Core C: Research Design and Analysis

Major Resources

Bioinformatics:

MicroArray Data Management Server

• Quad Processor AMD 848 Opteron 2.2 GHz
• 6 GB Ram
• 4 x 300GB SCSI RAID
• OS: Linux SUSE 9.1 Enterprise Edition

HPC Cluster

• 16 Nodes
• Dual Intel EM64T 3.2Ghz Intel Xeon Processors
• 2GB RAM
• Single 150GB 7200RPM SATA HD
• RedHat Enterprise Linux AS 3.0 Compatible

Affymetrix

Gene Chip Operating Software (GCOS)

• GCOS Administrator
• GCOS Manager
• GCOS Data Transfer Tool

Data Mining Tool

BLAST (Basic Local Alignment Search Tool) Server

Similarity search program designed to explore all of the available sequence databases of protein or DNA.

BLAT Server

Finds sequences of minimum 40 bases with 95% or greater similarity on entire genome. BLAT on proteins finds sequences of 80% or greater similarity of length of 20 amino acids or more.

DS_Gene

Multiple sequence alignment and analysis
Sequence editing and comparison
Fragment assembly
Restriction and proteolyc enzyme mapping
Primer analysis to predict PCR and sequencing primers and hybridization probes
Pattern, motif and gene finding

GeneSpring

Microarray data analysis
Gene lists
Functional classification
Regulatory sequences
Clusters
Pathways

StatMost

Statistical analysis
Graphical information

MathWorks®:

MATLAB ( RedHat Linux version )
Neural Network Toolbox
Statistics Toolbox
Fuzzy Logic Toolbox
Image Processing Toolbox