Mark L. Green, Ph.D.

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GRASE Bioinformatics and the Open Science Grid

• Mark L. Green, Ph.D.
• Head of Cyberinfrastructure

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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,
• Syracuses Center for Excellence in Environmental
  and Energy Systems,
• Rochesters Center for Excellence in Photonics
  and Microsystems,
• Albanys Center for Excellence in
  Nanoelectronics, and
• Stony Brooks Center for Excellence in Wireless
  Information Technology.

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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.

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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.

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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.

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ACDC Grid Portal Gateway
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Grid-enabling Application Template (GAT)
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Grid-enabling Application Template (GAT)
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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

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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.

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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).

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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 GenNYSis Center for Excellence in Cancer
  Genomics located at the University at Albany's
  East Campus in Rensselaer.

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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).

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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.

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ACDC Grid Portal

• Cyberinfrastructure Generated Virtual Facility
• Open Science Grid
• TeraGrid
• ACDC Grid
• Western New York
• Grid
• New York State Grid
• UB Campus Grid

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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
• grid-help_at_ccr.buffalo.edu
• Center for Computational Research
• URL http//www.ccr.buffalo.edu
• URL http//www.ccr.buffalo.edu/grid
• General contact info
• Mark L. Green mlgreen_at_ccr.buffalo.edu