About Us

The Bioinformatics Facility at the University of Connecticut provides computational power and technical support to both academia and industry. These services are available to faculty and students within the University system and are available at negotiated rates to other academic institutions, government, and industry. The Facility is located in the Biology/Physics Building of the UConn Storrs campus.

From left to right: Facility Heads Peter Gogarten and Paul Lewis;
Facility Scientist Pascal Lapierre; and Systems Manager Jeff Lary

The Bioinformatics Facility at the University of Connecticut provides computational power and technical support to both academia and industry. These services are available to faculty and students within the University system and are available at negotiated rates to other academic institutions, government, and industry. The Facility is located in the Biology/Physics Building of the UConn Storrs campus.

Bioinformatics facility scientist, Pascal Lapierre, advises individuals on the best use of the Facility's resources, and systems manager, Jeffrey Lary, maintains its servers. The Facility operates two main computer clusters open to the general research community and an additional satellite cluster dedicated to special projects.

Dr. Lapierre oversees the daily operation of the Bioinformatics Facility. A graduate of the University of Connecticut’s Genetics Program, Dr. Lapierre’s expertise includes data mining, genome analyses, and phylogenetic studies. He is proficient in PERL, Unix, and SQL and offers consulting services to faculty and students as well as assistance in various University collaborative research projects.

Instrumentation

The Bioinformatics Facility’s main cluster is comprised of a 17 node Dell Linux cluster running Redhat EL5. Each compute node is equipped with 2 x Quad-core 2.53 GHz Intel Xeon processors and 32 GB of memory. The storage capacity of the cluster includes a 6TB RAID Array. In addition, the Facility runs an older 18-node, 36 processor Apple Xserve Cluster. The storage capacity of the Xserve cluster includes a 2TB Apple Xserve RAID Array.

The Facility also maintains a satellite cluster that is available upon request. The cluster is a three node Linux cluster with 1500 GB of disk storage, using 2.13 GHz Quad Core Intel Xeon x3210 processors, with 4 or 16 GB of memory per node.

The Facility offers more than 170 Bioinformatics applications that can be accessed through a secure shell Unix command line on all clusters. This is extendable to licensed and other open source applications. A few of the current applications include:

• Beast
• BLAST Suite
• CLUSTALW
• DarkHorse
• EMBOSS
• FastTree
• GARLI
• gsAssembler (Newbler)
• HMMer
• HyPhy
• Mauve
• Mothur
• MrBayes
• MUSCLE
• MUMmer
• nhPhyM
• Paup*
• Phycas
• PHYLIP
• Phylobayes
• PhyML
• RaxML

The Apple Xserve cluster also has a Bioteam iNQuiry Informatics Clustering Kit with a Sun Grid Engine distributed resource management system that has a web-based front end to Bioinformatics applications. Additional programs may be installed on request.

Training and Education

Staff provide training and consultation in the use of instruments at no charge, but prospective users must schedule an appointment prior to a formal consulting session.

Genome Alignments Using Mauve

Graduate and undergraduate students interested in learning more about bioinformatics are encouraged to visit the Facility to discuss their research with Dr. Lapierre. Having the ability and knowledge to perform bioinformatics analyses is an asset in most areas and will help future researchers in job applications, performing better research, and improving their chances of obtaining grant funding.

Facility Scientist Pascal Lapierre Examining a Multiple Sequence Alignment

Cost for Services

No fees are presently charged to faculty and students within the University system. Services are available at negotiated rates to other academic institutions, government, and industry.

For more information contact Dr. Pascal Lapierre at (860) 486-8742 or pascal.lapierre@uconn.edu.

All rates are subject to periodic review and change.