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Signaling pathways are chains of interacting proteins, through which the cell converts a (usually) extracellular signal into a biological response. The number of known signaling pathways in the biological literature and on the Web has been increasing at a very high rate, thus demanding a need for efficient ways of storing, visualizing, querying, and mining signaling pathways. In this paper, first...
We present the design and implementation of SQL.CT, a prototype for managing, querying, and visualizing 3D CT (computed tomography) datasets. The system is motivated by scientific studies of fossil records. Our prototype is built on top of SQL server 2005 and uses both Web service and service broker technologies. The desktop client utilizes commodity graphics cards to interactively render 3D volumes...
Summary form only given. Advances in information technology contributed powerful tools for the development of scientific applications. Today scientists routinely exploit data mining and analysis tools, visualization tools, and increasingly leverage database and workflow management systems. Some of these tools run out-of-the-box, others require customization. But when it comes to metadata management,...
Materialized views are a well-known optimization strategy with the potential for massive improvements in query processing time, especially for aggregation queries over large tables. To realize this potential, the query optimizer has to know how and when to exploit materialized views. Reporting functions represent a novel technique to formulate sequence-oriented queries in SQL. They provide a column-wise...
Data analyses in scientific domains involve storage, retrieval, processing and visualization of large scale multidimensional datasets. The datasets incrementally grow by appending new data to the dataset without reorganizing the already allocated data storage. The datasets, typically modeled as k-dimensional arrays, are maintained in files where the array elements are allocated in a sequence of consecutive...
Summary form only given. Advances in networking and distributed computing allowed the establishment of production grid infrastructures. Today, large-scale production grid infrastructures such as EGEE in Europe, OSG in the US, and NAREGI in Japan are offering their services to many scientific and industrial applications, from domains as diverse as astronomy, biomedicine, computational chemistry, earth...
Many publish/subscribe systems have been built using wireless sensor networks, WSNs, deployed for real-world environmental data collection, security monitoring, and object tracking. However, research efforts on WSN-based publish/subscribe systems have largely focused on routing algorithms leaving data management issues mostly untouched. This paper considers a publish/subscribe system built on top...
Genealogy information is becoming increasingly abundant in light of modern genetics and the study of diseases and risk factors. As the volume of this structured pedigree data expands, there is a pressing need for better ways to manage, store, and efficiently query this data. Building on recent advances in semi-structured data management and proven relational database technology, we propose a general-purpose...
Nowadays, huge volumes of data, including scientific data, are organized or exported in tree-structured form. Querying capabilities are provided through tree-pattern queries. The need for integrating multiple data sources with different tree structures has driven, recently, the suggestion of query languages that relax the complete specification of a tree pattern. In this paper we adopt a query language...
In this paper we introduce the Holodex, a `holistic index' for databases that includes a facility for statistics and aggregate-like computations. The Holodex is an integration of the conventional index and summarization over traversals of the index. It can store customized summaries in its data structure, and in this way it can maintain, and provide fast access to, summarized information. The Holodex...
With the recent progress of spatial information technologies and communication technologies, it has become easier to track positions of a large number of moving objects in real-time. Mobility statistics plays an important role in the interactive analysis of a large collection of moving objects trajectories and its use of movement pattern prediction. The development of an effective mobility statistics...
Multiple sequence alignment represents a class of powerful bioinformatics tools with many uses in computational biology ranging from discovery of characteristic motifs and conserved regions in protein families to improved prediction of secondary and tertiary structure. Today, with rapidly growing data repositories offering scientists significantly more data with which to make better decisions, it...
Although the processing of data streams has been the focus of many research efforts in several areas, the case of remotely sensed streams in scientific contexts has received little attention. We present an extensible architecture to compose streaming image processing pipelines spanning multiple nodes on a network using a scientific workflow approach. This architecture includes (i) a mechanism for...
Routing plays an ever-important role in a society that relies heavily on individual means of transportation. Although efficient algorithmic solutions for navigation exist, an accurate and reliable weight database that forms the basis of an acceptable algorithmic solution is missing. This work defines algorithms and data management techniques that allow the derivation of dynamic weights from collected...
In spatial data exploration and analysis, the system would present a user with initial promising results and empower the user to modify runtime query parameters. The high degree of interactivity would significantly reduce users' waiting time for results that are not useful, and then having to re-issue a new query. To support this level of interaction during query processing, it necessitates the study...
Data summarization has been recognized as a fundamental operation in database systems and data mining with important applications such as data compression and privacy preservation. While the existing methods such as CF-values and DataBubbles may perform reasonably well, they cannot provide any guarantees on the quality of their results. In this paper, we introduce a summarization approach for numerical...
In many modern applications, there are no exact values available to describe the data objects. Instead, the feature values are considered to be uncertain. This uncertainty is modeled by probability distributions instead of exact feature values. A typical application of such an uncertainty model are moving objects where the exact position of each object can be determined only at discrete time intervals...
Bitmap indices have been widely used in scientific applications and commercial systems for processing complex, multi-dimensional queries where traditional tree-based indices would not work efficiently. A common approach for reducing the size of a bitmap index for high cardinality attributes is to group ranges of values of an attribute into bins and then build a bitmap for each bin rather than a bitmap...
A phenomenon appears in a sensor network when a group of sensors persist to generate similar behavior over a period of time. PhenomenaBases (or databases of phenomena) are equipped with phenomena detection and tracking (PDT) techniques that continuously run in the background of a sensor database system to detect new phenomena and to track already existing phenomena. The process of phenomena detection...
This paper investigates data-preservation, a feature of scientific workflow middleware (SWM) useful for supporting data provenance and "smart recomputation." We observe that in order for an SWM supporting data preservation to achieve decent performance, it should execute on top of copy-on-write file systems. Unfortunately, most file systems in-use at scientific computing facilities were...
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