TELE-COLLABORATION
TELE-COLLABORATION
Building a Local Rules Based Kinetic Simulator of Viral Capsid Assembly
Remote Interactive Design of Inhibitors using Molecular Modeling Techniques
Multisite Three-Dimensional Brain Visualization
Developing a Standard for the Digital Transmission of Pediatric Cardiology
Broad-bandwidth network use by the Medical Videoscope
Remote Optometric Consultation
Computational Simulation and Coil Design for High
Frequency / High-Field Magnetic Resonance Imaging
The Materials Research Science and Engineering Center (MRSEC) is a multidisciplinary research program focusing on thin film and particulate materials for ultra high-density information storage. MRSEC is supported by the National Science Foundation and is a critical component in the Center for Materials for Information Technology (MINT), which includes eighteen faculty members from six different academic departments, 30 graduate students and 10 postdoctoral associates. Many MINT/MRSEC research programs generate digital images from a variety of scanning microscopes used in surface analysis, elemental analysis, a new Auger-XPS facility, magnetic characterization, and from mechanical/chemical characterization equipment. Digital images generated from these machines sessions require data rates of at least 50 Mb/s and a wide range of QoS capability in order to be transmitted "live" during tele-collaboration. For example, in the NSF MRSEC project entitled "Computation of Materials Properties on Atomic and Mesoscopic Scales", researchers use supercomputers at the University of Kentucky and UCSD to perform calculations of molecular dynamics in polymer-magnetic particle paints used in coating magnetic disks and tapes. An Internet2-class connection to the University of Alabama (Tuscaloosa) will allow researchers to observe remote simulations in real-time on visualization stations available in the MINT Center. This remote visualization is currently impossible via the commodity Internet because graphical data sets for this three-dimensional rendering require data rates and latency guarantees which are not supported.
Building a Local Rules Based Kinetic Simulator of Viral Capsid Assembly
In a collaborative effort with the MIT Lab for Computer Science, UAB microbiologists are attempting to build a computer simulator model of virus capsid assembly from individual coat proteins. Features of the model permit insights into aspects of capsid assembly kinetics that cannot be addressed with current laboratory techniques. The simulator is designed to function as two separate programs. During development and upon completion, workstations at UAB will run the user interface for the code, while the numerical routines will run simultaneously on a multi-processor platform at MIT. Until now, collaboration has been limited with all simulations performed at MIT. A capability for remote use of the simulator from UAB will reduce delays in evaluating proposed simulations and increase interaction between the groups. By direct experience with the capabilities of the simulator, the biologists will be able to suggest improvements and design advanced experiments, thus allowing the computer scientists to more effectively incorporate laboratory results into refined simulations. For this approach to be feasible, the capacity to efficiently support an interactive graphical simulator running on two physically distant machines is required.
Remote Interactive Design of Inhibitors using Molecular Modeling Techniques
The Center for Macromolecular Crystallography (CMC) has active research programs in protein crystal growth, macromolecular structure determination, and structure-based drug design. The CMC is funded by NASA and is the point of contact for crystal growth experiments performed frequently during space shuttle missions. Planning is underway to have even more crystallography performed on the space station and the large amount of data generated could be more quickly disseminated with next generation networking facilities. Additionally, numerous drug design projects involve collaboration with experts from other institutions where a multidisciplinary team gathers around a graphics terminal, examines a target structure, and generates ideas for designing/improving an inhibitor using molecular modeling techniques. The possibility of doing this remotely in real time is a cost-effective alternative to physical co-location. Researchers in the CMC also participated in the first electronic conference of the Molecular Graphics and Modeling Society (EC1) held over the World Wide Web. The intent of the conference was to explore the latest specification of the virtual reality modeling language (VRML) including sound and animation; however, annoying lag times soon brought the proceedings to a halt. Virtual conferences such as EC1 have great promise with enhanced network services.
Multisite Three-Dimensional Brain Visualization
Functional imaging represents the technical frontier of brain and cognitive science. Spatiotemporal patterns of brain activity-related signals occurring while a human subject performs a perceptual, cognitive, or motor task can be superimposed on a structural image of the brain, permitting visualization of the space-time evolution of brain activity. Because of the high cost and complexity of the technology much functional imaging research requires collaborations among engineers, physicists, and neuroscientists who are often based at different institutions. The high resolution space-time functional image sets are composed of huge volumes of data (100 MB-10 GB). Investigators at UAB and collaborating institutions are developing software to permit researchers at different sites to simultaneously interact with three-dimensional dynamic graphic representations of a functional brain image data set. The interface will be designed to allow digital voice and video communication among the users, permit graceful turn taking among the participants, and manipulate the image data set in real-time. The requirement for remote, real-time access to large datasets without pre-transmission will require significant network resources and latency guarantees.
The Center for Nuclear Imaging Research (CNIR) at UAB is home to one of only seven high field (4.1 Tesla) whole body magnetic resonance imaging facilities in the world. Recently, the CNIR has been awarded a Research Resource grant from the National Institutes of Health to make this technology available to investigators throughout the US. Within UAB, collaborations exist between the CNIR, the Department of Biomedical Engineering, the Vision Science Research Center, and many units in the UAB Medical Center. External collaborations also exist between the CNIR and Yale University, Henry Ford Hospital (Detroit), Beth Israel Hospital (Harvard University), Columbia University (New York), and Auburn University (Alabama).
