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| BioE131/231
Introduction to Computational Biology.
Course info
- Code: Bioe131/231
- Title: Introduction to computational biology
- Instructor: Ian Holmes (follow the link to my page for my office hours)
- GSI: Oscar Westesson (office hours: During lab time. I will have additional O.H. if there is sufficient demand)
- When:
- Lecture log
Calendar & announcements
Mitch Skinner, developer of JBrowse, will be available in 381 Stanley on Tuesdays from 3-5pm to answer questions about JBrowse setup and configuration.
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See also the BioE131 fact sheet.
- Grading scheme
- 40% homework assignments
- 25% midterm exams
- 35% final project
- Extensions/Alternate Exam Dates
- Requests for extensions on homework due dates must be submitted to Ian Holmes via email at least 2 days before homework due date, clearly stating reason(s) for request.
- Please plan to attend the scheduled exam/presentation times. Requests for alternate exam/presentation dates must be submitted to Ian Holmes via email as soon as possible, clearly stating reason(s) for request. An alternate date request is only likely to be granted under extreme circumstances (family emergencies, major illness, etc.)
- Conflicting commitments on other courses will not usually be considered adequate reason to moving exams or homework deadlines unless the conflict is experienced by a majority of the class.
- Every year several requests failing to meet the above criteria are declined -- please do not invite mutual disillusion by asking for an exception.
- Teamwork
- We want to encourage you to work together, so for regular homework assignments, you may submit jointly with up to one other student as long as you identify who it was you worked with. However, we also want to encourage mixing, so you can contribute no more than three homework assignments with any one partner. After that you will have to rotate with someone else.
Student wiki
Notes and handouts
Slides
DISCLAIMER: The Powerpoint slides below were created using Microsoft Office on an Apple Mac.
They may not display properly on a Windows PC, or on OpenOffice.
I do not know of any conversion program that can convert Powerpoint files into PDFs in "batch" (command-line) mode.
Thus, in order to provide PDF copies, every PDF would have to be generated manually, and this would have to be repeated every time a change was made to the Powerpoint slides.
Inevitably, the PDFs would sometimes lag behind the PPT versions, creating huge potential for complexity and confusion.
If you cannot read the slides, and you did not take notes during class, please find someone in the class who has a Mac and ask them to do the conversion for you.
I apologize for the inconvenience.
Computational virus design
Scripting compbio applications
DNA pattern recognition & analysis
Genome and pathway databases
Information content of DNA
Other material
Some material is presented on the chalkboard rather than the projector, so there are no Powerpoint slides for these topics.
Wikipedia has a lot of material. For example:
- Biology & biophysics:
- Probability & information:
- Computational systems biology:
- Sequence analysis:
- etc. (please feel free to start your own page of links!)
Syllabus
Approximate sequence of lectures (see also BioE131 weekly schedule):
- Introductory case study
- Overview of syllabus; available means of assessment..
- group & individual presentations; literature reviews; class participation; homework; exam(s); project
- Review of fundamental molecular biology
- Biophysical principles of RNA and protein folding
- Overview of biological databases
- Introduction to Unix
- Introduction to Perl programming: loops, variables, subroutines; file manipulation; data structures
- Assemblers, compilers, interpreters & virtual machines: machine code, C, Perl and Java
- Biophysics of synthetic biology: RNA folding kinetics & viral genome design
- Sequence alignment algorithms: Needleman-Wunsch, Smith-Waterman, Gotoh, BLAST
- Genome annotation; biological ontologies, pathway databases
- Probabilistic inference; Bayes' theorem; experimental error; expectation and variance
- Quick refresher in basic distributional analysis...
- Basic combinatorics; binomials and multinomials
- Geometric, exponential, Poisson distributions
- Gaussian distribution; mixture distributions
- Quantitative measures of information; illustration via data compression
- Log-likelihood ratios and substitution matrices; coding & cryptography
- Probabilistic models for sequence motifs; "sequence logos"
- Algorithmic complexity & "big-O" notation: examples from compbio
- Finite state machines; multiple alignment; phylogenetic reconstruction
- Rate variation, evolutionary trace and phylogenetic profiling; applications to design
- Structural biology, protein structure prediction, protein design
- Clustering algorithms: K-means, K-medians; application to microarray data analysis
- Sequence assembly & metagenomics; examples (human microbiome; bioenergy)
- Computational biology at Berkeley
Lab practicals
- Unix
- Using Wiki
- Biological Databases
- Perl Basics
- Perl Hashes & Arrays
- Perl Pattern Matching
- RNA folding
- Sequence Alignment
- Information Content of DNA
- Bacterial Gene Prediction
- Primate Phylogeny
- Pathway Mining
- Protein Visualization
- Catch-up lab; project work
Homework exercises
Homework exercises will be assigned in labs and posted on the individual lab pages.
Programming assignments will be graded both for form (style) and function (correctness). Stylistic expectations will be outlined on the style guidelines page by the time the first assignment is given.
Textbooks
No textbook purchase is required to take the class.
References to the following textbook (which can be freely downloaded) appear occasionally as recommended reading:
- The MacKay Book: MacKay, DJC. Information Theory, Inference and Learning Algorithms. ISBN:0521642981
- Can be downloaded from here (copyright grants permission to view but not print)
The following Perl books from O'Reilly may be a useful supplement to what's taught in class:
- The following are the two "classic" Perl tutorial and reference books:
- The "Perl for Bioinformatics" series have more bioinformatics-oriented examples:
Other resources
Dates
Final project dates
- 20 Nov - final project announced; virus ProjectAssignments made
- 25 Nov - final project team names & membership lists due
- 4 Dec - final project peer-review viruses assigned
- 7 Dec - final project presentations
- 9 Dec - final project presentations
- 10 Dec - all submitted final project materials due (paths, zipfiles, statements)
- 17 Dec - all final project peer rankings due
Labs, homeworks and holidays
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Transposons, viruses & worms
Molecular biology databases