A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology

A Shared Ontology Approach to Semantic Representation of BIM Data

Architecture, engineering, construction and facility management (AEC-FM) projects involve a large number of participants that must exchange information and combine their knowledge for successful completion of a project. Currently, most of the AEC-FM domains store their information about a project in text documents or use XML, relational, or object-oriented formats that make information integration difficult. The AEC-FM industry is not taking advantage of the full potential of the Semantic Web for streamlining sharing, connecting, and combining information from different domains. The Semantic Web is designed to solve the information integration problem by creating a web of structured and connected data that can be processed by machines. It allows combining information from different sources with different underlying schemas distributed over the Internet. In the Semantic Web, all data instances and data schema are stored in a graph data store, which makes it easy to merge data from different sources. This paper presents a shared ontology approach to semantic representation of building information. The semantic representation of building information facilitates finding and integrating building information distributed in several knowledge bases. A case study demonstrates the development of a semantic based building design knowledge base

Impliance: A Next Generation Information Management Appliance

ably successful in building a large market and adapting to the changes of the last three decades, its impact on the broader market of information management is surprisingly limited. If we were to design an information management system from scratch, based upon today's requirements and hardware capabilities, would it look anything like today's database systems?" In this paper, we introduce Impliance, a next-generation information management system consisting of hardware and software components integrated to form an easy-to-administer appliance that can store, retrieve, and analyze all types of structured, semi-structured, and unstructured information. We first summarize the trends that will shape information management for the foreseeable future. Those trends imply three major requirements for Impliance: (1) to be able to store, manage, and uniformly query all data, not just structured records; (2) to be able to scale out as the volume of this data grows; and (3) to be simple and robust in operation. We then describe four key ideas that are uniquely combined in Impliance to address these requirements, namely the ideas of: (a) integrating software and off-the-shelf hardware into a generic information appliance; (b) automatically discovering, organizing, and managing all data - unstructured as well as structured - in a uniform way; (c) achieving scale-out by exploiting simple, massive parallel processing, and (d) virtualizing compute and storage resources to unify, simplify, and streamline the management of Impliance. Impliance is an ambitious, long-term effort to define simpler, more robust, and more scalable information systems for tomorrow's enterprises.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US