Shared Resources1

Shared ResourcesOver Lariat: 

Shared Resources Over Lariat Martin Gollery Nevada Center For Bioinformatics

http://bioinformatics.unr.edu: 

http://bioinformatics.unr.edu

Slide3: 

CFB Website Sequence Analysis NGC Sequencing Affymetrix Other Micro Proteomics 2D Gel Protein Seq Diff Display GCOS ArrayAssist Array Designer GeneSpring FinchServer TraceViewer Mascot Msfacts GPSExplorer Xcaliber 4700 explorer ProBLAST DeNovoX Peaks Melanie? Molecular Modeling Flow Cytometry Users and Collaborators Chemistry Math Comp Sci UC Davis UC Riverside Scripps

EMBOSS: 

EMBOSS

Sequence Manipulation Suite: 

Sequence Manipulation Suite

Sequence Analysis using Web Resources: 

Sequence Analysis using Web Resources

Modeling Tools: 

Modeling Tools CHARMM Sybyl Insight Amber Gamess Autodock MolPro

The New CFB Cluster-: 

The New CFB Cluster- 120 Opteron 244 CPU’s 60 2-CPU nodes 2 GB RAM/node Myrinet/GigE TeraByte RAID Waiting on renovation Provide access to NECG (Nevada Environmental Computational Grid) Core for IdeaNet Computational Grid (ICGRID)

DeCypher From TimeLogic: 

DeCypher From TimeLogic

Accelerated BLAST: 

Accelerated BLAST

Standard text output: 

Standard text output

Web Graphic Output: 

Web Graphic Output

ClustalW: 

ClustalW

Automatically build HMM’s: 

Automatically build HMM’s

Rapid Response allows flexibility: 

Rapid Response allows flexibility

Which kind of kinase?: 

Which kind of kinase?

Let’s Race! Run HMMPfam : 

Let’s Race! Run HMMPfam VS. Onyx 3800 with 32 CPU’s, 32 GB RAM

1 DeCypher = 56 Onyx 3800’s: 

1 DeCypher = 56 Onyx 3800’s

How Long does it really take?: 

How Long does it really take? “Researcher Time” = Query Transmission +Hardware Processing +Software alignment regeneration +Output formatting +Output Transmission

How Long does it really take?: 

How Long does it really take? “Researcher Time” = Query Transmission +Hardware Processing +Software alignment regeneration +Output formatting +Output Transmission Using conventional Internet, the bottleneck shifts to transmission time.

The Virtual Conference on Genomics & Bioinformatics: 

The Virtual Conference on Genomics & Bioinformatics WWW.VIRTUALGENOMICS.ORG SEPT 21-24 Uri Alon, Weizmann Institute of Science. Israel Wanda Andreoni, IBM Zürich Research Laboratory, Switzerland Kim Baldridge, Universität Zürich. Switzerland Patsy Babbitt. University of California, San Francisco. USA Irene Bosch, University of Massachusetts Medical School. USA Carlos Camacho, University of Pittsburgh, USA Colin C. Collins, Medicine and Cancer Research Institute, UCSF. USA Charles DeLisi, Boston University. USA Martin Gollery, University of Nevada at Reno. USA Fern Hunt, National Institute of Standards and Technology. USA S.S. Iyengar, Louisiana State University. USA Maricel Kann, National Institutes of Health. NCBI. USA Eugene Koonin, National Institutes of Health. USA Luis Rocha, Los Alamos National Laboratory. USA John B. Shabb, University of North Dakota. USA Wibke Sudholt, Universität Zürich. Switzerland Christoph W. Sensen, University of Calgary. Canada Richard Simon, National Institutes of Health. NCI. USA Jason Suen, California Institute of Technology, USA William Perrizo, North Dakota State University. USA Willy Valdivia-Granda. Orion Integrated Biosciences. USA Roie Yerushalmi, Weizmann Institute of Science. Israel

In Conclusion:: 

In Conclusion: The Nevada Center For Bioinformatics has many resources to share Some of these, such as the Cluster and the DeCypher, require Lariat to reach full potential Signup for an account at bioinformatics.unr.edu Get on the list for virtualgenomics.org