We developed Trap it!, a human-biology interaction (HBI) medium encompassing a touchscreen interface, microscopy, and light projection. Users can interact with living cells by drawing on a touchscreen displaying the microscope view of the cells. These drawings are projected onto the microscopy field as light patterns, prompting observable movement in phototactic responses. The system design enables stable and robust HBI and a wide variety of programmed activities (art, games, and experiments). We investigated its affordances as an exhibit in a science museum in both facilitated and unfacilitated contexts. Overall, it had a low barrier of entry and fostered rich communication among visitors. Visitors were particularly excited upon realizing that the interaction involved real organisms, an understanding that was facilitated by the eyepiece on the physical system. With the results from user study, we provide our observations, insights and guidelines for designing HBI as a permanent museum exhibit.

Achieving good performance on a modern machine with a multi-level memory hierarchy, and in particular on a machine with software-managed memories, requires precise tuning of programs to the machine's particular characteristics. A large program on a multi-level machine can easily expose tens or hundreds of inter-dependent parameters which require tuning, and manually searching the resultant large, non-linear space of program parameters is a tedious process of trial-and-error. In this paper we present a general framework for automatically tuning general applications to machines with software-managed memory hierarchies. We evaluate our framework by measuring the performance of benchmarks that are tuned for a range of machines with different memory hierarchy configurations: a cluster of Intel P4 Xeon processors, a single Cell processor, and a cluster of Sony Playstation3's.

We present a platform independent runtime interface for moving data and computation through parallel machines with multi-level memory hierarchies. We show that this interface can be used as a compiler target and can be implemented easily and efficiently on a variety of platforms. The interface design allows us to compose multiple runtimes, achieving portability across machines with multiple memory levels. We demonstrate portability of programs across machines with two memory levels with runtime implementations for multi-core/SMP machines, the STI Cell Broadband Engine, a distributed memory cluster, and disk systems. We also demonstrate portability across machines with multiple memory levels by composing runtimes and running on a cluster of SMP nodes, out-of-core algorithms on a Sony Playstation 3 pulling data from disk, and a cluster of Sony Playstation 3's. With this uniform interface, we achieve good performance for our applications and maximize bandwidth and computational resources on these system configurations.

We present a compiler for machines with an explicitly managed memory hierarchy and suggest that a primary role of any compiler for such architectures is to manipulate and schedule a hierarchy of bulk operations at varying scales of the application and of the machine. We evaluate the performance of our compiler using several benchmarks running on a Cell processor.

We present Sequoia, a programming language designed to facilitate the development of memory hierarchy aware parallel programs that remain portable across modern machines featuring different memory hierarchy configurations. Sequoia abstractly exposes hierarchical memory in the programming model and provides language mechanisms to describe communication vertically through the machine and to localize computation to particular memory locations within it. We have implemented a complete programming system, including a compiler and runtime systems for Cell processor-based blade systems and distributed memory clusters, and demonstrate efficient performance running Sequoia programs on both of these platforms.