Christine L. Yang

A collaborative informatics infrastructure for multi-scale science

The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informatics-based approach to synthesizing multi-scale information in support of systems-based research and is applying it within combustion science. An open source multi-scale informatics toolkit is being developed that addresses a number of issues core to the emerging concept of knowledge grids including provenance tracking and lightweight federation of data and application resources into cross-scale information flows. The CMCS portal is currently in use by a number of high-profile pilot groups and is playing a significant role in enabling their efforts to improve and extend community maintained chemical reference information.

DAVE: a plug and play model for distributed multimedia application development

This paper presents a model being used for the development of distributed multimedia applications. The Distributed Audio Video Environment (DAVE) was designed to support the development of a wide range of distributed applications. The implementation of this model is described. DAVE is unique in that it combines a simple “plug and play” programming interface, supports both centralized and fully distributed applications, provides device and media extensibility, promotes object reusability, and supports interoperability and network independence. This model enables application developers to easily develop distributed multimedia applications and create reusable multimedia toolkits. DAVE was designed for developing applications such as video conferencing, media archival, remote process control, and distance learning.

The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches.

Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research laboratory or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a Web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of this is to not only provide a common data sharing and archiving system, but also to assist in the building of new collaborations and to spur the development of new tools and technologies.

The Diesel Combustion Collaboratory: Combustion Researchers Collaborating over the Internet

The Diesel Combustion Collaboratory (DCC) is a pilot project to develop and deploy collaborative technologies to combustion researchers distributed throughout the DOE national laboratories, academia, and industry. The result is a problem-solving environment for combustion research. Researchers collaborate over the Internet using DCC tools, which include: a distributed execution management system for running combustion models on widely distributed computers, including supercomputers; web-accessible data archiving capabilities for sharing graphical experimental or modeling data; electronic notebooks and shared workspaces for facilitating collaboration; visualization of combustion data; and video-conferencing and data-conferencing among researchers at remote sites. Security is a key aspect of the collaborative tools. In many cases, we have integrated these tools to allow data, including large combustion data sets, to flow seamlessly, for example, from modeling tools to data archives. In this paper the authors describe the work of a larger collaborative effort to design, implement and deploy the DCC.

Portal-based knowledge environment for collaborative science.

The Knowledge Environment for Collaborative Science (KnECS) is an open‐source informatics toolkit designed to enable knowledge Grids that interconnect science communities, unique facilities, data, and tools. KnECS features a Web portal with team and data collaboration tools, lightweight federation of data, provenance tracking, and multi‐level support for application integration. We identify the capabilities of KnECS and discuss extensions from the Collaboratory for Multi‐Scale Chemical Sciences (CMCS) which enable diverse combustion science communities to create and share verified, documented data sets and reference data, thereby demonstrating new methods of community interaction and data interoperability required by systems science approaches. Finally, we summarize the challenges we encountered and foresee for knowledge environments. Copyright

DAVE: a plug-and-play model for distributed multimedia application development

We created the Distributed Audio Video Environment for developing applications. DAVE is unique in that it provides a distributed plug-and-play application programming interface, is object-oriented, offers device and media extensibility, uses traditional Unix network facilities for transmission, and employs existing audio and video hardware commonly found on many workstations. To demonstrate DAVEs usefulness, we used it to develop two multimedia applications applicable to collaborative engineering: desktop videoconferencing and video broadcasting/receiving. DAVEs object-oriented techniques provide a high level of abstraction for devices. Application developers can treat media devices (such as cameras and microphones) as distributed resources, much as workstations treat graphics and windows. This flexibility and accessibility lets developers easily integrate multimedia into existing distributed environments. Through inheritance and data independence, developers can define additional devices and media types and integrate them into the environment. This plug-and-play approach provides easy access for application developers who want to avoid learning the details of media devices or who want to dynamically change their applications at runtime. >

Group tele-immersion:enabling natural interactions between groups at distant sites.

We present techniques and a system for synthesizing views for video teleconferencing between small groups. In place of replicating one-to-one systems for each pair of users, we create a single unified display of the remote group. Instead of performing dense 3D scene computation, we use more cameras and trade-off storage and hardware for computation. While it is expensive to directly capture a scene from all possible viewpoints, we have observed that the participants viewpoints usually remain at a constant height (eye level) during video teleconferencing. Therefore, we can restrict the possible viewpoint to be within a virtual plane without sacrificing much of the realism, and in cloning so we significantly reduce the number of required cameras. Based on this observation, we have developed a technique that uses light-field style rendering to guarantee the quality of the synthesized views, using a linear array of cameras with a life-sized, projected display. Our full-duplex prototype system between Sandia National Laboratories, California and the University of North Carolina at Chapel Hill has been able to synthesize photo-realistic views at interactive rates, and has been used to video conference during regular meetings between the sites.