Crystal Grid Reciprocal Net XPort Crystal Grid Framework Chemical Informatics and...

Chemical Informatics and Cyberinfrastructure Collaboratory - 2005

Crystal Crystal GridGrid

Reciprocal NetReciprocal Net XPortXPort Crystal Grid FrameworkCrystal Grid Framework

The Crystal Grid

A joint project of the

•Indiana University Molecular Structure Center

•KAPL Pervasive Technology Laboratory

•Computer Science Department

•Informatics Research Institute

Presentation by: John C. Huffman, Informatics Research Institute




The Crystal GridThe Crystal Grid

XPort

Reciprocal Net

CIMA

Crystal Grid Framework

IUScholarWorks




XPort:

“X-ray Portal”, funded (for one year) by the DOE as part of the Internet-2 initiative. The funding for all Internet-2 projects was terminated early in the second year.

The goal of the XPort project was to utilize grid-accessible hardware to create an X-ray portal. The idea was to utilize video cameras and communication systems to allow a remote user to “participate” in an experiment.




Reciprocal Net:

The Reciprocal Net was funded as a part of the National Science Foundation Division of Undergraduate Education National Science Digital Library (NSDL).

The main thrust of the Reciprocal Net was to create a distributed molecular database that placed servers in crystallography laboratories throughout the United States and the world.




CIMA:

Common Instrument Middleware Architecture (CIMA) is a part of the National Science Foundation Middleware Initiative (NMI).

The Common Instrument Middleware Architecture (CIMA) project, supported by the NMI, is aimed at "Grid enabling" instruments as real-time data sources to improve accessibility of instruments and to facilitate their integration into the Grid. CIMA middleware is based on current Grid implementation standards and accessible through platform independent standards such as the Open Grid Services Architecture (OGSA) and the Common Component Architecture (CCA).




Crystal Grid Framework:

The Crystal Grid Framework is funded by the Science and Engineering Information Integration program in the Division of Information & Intelligent Systems of the National Science Foundation

The CrystalGrid Framework (CGF) project will investigate issues in acquisition, transport, and curation of data over the entire data space of the field of X-ray crystallography, and within that context, methods for managing wide heterogeneity in data representations, formats, and containers, taking into account the realities of multiple administrative domains and diverse instruments and equipment.




Why “Grid Enable” (or “Cyber-enhance) X-ray Crystallography?

“Cyber-enhancement” will allow:

• Remote access (and monitoring) during data collection

• Near real-time access to data using simple web browsers

• Development of standards for data formatting and archiving

• Remote collaboration and assistance

• A repository for raw crystallographic data that is now discarded

• Access to crystallographic data that would otherwise be lost

• Education and public outreach




The Reciprocal Net is the most mature of these projects.

Currently, there are eighteen laboratories involved including the ChemMatCARS beamline at Argonne National Laboratory, the National Crystallographic Service of the UK, the University of Sydney (Australia), Los Alamos National Laboratory, and thirteen university laboratories in the US and Canada.





Each laboratory maintains its own server and controls the access to all data stored on that server. There is no “master” administrator.

The JaMM applets for viewing the molecules allows the non-technical users to perform all the necessary graphics using only a web browser.





For the “end user” the graphics capability are the most desired feature. The chemist can easily generate publication quality graphics without having to learn how to use complex programs.




The Reciprocal Net is the most mature of these projects.The Reciprocal Net is the most mature of these projects.

The “Common Molecules” server, with about 600 molecules receives about 750,000 hits per month (about 18,000 unique visitors).

The site was selected as one of the top science and engineering sites on the web by Scientific American for 2004.




The Reciprocal Net is the most mature of these projectsThe Reciprocal Net is the most mature of these projects.

Using the same underlying database, the user view is designed for general education use. The user still has all the graphics capability of the “research” molecules.




CIMA

The CIMA project builds on the visualization and monitoring hardware initially implemented in the DOE XPort project.

The primary difference is the data collection and archiving functions. Not only are the “raw” CCD frames collected, but environmental metadata, crystal images, etc. are harvested in a way that allows the user to monitor the progress of the data.




CIMA The data are stored on an institutional repository to insure availability and security. Current or completed data sets can be examined remotely using web services.




