
- Python code for performing PCA yourself
Apr 9, 2015 - Classifiers I
- Today's slides
- Classifying leukemias
- For those of you using classifiers for your projects, here's the best open software for do-it-yourself classifiers and data mining: Weka
Apr 7, 2015 - Clustering II
- We're finishing up the slides from Apr. 2.
- Fuzzy k-means
- SOM gene expression
- Links to various applications of SOMs: 1, 2, 3, 4. You can run SOMs on the following web site. You can also run SOM clustering with the Open Source Clustering package (an alternative to Eisen's Cluster) with '-s' option, or GUI option. See http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM for detail. (FYI, it also supports PCA). If you are not happy with Cluster's SOM function, the statistical package R also provides a package for calculating SOMs (http://cran.r-project.org/web/packages/som/index.html).
Apr 2, 2015 - Functional Genomics & Data Mining - Clustering I
- Today's slides
- Clustering
- Review of phylogenetic profiles
- B cell lymphomas
- Primer on clustering
- K-means example (.ppt)
Problem Set 3, due before midnight Apr. 14, 2015. You will need the following software and datasets:
- The clustering and treeview software is available here. Previous students have said the Mac/Linux versions of the tree viewing program can be a bit buggy; however, the Windows version (TreeView) seems to be fine.
- Yeast protein sequences
- Yeast protein phylogenetic profiles
- Yeast mRNA expression profiles
Mar 31, 2015 - Motifs
- News of the day
- Those of you with a passion to teach math to the next generation might be interested in the Apollo 20 Fellowship
- Today's slides
- NBT Primer - What are motifs?
- NBT Primer - How does motif discovery work?
- The biochemical basis of a particular motif
- Gibbs Sampling
- AlignAce
Mar 26, 2015 - Mapping protein complexes
- Guest speaker: Blake Borgeson
Mar 24, 2015 - Mass spectrometry proteomics
- Welcome back from Spring Break. Apparently, we had some down time on Rosalind, so I'm extending the HW3 deadline to 11:59PM March 26...
- Guest speaker: Dr. Daniel Boutz
Mar 17-19, 2015 - SPRING BREAK
Mar 12, 2015 - Genomes II, Gene Expression
- For those of you interested in summer coding: SciRuby summer of code project
- For those of you interested in doing your homework/research with more experienced coders in the room, there will be a weekly Open Coding Hour in the CCBB conference room / collaboratorium (GDC 7.514) each Tuesday from 5-7 PM. Scott Hunicke-Smith will begin each Open Coding Hour with 10 minutes of computing tricks. Accompanying google group in-house programming question and answer forum.
- Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is due by 11:59PM March 24.
- A gentle reminder that HW2 is due by 11:59PM tonight
- We're finishing up the slides from Mar. 10, then on to RNA expression. Note: we'll increasingly be discussing primary papers in the lectures. Here are a few classics and reviews that will come up.
- Gene expression by ESTs
- Gene expression by SAGE
- Affy microarrays 1 & Affy microarrays 2
- cDNA microarrays
- RNA-Seq
- Clustering by gene expression
- Cell cycle data
Mar 10, 2015 - Genome Assembly
- Today's slides
- DeBruijn Primer and Supplement
- Here are a few explanations of using the BWT for indexing: 1 2 3
Mar 5, 2015 - *** ICE STORM 2015***, UT classes cancelled
Mar 3, 2015 - Gene finding II
- We're finishing up the slides from Feb. 26, then moving on into Genome Assembly
- Due March 12 by email - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators. This assignment will account for 5 points out of your 25 total points for your course project.
- Here are a few examples of final projects from previous years: 1, 2, 3, 4, 5 6 7 8 9 10 11 12 13 14
- Office hours tomorrow overlap a seminar (MBB 1.210, 4-5PM) from Prof. Wah Chiu of the Baylor College of Medicine, "Visualizing Viruses Inside and Outside the Cells". The talk will be better, so I propose office hours be skipped in favor of the talk. Here are a few snippets from Prof. Chiu's research to whet your appetite: Infected cyanobacteria, Lemon-shaped viruses, drug efflux pumps, and building "3D cellular context"
Feb 26, 2015 - Gene finding
Reading:
Feb 24, 2015 - HMMs II
- News of the day: Mammoths!
- We're finishing up the slides from Feb. 19.
Problem Set 2, due before midnight Mar. 10, 2015:
- Problem Set 2.
- You'll need these 3 files: State sequences, Soluble sequences, Transmembrane sequences
Feb 19, 2015 - Hidden Markov Models
- re: our discussion of databases, another view of the remarkable growth of data, e.g. UniProt
- Today's slides
Reading:
- HMM primer and Bayesian statistics primer, Wiki Bayes
- Care to practice your regular expressions? (In python?)
