Server at Davidson College



You have discovered the web server for the Genome Consortium for Active Teaching (GCAT) at Davidson College. This provides students and faculty unparalleled capacity and access. Generation I of the server was launched August 7, 2003 and Generation II was launched January 1, 2010. Soon, there will be a lot more on these pages.

Genomics Tools

MAGIC Tool: public domain and open source software for microarray data analysis
DAB: divide and BLAST for discovering evolutionary origins of protein domains
Hemoglobin Mutagenesis: use cDNA sequence to create wild-type and mutant proteins online
Microarray Clustering Tool: clusters a combination of genes from various experiments
Kyte-Doolittle Hydropathy Plots: allows user to perform Kyte-Doolittle hydropathy plots on their sequence
DeRisi Lab: explore the yeast diauxic shift microarray data published by DeRisi, et al.
Word or Excel files for exploring correlation coefficients

Synthetic Biology Tools

GCAT-alog: online catalog of freezer stocks
The Oligator: chooses oligos for a DNA sequence greater than 22 bp, removes BioBrick restriction sites, adds BioBrick ends, and adds Golden Gate assembly sticky ends
The DIY Oligator: A program that allows the user to manually select oligos for constructing a longer DNA sequence.
The WiserOptimizer: a split site optimization tool for Golden Gate Assembly
The Loligator: processes oligos for 20 µL boiled and cooled oligos
The Success-O-Rater: determines the number of trials needed to find a successful sample
PCR Primer Design: adds BioBrick ends to an input DNA sequence and designs PCR primers
Optimal Agarose Concentration: selects the optimum percent agarose gel concentration for a given length of dsDNA
GGAJET: Golden Gate Assembly Junction Evaluative Tool
Prime Time Primer Designer: A Golden Gate Assembly Tool
Optimal & Random mRNA Sequence Calculator: Finds the optimal mRNA sequence and a Random mRNA sequence based on codon usage frequencies
Lab Protocols: Davidson Protocols for the 2010 iGem Project

Faculty

Dr. A. Malcolm Campbell, Professor of Biology
Dr. Laurie J. Heyer, Associate Professor of Mathematics

Curriculum

Genomics Concentration, an interdisciplinary concentration with research opportunities for undergraduates
Intro to Genomics and Lab Methods in Genomics, taught each fall by Malcolm Campbell
Intro to Bioinformatics, taught by Laurie Heyer
Biology and Mathematics courses offered by Davidson College
Discovering Genomics, Proteomics and Bioinformatics, the first true genomics textbook