Manageability comparison: Oracle database 10g and Oracle 9i database

In this paper we performed a basic and common DBA tasks on the two products and measured the time taken and the steps required to complete each task, to assess their relative manageability. The time taken to complete the tasks was then weighted according to their frequency of use in a typical DBA workday to arrive at an overall time savings percentage.[manageability comparison] [software application] [management system]

Organic Rules and Certification

Development of the database, www.organicrules.org: The database was developed by ICROFS (DARCOF) and FiBL in 2005 - 2006 for comparison of European and international standards with the EU Regulation 2092/91 in the EU FP6 project, ”EEC 2092/91 Revision” (www.organic-revision). In the EU FP7 project, Economic Analysis of Certification Systems in Organic Food and Farming, www.CERTCOST.org (2008-2011). The database has been further developed by ICROFS. The information for the database is collected by the 9 partners of the CERTCOST project, and it is edited by Lizzie Melby Jespersen, ICROFS

A description of an automated database comparison program

An interactive FORTRAN computer comparison program designed to automatically locate regions of incongruity between two databases is described. The software, guided by user input parameters, incrementally compares the databases and generates plots of these regions in the databases which do not compare within a specified tolerance. Additionally, tools are provided within the software which enable the user to statistically reduce the number of data points in the databases compared. To facilitate the description of these tools, the procedures used to compare two aerodynamic databases for an F-18A fighter aircraft are detailed

A database of orthologous exons in primates for comparative analysis of RNA-seq data

RNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exon- and transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon

Searching a biomedical bibliographic database from the Ukraine: the Panteleimon database

The Panteleimon database is available via the Internet and is a public access, database, capable of being searched in English, Russian and Ukrainian, covering medical, pharmaceutical, and chemical publications, published in he Ukraine and Russia from 1998. Describes the formulation of a search strategy for the Panteleimon database, for the identification of citations to randomized controlled trials (RCTs), and the comparison of the search results with records included in the Cochrane Library's Cochrane Central Register of Controlled Trials (CENTRAL) database, to evaluate how comprehensive the coverage of the CENTRAL database is for the literature of the Ukraine. The results indicated that Panteleimon is an easily accessible bibliographic database offering easy access to the Ukrainian biomedical literature. The English language retrieval functions picked up most of the reports of RCTs/CCTs (91 per cent precision but the lower recall of 55 per cent indicates the need to search using Russian and Ukrainian terms for completeness. The overall precision of 26 per cent compares favourably with a search for RCTs in EMBASE, carried out by the UK Cochrane Centre, where 70,000 reports of RCTs were identified from 300,000 records down-loaded (precision 23 per cent). (Quotes from original text

RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de

Performance of VIDEBAS in an operational environment

VIDEBAS is a relational database management system in which a database consists of two parts, namely a “real-only” and an “update” part. The first part remains unmodified until the next reorganization and exploits redundancy to achieve fast access to data. A prototype of VIDEBAS has been built. In this paper a performance comparison between this relational system and a DBTG-system (UDS) is made. The used external memory and the number of page accesses to retrieve and update tuples is estimated. Although it is commonly assumed that in an operational environment relational systems are slower than network systems the opposite appears. On the other hand UDS needs less external memory