Larry Smarr

CAMERA: a community resource for metagenomics.

The CAMERA (Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis) community database for metagenomic data deposition is an important first step in developing methods for monitoring microbial communities.

The OptIPuter

This architecture/infrastructure of parallel optical networks couples data exploration, visualization, and collaboration technologies through IP at multi-gigabit speeds.

The StarCAVE, a third-generation CAVE and virtual reality OptIPortal

A room-sized, walk-in virtual reality (VR) display is to a typical computer screen what a supercomputer is to a laptop computer. It is a vastly more complex system to design, house, optimize, make usable, and maintain. 17 years of designing and implementing room-sized CAVE VR systems have led to significant new advances in visual and audio fidelity. CAVEs are a challenge to construct because their hundreds of constituent components are mostly adapted off-the-shelf technologies that were designed for other uses. The integration of these components and the building of certain critical custom parts like screens involve years of research and development for each new generation of CAVEs. The difficult issues and compromises achieved and deemed acceptable are of keen interest to the relatively small community of VR experimentalists, but also may be enlightening to a broader group of computer scientists not familiar with the barriers to implementing virtual reality and the technical reasons these barriers exist. The StarCAVE, a 3rd-generation CAVE, is a 5-wall plus floor projected virtual reality room, operating at a combined resolution of ~68 million pixels, ~34 million pixels per eye, distributed over 15 rear-projected wall screens and 2 down-projected floor screens. The StarCAVE offers 20/40 vision in a fully horizontally enclosed space with a diameter of 3 m and height of 3.5 m. Its 15 wall screens are newly developed 1.3 mx2 m non-depolarizing high-contrast rear-projection screens, stacked three high, with the bottom and top trapezoidal screens tilted inward by 15^@? to increase immersion, while reducing stereo ghosting. The non-depolarizing, wear-resistant floor screens are lit from overhead. Digital audio sonification is achieved using surround speakers and wave field synthesis, while user interaction is provided via a wand and multi-camera, wireless tracking system.

The OptIPortal, a scalable visualization, storage, and computing interface device for the OptiPuter

The OptIPortal is a tiled display that is the visual interface to the OptIPuter, a global-scale computing system tied together by tens of gigabits of networking. The main point of the OptIPuter project is to examine a future in which networking is not a bottleneck to local, regional, national and international computing. OptIPortals are designed to allow collaborative sharing over 1-10 gigabit/second networks of extremely high-resolution graphic output, as well as video streams. OptIPortals typically consist of an array of 4 to 70 LCD display panels (either 2-megapixel or 4-megapixel each), driven by an appropriately sized cluster of PCs, with optimized graphics processors and network interface cards. Rather than exist as one-of-a-kind laboratory prototypes, OptIPortals are designed to be openly and widely replicated, balancing the state of the art of PCs, graphic processing, networks, servers, software, middleware, and user interfaces, and installed in the context of a laboratory or office conference room. Discussed in detail are the design decisions made to achieve a replicable tiled display that can be built by computational science researchers in various disciplines.

Quantifying your body: A how-to guide from a systems biology perspective

During the coming decade we will see an accelerated digital transformation of healthcare. Leading this change within the institutional medical community are both the move to digital medical records and the use of digital biomedical measurement devices. In addition to this institutional evolution, there is a non-institutional, bottom-up, unorganized, highly idiosyncratic movement by early adopters to quantify their own bodies. In this article, I share my decade-long personal experience of tracking many blood and stool biomarkers, which provide insight into the health or disease of major subsystems of my body. These results are interpreted in the context of the genetics of my human DNA and that of the microbes in my gut. Even though I am a computer scientist and not a medical professional, by using commercially available tests and a systems biology integrative approach, I have become an early example of Leroy Hoods vision of the emergence of predictive, preventive, personalized, and participatory (P4) medicine. It is an individuals story illustrating how each of us can contribute to realizing this paradigm shift.

The future of the CAVE

The CAVE, a walk-in virtual reality environment typically consisting of 4–6 3 m-by-3 m sides of a room made of rear-projected screens, was first conceived and built in 1991. In the nearly two decades since its conception, the supporting technology has improved so that current CAVEs are much brighter, at much higher resolution, and have dramatically improved graphics performance. However, rear-projection-based CAVEs typically must be housed in a 10 m-by-10 m-by-10 m room (allowing space behind the screen walls for the projectors), which limits their deployment to large spaces. The CAVE of the future will be made of tessellated panel displays, eliminating the projection distance, but the implementation of such displays is challenging. Early multi-tile, panel-based, virtual-reality displays have been designed, prototyped, and built for the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia by researchers at the University of California, San Diego, and the University of Illinois at Chicago. New means of image generation and control are considered key contributions to the future viability of the CAVE as a virtual-reality device.

International real-time streaming of 4K digital cinema

This paper describes the worlds first real-time, international transmission of 4K digital cinema and 4K Super High Definition (SHD) digital video at iGrid 2005, hosted at the California Institute of Telecommunications and Information Technology (Calit2) at the University of California, San Diego. Nearly six hours of live and pre-recorded 4K motion picture and audio content was streamed to iGrid in San Diego from the Research Institute for Digital Media and Content (DMC) at Keio University in Tokyo.To implement this demonstration, several new technologies were introduced, including a prototype high-performance 4K compressed multicasting system called JPEG 2000 Flexcast, and Soundscape, a practical scheme for synchronizing audio and video transmitted from different locations over IP networks.These iGrid 2005 demonstrations proved that it is now feasible to implement networked professional audio/video applications - production, post-production and distribution - even at 4K quality over IP networks up to 15,000 km long. The demonstrations also showed the new 4K motion picture technology being introduced for digital cinema can be usefully applied to other network applications such as remote telepresence, distance learning and scientific visualization.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, and distribution of metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. The omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and, importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement.

Editorial: Special section: OptIPlanet - The OptIPuter global collaboratory

The technological developments made by OptIPuter research project as an OptIPlanet Collaboratory of virtual organizations, in various scientific and technology domains, enhancing and contributing to this evolving cyberinfrastructure to solve complex global problems, are summarized. OptIPuter project has developed an optical control plane, an infrastructure and distributed intelligence, to control the establishment and maintenance of connections in a network and algorithms for engineering an optimal path among endpoints. The Scalable Adaptive Graphics Environment (SAGE) visualization middleware developed by OptIPuter partner Electronic Visualization Laboratory, is an operating system for tiled-display environments, which allows users to launch distributed visualization applications on remote computer clusters.

The OptIPuter: high-performance, QoS-guaranteed network service for emerging E-science applications

Emerging large-scale scientific applications have a critical need for high bandwidth and predictable-performance network service. The OptlPuter project is pioneering a radical new type of distributed application paradigm that exploits dedicated optical circuits to tightly couple geographically dispersed resources. These private optical paths are set up on demand and combined with end resources to form a distributed virtual computer (DVC). The DVC provides high-quality dedicated network service to applications. In this article we compare the OptIPuters approach (DVC), which exploits network resources to deliver higher-quality network services, to several alternative service models (intelligent network and asynchronous file transfer). Our simulations show that there are significant differences among the models in their utilization of resources and delivered application services. Key takeaways include that the OptlPuter approach provides applications with superior network service (as needed by emerging e-science applications and performance-critical distributed applications), at an expense in network resource consumption. The other approaches use fewer network resources, but provide lower-quality application service