CIMA

The data can be examined frame-by-frame prior to processing, and images can be combined to create mpeg files of the complete experiment..




A primary CIMA requirement is that the original instrument should not be modified in any way (or at least minimally)

Instrument proxy-box

Instrument and local sensors

University maintained systems(Data Capacitor)

University maintained Mass Storage systems(HPSS)




Remote collaboration and assistanceRemote collaboration and assistance

Several techniques are being explored with Polycom videoconferencing being the current preferred solution. The Polycom unit is relatively inexpensive and can be readily moved to a classroom or office. The Polycom unit in the IUMSC uses auxiliary video input signals to show the crystal images. In a worst case scenario it would be possible to simply phone the laboratory and use the video images from the web pages.

The smaller version of the Polycom, the ViaVideo, is also sufficient for many collaborations and easier to set up.




Remote collaboration and assistanceRemote collaboration and assistance

The IUMSC has over 15 video cameras that can monitor any phase of the crystallography experiment. Cameras can be easily selected and controlled using a web browser.




Modes of collaborationModes of collaboration

The CIMA crystallography portal is designed for a diverse matrix of users and instruments:

Instrument

In Lab 1

Instrument

In Lab 2

Data storage

Facilities

Local Users

Local Users

Remote Users

Web

Interface

Tele-colla-boration

Observers




Education and public outreachEducation and public outreach

One use of the current system was been the development of a “virtual crystallography” laboratory. A group of students and faculty from Ball State University remotely participated in the entire process of determining a molecular structure. They were able to observe mounting a crystal; collection of data; solution of the structure; and examination of results on the Reciprocal Net. The response was positive and we are currently working with 12 other Indiana institutions to provide the “virtual crystallography” exercise to advanced inorganic and other classes.




IUScholarWorks:

Provides an institutional repository for indexable, searchable reports that tie the final crystallographic results to the raw data.




CIMA CollaboratorsCIMA Collaborators

There are many groups located throughout the country that are involved in the development of the CIMA system. Several groups in the Computer Science Department of the School of Informatics are involved in developing the portal and other software we are incorporating.

In addition, there are several crystallography laboratories who either have implemented or are in the process of implementing the CIMA crystallography software. These include:

• Purdue University• ChemMatCARS at Argonne National Laboratory• IU Bloomington Biology Department Macromolecular groups• University of Minnesota• University of Sydney• National Crystallography Service (Great Britain)




Expanding CIMAExpanding CIMA

Additional crystallography portals located at:Additional crystallography portals located at:•ChemMatCARS beamline (ANL)ChemMatCARS beamline (ANL)•Purdue UniversityPurdue University•IU Biology (macromolecular crystallography groups)IU Biology (macromolecular crystallography groups)•University of MinnesotaUniversity of Minnesota

Mass SpectroscopyMass SpectroscopyNuclear Magnetic Resonance SpectroscopyNuclear Magnetic Resonance Spectroscopy




Contributors:Contributors:

35 students, faculty, staff involved in the Reciprocal Net project35 students, faculty, staff involved in the Reciprocal Net project

15 faculty, staff, students involved in CIMA15 faculty, staff, students involved in CIMA

Crystal Grid Framework—Students at IU and SUNY BinghamtonCrystal Grid Framework—Students at IU and SUNY Binghamton




We acknowledge financial support for this work from the We acknowledge financial support for this work from the National Science Foundation. (SCI 0330568, DBI 0446802, National Science Foundation. (SCI 0330568, DBI 0446802, MRI 0116050, CNS-MRI 0521433)MRI 0116050, CNS-MRI 0521433)

NSF Middleware InitiativeNSF Middleware Initiative: www.nsf-middleware.org,: www.nsf-middleware.org,CIMA project:CIMA project: www.instrument-middleware.org www.instrument-middleware.orgNSF CRIF:MU ProgramNSF CRIF:MU ProgramNSF Major Research Instrumentation ProgramNSF Major Research Instrumentation Program

Financial support also provided by the IU Office of Research, Financial support also provided by the IU Office of Research, College of Arts and Sciences.College of Arts and Sciences.




Further information can be readily located starting from the Further information can be readily located starting from the IUMSC web site:IUMSC web site:

http://www.iumsc.indiana.edu

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