Winter 2006 - BME 060

BME 060 - Winter 2006
Programming for Biologists and Biochemists -
Syllabus

Week 1

		Thurs, Jan 5th
Schedule		Introduction: biology's digital age
Lecture Notes		Introduction [pdf] [ppt]
Reading		Tisdall: Chap 1-4

Week 2

	Tues, Jan 10	Thurs, Jan 12
Schedule	Data manipulation and computation	Finding and eliminating bugs
Lecture Notes	Building Blocks [pdf] [ppt]	Debugging [pdf] [ppt]
Reading	Tisdall: Chap 5	Tisdall: Chap 6, pgs 104-116

Week 3

	Tues, Jan 17	Thurs, Jan 19
Schedule		Making your code resuable with subroutines and functions
Lecture Notes	Variables & I/O [pdf] [ppt]	Subroutines [pdf] [ppt]
Reading	Tisdall: Chap 6, pgs 87-103, Appendix B pg 330-333	Tisdall: Chap 6

Week 4

	Tues, Jan 24	Tues, Jan 26
Schedule	Basic pattern matching	Libraries
Lecture Notes	Regular Expressions I [pdf] [ppt]	Libraries [pdf] [ppt] In class example: Searching for patterns in a URL. The two files we wrote were: search_url.pl and webLib.pm. Put these in the same directory and you should be able to call it with a command like: > search_url.pl http://www.cnn.com death
Reading	Tisdall: Chap 5 pg 67-70,81-84	Tisdall: Chapter 6 pg 102-103, Appendix B pg 341-343

Week 5

	Tues, Jan 31	Thurs, Feb 2
Lecture Notes	References & Hashes II [pdf][ppt]	Statistics
Reading	Tisdall: Continue Chapter 6, pg 99-102 Tisdall: Appendix B pg 320-321

Week 6

	Tues, Feb 7	Thurs, Feb 9
Lecture Notes	Regular Expressions II [pdf] [ppt]
Reading	Tisdall, Chap 9, Appendix B 334-340

Week 7

	Tues, Feb 14	Thurs, Feb 16
Lecture Notes	Parsing a PDB file
Reading	Announcements [pdf] [ppt] Example script we wrote in class to find records in a PDB file [atoms.pl]

Week 8

	Tues, Feb 21	Thurs, Feb 23
Schedule	Communicating with UNIX from inside your Perl program
Lecture Notes	Communicating [pdf] [ppt]
Reading	BioPerl Tutorial [HTML] [TXT], sections III.3 and III.4 Use the BioPerl tuturial script, bptutorial. To do this, change directory to: /afs/cats.ucsc.edu/courses/bme060-js/software/bioperl-1.4 To read the manual, type: perldoc bptutorial.pl To see documentation on Bio::Seq type: perl bptutorial.pl 100 Bio::Seq

Week 9

	Tues, Feb 28	Thurs, Mar 2
Schedule	Lecture on Object-oriented programming
Lecture Notes	Networks and Object-oriented Programming [pdf] [ppt]
Reading	Tisdall: Chapter 12, pgs 294-300

Week 10

	Tues, Mar 7	Thurs, Mar 9
Schedule
Lecture Notes	BioPerl I [pdf] [ppt]	We worked together to write a script that reads a list of gene names from the command line, fetches their associated sequences from Genbank, and then prints them out in 3 different formats. This example used BioPerl objects to do the heavy lifting.
Reading	Read Brian Osborne's BioPerl Tutorial for Beginners [HTML]	The main script we wrote is in the getGenbank.pl script. This script uses the readAliases() function from libLab5.pm, so make sure that package is in the directory if you run the getGenbank.pl script. While you could use this for human genes, we tested it on yeast genes. We used a small yeast alias file called yeast.alias.txt. Note that you could instead use the human.alias.txt file from lab 6 here instead. Of course then you would need to type a valid human gene, instead of a yeast gene, into the command prompt. To run the program, type the following command in a directory where both libLab5.pm and yeast.alias.txt are present: perl getGenbank.pl YAP2 This should print out the protein sequence coded by the YAP2 gene in the Genbank, Ensembl, and FASTA formats in that order (see my yap2.out.txt file for an example of what should be printed out).

Week 11

	Tues, Mar 14	Thurs, Mar 16
Schedule	Instructor / TA Evals	In class BioPerl workshop using BLAST.
Lecture Notes	BioPerl II [pdf] [ppt]	We wrote a script that uses BLAST to identify homologous sequences in yeast for a set of given human sequences.
Reading		We first used our getGenbank.pl script from last time to get the FASTA sequence of the human STK24 gene. This gene has a known yeast homolog (the yeast STE20 gene). We saved the amino acid sequence of the STK24 protein in the stk24.fa file. We wrote a new script call blast.pl to find homologous sequences for a set of supplied protein sequences given in FASTA format. This script helps solve part II of lab 6. To call the program, we can send the FASTA sequence(s) to the blast.pl program's standard input using the following UNIX command: perl blast.pl < stk24.fa Remember that the code does not work at this stage because NCBI has recently changed their output format. In the future, we will instead use the XML-based BioPerl parser so that it does not break when NCBI updates their format.

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