Biotools II

1
Biotools II
2
Midterm info

• Bring your textbook
• 4 problems, similar to assigned hws
• For example
• though (evaluation) question
• math
• Data sources
• Sequencing technique

3
New on AFS!

• Bioperl (actually, this is old)
• Biopython
• Biojava

4
biopython

• afs1-afs36
• Issues
• Must use full path /usr/local/bin/python2.2(othe
  rwise default py2.0 is used)
• Libs in limestone/usr/local/lib/python2.2
• 1.10 test suite ok except for local db

5
additional packages

• egenix-mx-base-2.0.4
• numarray-0.4
• ReportLab_1_11
• Python Imaging Library, PIL
• (All in the same lib directory)

6
biojava

• The jar files to use biojava are located in
  /afs/cad/solaris/biojava.
• Here they arebiojava-1.22.jar
  jakarta-regexp.jar xml.jar
• bytecode-0.91.jar xerces.jar
• For instructions on setting the classpath to use
  these jar files please see -- http//www.biojava.o
  rg/docs/started.html