Bioinformatics

estLIMS©, an automated EST analysis pipeline and LIMS system.

• As a LIMS, it tracks Principal Investigators, projects, samples, costs.
• As an EST analysis pipeline, estLIMS©:
• processes sequence files
• cleanses and clusters raw sequence files using phred, phrap, cross-match, consed
• incorporates a custom-cleanse and vector calling
• annotates for automatic NCBI submission and FASTA output
• Use estLIMS© at your desktop, for free, with the Center’s support

DeCypher® system and server

• The DeCypher® Accelerated Biocomputing Solutions is a system for accelerated bioinformatics algorithms. The system makes use of a hardware accelerator card to optimize bioinformatics search and analysis algorithms [e.g. BLAST], and delivers the computational power of at least 75 processor cores.
• DeCypher® runs all types of BLAST searchers
• Standard query databases are included, specialized databases can be installed
• Use DeCypher® at your desktop, for free, with the Center’s support

Molecular Modeling Software and Computers

• The Center provides comprehensive tools for molecular modeling and visualization with licenses for the the following software packages: SYBYL®, Insight II (Accelrys), and Discovery Studio Modeler (Accelrys). These large commercial packages provide an overall modeling environment in which one can use modules to perform diverse calculations ranging from sequence analysis to structure prediction to thermodynamic and kinetic analysis of atomic interactions.
• The Center supports AMBER, which is currently running on the university research grid
• SGI Octane2 and Fuel workstations with stereoscopic graphic capabilities designated for molecular modeling
• Use these from your desktop (or ours), without cost
• Click here for other molecular modeling resources at the center.

Microarray Analysis Software

• The popular GeneSifter™ microarray analysis software provides analysis and storage support for common platforms (Affymetrix, Agilent, Codelink, etc.) as well as for custom arrays. GeneSifter includes analysis options that enable researchers to determine both statistical and biological significance of microarray data in a simple to use Web-based system. GeneSifter is currently available through the Center. Please contact Karen Schlauch (schlauch@unr.edu) for access to this software.
• XRAY is a user-friendly add-in for Microsoft® Excel®. It can be used for general quality control as well as generating gene lists via statistical tests.
• Custom Analyses are also available from the Center. These are based on your research needs, platforms, and design. We can provide robust experimental design, rigorous quality control, hypotheses tests to compare experimental conditions, PCA, pathway analysis, Gene Set Enrichment Analysis, etc.
Please contact Karen Schlauch (schlauch@unr.edu) for your custom analysis needs.

Computing

• The University Research Grid supplies a combined 518 GB of RAM and 386 processor cores. A dual Sun Fire X4500 server provides 24 TB of storage. Please contact Chad Feller (feller@unr.edu) for access to this supercomputing power.

Storage

• The Center maintains several servers with more than 50TB of space
for data storage.

Consulting

• The Center is open daily for consulting in a number of bioinformatics areas, including the development of experimental designs, data analysis and mining, programming, streamlining, etc.
• We also can supply you with access to the university research grid, as well as access to personal computers or workstations, and data storage servers.
• For long-term goals, and projects, please email Marcel Levy (mlevy@unr.edu) and make an appointment to discuss your needs.