Teaching > BioE131 > BioE131LectureNotes

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BioE131 lecture notes and class materials

Main lectures

PDFs of the slides from class lectures will be posted here, after each group of lectures has concluded, and corrections have been incorporated.

1. Signals in compbio
2. Formats & databases
3. Scripting
4. RNA design
5. RNA folding
6. Probability
7. Information
8. Pairwise alignment
9. Multiple alignment
10. Phylogeny
11. Biological ontologies
12. Genome annotation and browsers

Note that many of these filesspan multiple lectures (for example, Signals in compbio covers roughly the first two lectures).

Other notes and handouts

1. * Recursion and Dynamic Programming (-- BenjaminEpstein)

Past slides

These are older slides (from 2009).

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

• Transposons, viruses & worms (PDF)
• %PPT% Molecular biology databases (Powerpoint)
• %PPT% Bioengineering RNA (Powerpoint)
• %PPT% RNA folding algorithms (Powerpoint)

Scripting compbio applications

• %PPT% Scripting in bioinformatics (Powerpoint)

DNA pattern recognition & analysis

• %PPT% Alignment basics (Powerpoint)
• %PPT% Homology (Powerpoint)
• %PPT% Multiple alignment (Powerpoint)
• %PPT% Phylogeny (Powerpoint)

Genome and pathway databases

• %PPT% Biological ontologies (Powerpoint)
• %PPT% Genome annotation & pathway mining (Powerpoint)
• %PPT% GFF: Gene Finding Format (Powerpoint)

Information content of DNA

• %PPT% Probability & information (Powerpoint)
• %PPT% Algorithmic complexity + review (Powerpoint)

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:
  • Wikipedia:Central_dogma_of_molecular_biology
  • Wikipedia:Protein_structure_prediction
  • Wikipedia:RNA_structure
• Probability & information:
  • Wikipedia:Bayesian_inference
  • Wikipedia:Information_theory
• Computational systems biology:
  • Wikipedia:Gene_ontology
• Sequence analysis:
  • Wikipedia:Sequence_alignment
    • Wikipedia:Needleman-Wunsch
    • Wikipedia:Smith-Waterman
  • Wikipedia:Phylogenetics
• etc. (please feel free to start your own page of links!)

-- IanHolmes - 31 Aug 2010

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