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This paper presents an overview of EXODUS, an extensible database system project that is addressing data management problems posed by a variety of challenging new applications. The goal of the project is to facilitate the fast development of high-performance, application-specific database systems. EXODUS provides certain kernel facilities, including a(More)
<italic>In this paper, we present the design of the EXTRA data model and the EXCESS query language for the EXODUS extensible database system. The EXTRA data model includes support for complex objects with shared subobjects, a novel mix of object- and value-oriented semantics for data, support for persistent objects of any type in the EXTRA type lattice, and(More)
We recently reported that laminin-5, expressed by human mesenchymal stem cells (hMSC), stimulates osteogenic gene expression in these cells in the absence of any other osteogenic stimulus. Here we employ two-dimensional liquid chromatography and tandem mass spectrometry, along with the Database for Annotation, Visualization and Integrated Discovery (DAVID),(More)
— Algebraic query processing and optimization for relational databases is a proven and reasonably well-understood technology. Recently the algebraic approach has been extended to more advanced data models (nested relations, complex objects, object-oriented systems). Here we continue this evolution by presenting novel algebraic operators and transformations(More)
This paper describes a new object-oriented model and query algebra that will be used as an input language for the query optimizers that are being built as a part of the EREQ project. The model adopts a uniform view of objects and values and separates syntactic, semantic, and implementation concerns. The algebra addresses issues of type-deened equality and(More)
Relational database systems and most object-oriented database systems provide support for queries. Usually these queries represent retrievals over sets or multisets. Many new applications for databases, such as multimedia systems and digital libraries, need support for queries on complex bulk types such as lists and trees. In this paper we describe an(More)
BACKGROUND Systems biology refers to multidisciplinary approaches designed to uncover emergent properties of biological systems. Stem cells are an attractive target for this analysis, due to their broad therapeutic potential. A central theme of systems biology is the use of computational modeling to reconstruct complex systems from a wealth of reductionist,(More)
One of the hallmark events regulating the process of osteogenesis is the transition of undifferentiated human mesenchymal stem cells (hMSCs) found in the bone marrow into mineralized-matrix producing osteoblasts (hOSTs) through mechanisms that are not entirely understood. With recent developments in mass spectrometry and its potential application to the(More)
This paper formulates a set of rules to classify genotypes of the Mycobacterium tuberculosis complex (MTBC) into major lineages using spoligotypes and MIRU-VNTR results. The rules synthesize prior literature that characterizes lineages by spacer deletions and variations in the number of repeats seen at locus MIRU24 (alias VNTR2687). A tool that efficiently(More)