Tool-Building in Bioinformatics

• Main Page
• Announcements
• Weekly Schedule
• Lecture Notes
• Process Management
• Wrapping ClustalW
• Web-services
• Searching NCBI
• 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. The lecture notes are all written by Thomas Mailund.

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
  
  
• SQL Databases
  
  Lecture: Accessing Databases
  
  Lecture: Creating and Modifying Databases
  
  Exercises: A Database of Multiple Alignments
  
  
• Making WWW interfaces
  
  Lecture: CGI Scripts
  
  Exercises: CGI Interface to Clustal W
  
  
• 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)