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Mark L. Green, Ph.D.Head of Cyberinfrastructure
GRASE Bioinformatics and the Open Science Grid
University at Buffalo
The State University of New York
22 University at Buffalo
The State University of New YorkCenter for Computational Research
New York State Center of Excellence in Bioinformatics & Life Sciences
The $1B New York State Centers of Excellence program includes the Center of Excellence in Bioinformatics &
Life Sciences at SUNY-Buffalo, Syracuse’s Center for Excellence in
Environmental and Energy Systems, Rochester’s Center for Excellence in
Photonics and Microsystems, Albany’s Center for Excellence in
Nanoelectronics, and Stony Brook’s Center for Excellence in
Wireless & Information Technology.
33 University at Buffalo
The State University of New YorkCenter for Computational Research
New York State Center of Excellence in Bioinformatics & Life Sciences
CEBLS led the University at Buffalo in partnership with Roswell Park Cancer Institute and Hauptman-Woodward Medical Research Institute.
Corporate partners include GE Healthcare, Biogen, Cognigen, General Electric Global Research, Invitrogen Corporation, Silicon Graphics Incorporated, Stryker Corporation and 3M (Diagnostics and Pharmaceuticals.
44 University at Buffalo
The State University of New YorkCenter for Computational Research
New York State Center of Excellence in Bioinformatics & Life Sciences
The Center in Buffalo is supported by More than $200 million in private industry and
venture capital, $61 million in funding from the State to support
construction and an estimated $74 million in federal support.
Mission: The Center will specialize in drug design
research, computational and three-dimensional visualization, product commercialization and workforce training.
55 University at Buffalo
The State University of New YorkCenter for Computational Research
Buffalo Niagara Medical Campus (BNMC)
The BNMC has developed a unique partnership in which the University at Buffalo, Roswell Park Cancer Institute, Olmsted Center for the Visually Impaired, Kaleida Health, Hauptman-Woodward Medical Research Institute, Buffalo Medical Group Foundation and Buffalo Hearing & Speech Center
are working in collaboration with the surrounding neighborhoods and local government to cultivate a world-class medical campus in downtown Buffalo.
66 University at Buffalo
The State University of New YorkCenter for Computational Research
77 University at Buffalo
The State University of New YorkCenter for Computational Research
ACDC Grid Portal Gateway
88 University at Buffalo
The State University of New YorkCenter for Computational Research
Grid-enabling Application Template (GAT)
99 University at Buffalo
The State University of New YorkCenter for Computational Research
Grid-enabling Application Template (GAT)
1010 University at Buffalo
The State University of New YorkCenter for Computational Research
Bioinformatics Related
Shake-and-Bake (SnB) Molecular Structure Determination Application
Buffalo-and-Pittsburgh (BnP) SnB and PHASES Complete Protein Phasing
SledgeHMMER Sequence analysis using profile hidden Markov models
QMolDyn Quantum Molecular Dynamics
ARACNE Algorithm for the Reconstruction of Accurate Cellular
Networks
1111 University at Buffalo
The State University of New YorkCenter for Computational Research
Bioinformatics
Shake-and-Bake (SnB) - Molecular Structure Determination Application
Description: SnB is a computer program based on Shake-and-
Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data.
User group: The Hauptman-Woodward Medical Research
Institute (HWI) is an independent, non-profit, biomedical research facility located in the heart of downtown Buffalo's medical campus.
1212 University at Buffalo
The State University of New YorkCenter for Computational Research
Bioinformatics
Buffalo-and-Pittsburgh (BnP) - SnB and PHASES Complete Protein Phasing
Description: The result is BnP, an application interface that
facilitates communication between SnB (a direct-methods program that has used the Shake-and-Bake procedure to solve substructures) and PHASES (a program package that computes the phase angles for protein structures).
User group: The Hauptman-Woodward Medical Research
Institute (HWI).
1313 University at Buffalo
The State University of New YorkCenter for Computational Research
Bioinformatics
SledgeHMMER – Sequence analysis using profile hidden Markov models
Description The SledgeHMMER input file contains about 2.5
million protein sequences representing almost all non-redundant protein sequences in the public domain. The database file contains ~8000 Hidden Markov Models of protein families commonly known as the Pfam Database.
User Group: The Gen*NY*Sis Center for Excellence in Cancer
Genomics located at the University at Albany's East Campus in Rensselaer.
1414 University at Buffalo
The State University of New YorkCenter for Computational Research
Bioinformatics
QMolDyn – Quantum Molecular DynamicsDescription
QUANTUM DOTS, also known as nanocrystals, are a non-traditional type of semiconductor with limitless applications as an enabling material across many industries.
User group: Albany NanoTech is a university-based global
research, development, technology deployment and education resource supporting accelerated high technology commercialization. Co-located with the new College of NanoScale Science and Engineering at the University at Albany (SUNY).
1515 University at Buffalo
The State University of New YorkCenter for Computational Research
Bioinformatics
ARACNE – Algorithm for the Reconstruction of Accurate Cellular Networks
Description ARACNE (Algorithm for the Reconstruction of
Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells
User group: AMDeC Foundation, Inc. (AMDeC) is a not-for-profit
consortium of thirty-five New York medical schools, academic health centers, and research institutions, created to advance biomedical research and technology in New York.
1616 University at Buffalo
The State University of New YorkCenter for Computational Research
ACDC Grid Portal
Cyberinfrastructure Generated Virtual Facility Open Science Grid TeraGrid ACDC Grid Western New York
Grid New York State Grid UB Campus Grid
1717 University at Buffalo
The State University of New YorkCenter for Computational Research
Contact Information
ACDC Grid and Operations Dashboards URL: http://osg.ccr.buffalo.edu
ACDC Grid Portal URL: https://grid.ccr.buffalo.edu
For GRASE VO Membership, email: [email protected]
Center for Computational Research URL: http://www.ccr.buffalo.edu URL: http://www.ccr.buffalo.edu/grid
General contact info Mark L. Green: [email protected]
