The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informaticsbased approach to synthesizing multi-scale information to support a systems-based research approach and is applying it in support of combustion research. 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.

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 lab 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 which 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 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.

Multithreading can significantly increase the performance of large agent-based simulations on multicore systems, but agent-based software packages do not commonly offer adequate support for multithreading. This report describes alterations and additions made to the MASON agent-based simulation package that allow the application programmer to make use of multiple threads easily and without radical change to conventional agent-based programming style. The report confirms performance gains with the results of test runs.

SUMMARYThe 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.