Feb 17, 2015 - Next-generation Sequencing (NGS)
- Guest speaker: Dr. Scott Hunicke-Smith, director of the Genome Sequencing and Analysis Facility.
- Illumina/Solexa Sequencing (Youtube Video)
- Genome Analyzer (Youtube Video)
Feb 12, 2015 - 3D Protein Structure Modeling
- Congratulations to this year's Dan David Prize winners, awarded in bioinformatics (!) to David Haussler, Cyrus Chothia, and Michael Waterman !!!
- Guest speaker: Dr. Kevin Drew, formerly of New York University and now at the UT Center for Systems and Synthetic Biology
- Today's slides
- The Rosetta software suite for 3D protein modeling, and what it can do for you
- The Protein Data Bank, HHPRED, MODELLER, and Pymol
Feb 10, 2015 - Biological databases
- Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is due by 11:59PM February 19.
- Just a note that we'll be seeing ever more statistics as go on. Here's a good primer from Prof. Lauren Myers to refresh/explain basic concepts.
- Today's slides
Feb 5, 2015 - Guest lecture: Intro to Appsoma
- We'll have a guest lecture by Zack Simpson, a Fellow of the UT Center for Systems and Synthetic Biology. For the curious, Science magazine wrote a nice feature on Zack several years ago (posted here). Zack co-founded the bioinformatics startup company Traitwise (full disclosure: I'm on their scientific advisory board) and is the lead developer of Appsoma, a web-based scientific cloud computing platform that has a number of enhancements (and dedicated computer clusters) specifically for UT students.
Feb 3, 2015 - BLAST
- Our slides today are modified from a paper on Teaching BLAST by Cheryl Kerfeld & Kathleen Scott.
- The original BLAST paper
- The protein homology graph paper. Just for fun, here's a link to a stylized version we exhibited in the engaging Design and the Elastic Mind show at New York's Museum of Modern Art.
- Repeats in the human genome, tallied here
Jan 29, 2015 - Sequence Alignment II
- We're finishing up the slides from Jan. 27. Note that I added a few more slides.
- Dynamic programming primer
- An example of dynamic programming using Excel, created by Michael Hoffman (a former UT undergraduate who took the prior incarnation of this class)
- A few examples of proteins with internally repetitive sequences: 1, 2, 3
Jan 27, 2015 - Sequence Alignment I
- One of my favorite news items last year: China cloning on an 'industrial scale'. Favorite quote: "If it tastes good you should sequence it..." BGI is one of the biggest (the biggest?) genome sequencing centers in the world and employs >2,000 bioinformatics researchers.
- Today's slides
Problem Set I, due before midnight Feb. 5, 2015:
- Problem Set 1
- T. volcanium genome
- 3 mystery genes (for Problem 5): Mgene1, Mgene2, Mgene3
Reading:
- BLOSUM primer
- The original BLOSUM paper (hot off the presses from 1992!)
- BLOSUM miscalculations improve performance
- There is a good discussion of the alignment algorithms and different scoring schemes here
Jan 22, 2015 - Intro to Python
- Note the new TA office hour times & locations (M/F 10-11, MBB 3.304/3.204)
- Latest rumor on the street...
- Today's slides
- Python primer
- E. coli genome
Jan 20, 2015 - Introduction
- Today's slides
- Some warm-up videos to get you started on Python: Code Academy's 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 BCH364C/391L 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 27.
- 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.) However, if you've never programmed before, definitely check this out!!!
- 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 graduate students and upper division undergrads (with permission) 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, 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 percent per day late (rounding up), i.e., a 50 point assignment turned in 1.5 days late would be penalized 20%, or 10 points.
Homework, problem sets, and the project total to a possible 100 points. There will be no curving of grades, nor will grades be rounded up. We’ll use the plus/minus grading system, so: A= 92 and above, A-=90 to 91.99, etc. Just for clarity's sake, here are the cutoffs for the grades: 92% ≤ A, 90% ≤ A- < 92%, 88% ≤ B+ < 90%, 82% ≤ B < 88%, 80% ≤ B- < 82%, 78% ≤ C+ < 80%, 72% ≤ C < 78%, 70% ≤ C- < 72%, 68% ≤ D+ < 70%, 62% ≤ D < 68%, 60% ≤ D- < 62%, F < 60%.
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 May 4, 2015.
- How to make a web site for the final project
- Google Site: https://support.google.com/sites/answer/153197?hl=en