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

Bioinformatics facility scientist, Pascal Lapierre, advises individuals on the best use of the Facility's resources, and system manager, Jeffrey Lary, maintains its servers. The Facility operates a main computer cluster open to the general research community and three satellite clusters 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 composed of an 18-node, 36 processor Apple Xserve with 2.3 GHz Power PC G5 and 2 to 8 GB memory/node. The storage capacity of the cluster includes a 2TB Apple Xserve RAID Array consisting of 6-400 GB disks plus one “hot spare”.

The Facility also maintains three satellite clusters that are available upon request. The clusters are a three node, 10 CPU, 2 GB memory per node, 2.3 GHz PowerPC G5 with 500 GB of disk storage; a three node Linux cluster with 500 GB of disk storage, using 2.13 GHz Quad Core Intel Xeon x3210 processors, with 4 or 16 GB of memory per node; and a five node 1 GHz dual cpu PowerPC G4 cluster that can be used for parallel computing calculations when raw computational power is not required.

The Facility offers more than 170 Bioinformatics applications that can be accessed using a web-based portal or through a secure shell Unix command line. This is extendable to licensed and other open source applications. Current applications include EMBOSS, PHYLIP, HMMer and Blast suites, Clustalw, Paup, MrBayes, HyPhy, PhyML, Mauve, MUMmer, Beast, GARLI, RaxML, and others. The Facility 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.