Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU r...

When mapping high-throughput signal processing applications onto heterogeneous platforms, parts of these applications will most likely be mapped into re-configurable components. The current trend of automating such mappings assumes that one can transform application specification to implementation specification without delving deep into details. This implies that one has to rely on the (re-)use...

The current state of the art for provenance in data stream management systems (DSMS) is to provide provenance at a high level of abstraction (such as, from which sensors in a sensor network an aggregated value is derived from). This limitation was imposed by high-throughput requirements and an anticipated lack of application demand for more detailed provenance information. In this work, we firs...

Combinatorial technology has been evaluated as the revolutionary approach to overcome the limitation of conventional research and to advance research in the development of novel materials and catalysts. For the past decade, because of the advance in library synthetic method and characterization tools, combinatorial and high-throughput methodology surprisingly matured and nowadays has been exten...

Knowledge of the internal behavior of applications often gets lost over the years. This circumstance can arise, for example, from missing documentation. Application-level monitoring, e.g., provided by Kieker, can help with the comprehension of such internal behavior. However, it can have large impact on the performance of the monitored system. High-throughput processing of traces is required by...

Outlying values in predictors often strongly affect the results of statistical analyses in high-dimensional settings. Although they frequently occur with most high-throughput techniques, the problem is often ignored in the literature. We suggest to use a very simple transformation, proposed before in a different context by Royston and Sauerbrei, as an intermediary step between array normalizati...

The challenge of recovering the topology of massive neuronal circuits can potentially be met by high throughput Electron Microscopy (EM) imagery. Segmenting a 3-dimensional stack of EM images into the individual neurons is difficult, due to the low depth-resolution in existing high-throughput EM technology, such as serial section Transmission EM (ssTEM). In this paper we propose methods for det...

Repurposing and repositioning drugs--discovering new uses for existing and experimental medicines-is an attractive strategy for rescuing stalled pharmaceutical projects, finding treatments for neglected diseases, and reducing the time, cost and risk of drug development. As this strategy emerged, academic researchers began performing high-throughput screens (HTS) of small molecules--the type of ...

MOTIVATION High-throughput screening (HTS) is an early-stage process in drug discovery which allows thousands of chemical compounds to be tested in a single study. We report a method for correcting HTS data prior to the hit selection process (i.e. selection of active compounds). The proposed correction minimizes the impact of systematic errors which may affect the hit selection in HTS. The intr...