Developing a Standard for the Digital Transmission of Pediatric Cardiology
Echocardiography (cardiac ultrasound) equipment is commonly available in outlying hospitals, but the skills necessary for the performance and interpretation of echocardiograms in children is often available only in large urban medical centers. The executive committee of the Section on Cardiology of the American Academy of Pediatrics has stated "the challenge is to bring the technology and expertise to the community hospital and to assure prompt transfer of the infant with life-threatening congenital heart disease, but to avoid unnecessary transfers." To be effective, the basic requirements for this class of remote diagnostic interaction include transfer of extremely high-quality full-motion video, audio and phonocardiography of heart sounds and murmurs in addition to conventional videoconferencing links. Unfortunately, conventional encoding and transmission technologies are inadequate for high-definition, time-sensitive, unconventional diagnostic imagery like echocardiography. The UAB Division of Pediatric Cardiology has experimented with commercially available telemedicine devices and telecommunications technologies (such as bonded ISDN lines). These systems have been found to be cumbersome, suboptimal in quality, and unreliable.
In order to develop an effective telemedicine standard for pediatric cardiology, researchers in the UAB Division of Pediatric Cardiology, School of Engineering and Medical Television Facility have developed a collaborative relationship with the Division of Pediatric Cardiology at the University of Arizona in Tucson, an NSF-funded institution for vBNS connectivity. This collaborative effort will be focused on testing and/or development of standards for the transfer of diagnostic quality multimedia data over digital networks, including, but not limited to MPEG (Motion Picture Experts Group-Video Standard I), MPEG-2, full motion JPEG for video, and similar standards for audio data. Application-level evaluation instruments will be designed and implemented to assess the quality of transmitted data, the effectiveness and timeliness of diagnostic encounters via a variety of advanced telecommunications infrastructures, and the requirements and procedures for establishment of switched channels for short-term, high-bandwidth, mixed-mode data consisting of isochronous and prioritized packet streams utilizing technologies available via the vBNS and Next Generation Internet. UAB plans to field test this telemedicine application with Druid City Hospital in Tuscaloosa using an existing fiber connection via UA.
Observing Remote Astronomy
The University of Alabama astronomy group has been involved in testing the remote use of instruments with the National Optical Astronomy Observatories. Remote observation based on currently available transmission technology such as the commodity Internet has been hampered because researchers do not have the guaranteed sustained bandwidth to view full-resolution images in real-time. The intermittent nature of packet-switched technology can cause researchers to lose control connection altogether, thus wasting valuable observation time.
Typically, for a single large optical charge-coupled device, a 2048x2048 image (32 bits/pixel) is taken every 5 minutes (averaging over short calibration exposures and longer science frames). For infrared (IR) data, where atmospheric emission dictates more frequent readouts, a 1024x1024 array might take data every 30 seconds, with calibrations at 5 times this rate. The IR data rate is several times higher than that of optical data; for IR calibration measurements, a data rate of 0.7 MB/s is generated, plus a small fraction of this for communications and control. The facility recently added two-dimensional spectroscopy through the use of Fabry-Perot etalons as tunable filters of very narrow passband. These latter observations generate data at high rates, requiring multiple images with the etalon tuned to randomly shifted wavelengths within the desired range. Simulations of astrophysical jets and their interactions with surrounding media each generate several GB of output that must be transferred and analyzed.
Current Internet availability limits the scope of analyses that can be done, and it creates an inevitable time loss in turnaround based on analysis of previous runs. Clearly, these data streams require Internet2-class transmission, scheduling, and bandwidth guarantees since observation of astronomical phenomena cannot be "rescheduled".
Broad-bandwidth network use by the Medical Videoscope
The Computer-Assisted Neurosurgery (CANS) facility at UAB develops interactive technology using digital medical imaging (CT, MRI, SPECT, etc.) to directly guide surgery. A new project uses binocular rendering of medical images to stereoscopically superimpose the graphics onto the operative field. The instrument that will accomplish this, the 'Medical Videoscope', is a computer-coupled high-resolution binocular operating microscope. A significant application of this technology is transmission of a binocular stereoscopic rendering of the surgical field to a remote (off-campus) surgical expert who will, using a similar viewing device, enter into the virtual operative field and, via return transmission, 'virtually' assist the surgeon in the actual operative field. The success of the remote tele-assistance component depends on unfailing, high-speed, broad-bandwidth network transmission. Internet2 seems an ideal network infrastructure upon which to begin developing and testing this system due to the availability of high-order QoS guarantees and a multiplicity of remote collaborators with appropriate technical and medical expertise.
http://www.cans.uab.eduRemote Optometric Consultation
Utilizing remote diagnostic expertise in the diagnosis and treatment of ocular disorders. For example, this application might involve live imaging of the ocular fundus for diabetes screening.
Computational Simulation and Coil Design for High Frequency / High-Field Magnetic Resonance Imaging
In collaboration with the Magnetic Resonance Imaging Center at Mass. General Hospital / Harvard Medical School, computational algorithms will be applied to medical data sets. The calculations will occur at Mass. General while visualization of these computations occurs simultaneously at UAB. This work will be greatly facilitated by high-speed connection for production runs and for retrieval of large data sets. The slow speed of present Internet connections makes real-time visualization of remote calculations impractical because of the large data flow needed for image updates. Additional computation, involving datasets of 1GB or more in size, will be retrieved to the UAB site for use in thermal analysis using software licensed for use on the Alabama Cray Supercomputer. Thus high-speed connectivity is needed to carry out the overall work from modeling to analysis.
A collaboration with the Department of Biomedical Engineering to examine mechanisms of cortical reorganization. Transfer of large image data files is involved.
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