Tool-Building in Bioinformatics

• Main Page
• Announcements
• Weekly Schedule
• Lecture Notes
• Process Management
• Wrapping ClustalW
• Web-services
• Searching NCBI
• Rpy
• Python Object Persistence
• Accessing Databases
• Creating and Modifying Databases
• A Database of Multiple Alignments
• CGI Scripts
• CGI Interface to Clustal W
• Distributed Systems
• Remote Method Invocation
• Threads and Worker Pools
• Mandatory Projects

About the Lecture Notes

This page lists the set of lecture notes we plan to use in this course.

Each note comes in two parts: the main lecture and a set of exercises for the lecture. The main lecture note contains minor exercises that are to be done while reading the lecture note; the exercises note contains exercises that are to be done after reading the main note.

The Lecture Notes

• Pipelining programs using Python
  
  Lecture: Communication with external programs in Python
  
  Exercises: Wrapping Clustal W
  
  
• Extracting information from the web
  
  Lecture: Web-Services
  
  Exercises: Searching NCBI
  
  
• R from Python
  
  Lecture: Rpy
  
  
• Python Object Persistence
  
  Lecture: pickle and shelve
  
  
• SQL Databases
  
  Lecture: Accessing Databases
  
  Lecture: Creating and Modifying Databases
  
  Exercises: A Database of Multiple Alignments
  
  

Additional lecture notes not part of this years course:

• Network Programming
  
  Lecture: Distributed Systems
  
  Lecture: Remote Method Invocation (RMI)
  
  Lecture: Threads and Worker Pools
  
  Exercises: No exercises (yet)
  
  
• Making WWW interfaces
  
  Lecture: CGI Scripts
  
  Exercises: CGI Interface to Clustal W