Mark L. Green, Ph.D. Head of Cyberinfrastructure GRASE Bioinformatics and the Open Science Grid University at Buffalo The State University of New York

University at Buffalo The State University of New York Center for Computational Research 2 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.

University at Buffalo The State University of New York Center for Computational Research 3 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.

University at Buffalo The State University of New York Center for Computational Research 4 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.

University at Buffalo The State University of New York Center for Computational Research 5 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.

University at Buffalo The State University of New York Center for Computational Research 6

University at Buffalo The State University of New York Center for Computational Research 7 ACDC Grid Portal Gateway

University at Buffalo The State University of New York Center for Computational Research 8 Grid-enabling Application Template (GAT)

University at Buffalo The State University of New York Center for Computational Research 9 Grid-enabling Application Template (GAT)

University at Buffalo The State University of New York Center for Computational Research 10 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

University at Buffalo The State University of New York Center for Computational Research 11 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.

University at Buffalo The State University of New York Center for Computational Research 12 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).

University at Buffalo The State University of New York Center for Computational Research 13 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.

University at Buffalo The State University of New York Center for Computational Research 14 Bioinformatics  QMolDyn – Quantum Molecular Dynamics  Description  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).

University at Buffalo The State University of New York Center for Computational Research 15 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.

University at Buffalo The State University of New York Center for Computational Research 16 ACDC Grid Portal  Cyberinfrastructure Generated Virtual Facility  Open Science Grid  TeraGrid  ACDC Grid  Western New York Grid  New York State Grid  UB Campus Grid

University at Buffalo The State University of New York Center for Computational Research 17 Contact Information  ACDC Grid and Operations Dashboards  URL:  ACDC Grid Portal  URL:  For GRASE VO Membership,   Center for Computational Research  URL:  URL:  General contact info  Mark L. Green: