Scientific story (html)
In brief: You are studying the developmental process that leads to sporulation in Bacillus subtilis, an organism that is closely related to the bacterium that causes Anthrax. You hope to learn which genes are expressedBioinformatic tools
during different stages of sporulation. It so happens that you have a few B. subtilis microarrays and some half-finished software kicking about. Will they help?
Reverse EngineeringMolecular biology concepts
Reverse engineer the output from Michael Eisen's Cluster program.
Apply the concepts of cluster analysis to the exploration of microarray datasets.
Regulation of gene expressionPerl focus: Trees and Recursion. Advanced Hashes.
Spotted DNA microarray technology
Hierarchies in biological systems
MergeSort.pl A subroutine for sorting a list (for Monday)Notes & Problem Set
Perl already knows how to sort a list, but this simple program illustrates how
recusion is a natural tool when solving problems that have a natural representation as a tree
Data: Small data file for testing MyCluster.pl or exploring Cluster (ratiodata.txt)
Data: Real microarray data file with data from B. subtilis microarrays for use with MyCluster.pl (BacillusData2.txt)
Data: Much bigger data file (from mouse microarrays) suitable for demonstrating Mike Eisen's Cluster (Final_with_zeros.txt)
Introduction to clustering (Clustering_BNFO601.ppt)
Combined Notes and Problem set (DOC)