Book reviews online

As the number of new academic books published each year continues to rise, such that it becomes evermore difficult to keep abreast of them in one's discipline, the book‐review procedure takes on an increasing importance. This paper outlines the design and development of an automated system for handling book reviews. Descriptions are given of some prototypes that have been developed for use on an intranet server and/or the Internet. These systems, based on SGML and HTML, are briefly discussed and compared

Calming the Tempest: The Benefits of Using Prospero for Electronic Document Delivery in a Large Academic Library

To effectively supplement a library???s collection, Interlibrary Loan departments must strive to produce materials quickly. As libraries acquire more online databases, ILL departments experience a reciprocal increase in article requests submitted. Facing increased demands, how can ILL departments improve and maintain timely and efficient service? The Information Resource and Retrieval Center at the University of Illinois at Urbana-Champaign responded to this challenge by integrating Electronic Document Delivery to the benefit of library users. This article describes UIUC???s decision to use Prospero for EDD and the trials and triumphs of Prospero???s successful implementation.published or submitted for publicationis peer reviewe

GenomeVIP: A cloud platform for genomic variant discovery and interpretation

Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional “download and analyze” paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets.</jats:p

Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches

BACKGROUND: Sequence similarity searching is a powerful tool to help develop hypotheses in the quest to assign functional, structural and evolutionary information to DNA and protein sequences. As sequence databases continue to grow exponentially, it becomes increasingly important to repeat searches at frequent intervals, and similarity searches retrieve larger and larger sets of results. New and potentially significant results may be buried in a long list of previously obtained sequence hits from past searches. RESULTS: ReHAB (Recent Hits Acquired from BLAST) is a tool for finding new protein hits in repeated PSI-BLAST searches. ReHAB compares results from PSI-BLAST searches performed with two versions of a protein sequence database and highlights hits that are present only in the updated database. Results are presented in an easily comprehended table, or in a BLAST-like report, using colors to highlight the new hits. ReHAB is designed to handle large numbers of query sequences, such as whole genomes or sets of genomes. Advanced computer skills are not needed to use ReHAB; the graphics interface is simple to use and was designed with the bench biologist in mind. CONCLUSIONS: This software greatly simplifies the problem of evaluating the output of large numbers of protein database searches

A Service-Oriented Healthcare Message Alerting Architecture in an Asia Medical Center: A Case Study

This paper illustrates how our development team has used some information technologies to let physicians obtain an instant abnormal laboratory result report for critical patient care services. We have implemented a healthcare message alerting system (HMAS) on a healthcare short message service (HSMS) engine and the distributed healthcare-oriented service environment (DiHOSE) in the National Taiwan University Hospital (NTUH). The HSMS engine has a general interface for all applications which could easily send any kind of alerting messages. Fundamentally, the DiHOSE uses HL7 standard formats to process the information exchange behaviors and can be flexibly extended for reasonable user requirements. The disease surveillance subsystem is an integral part of NTUH new hospital information system which is based on DiHOSE and the disease surveillance subsystem would send alerting messages through the HSMS engine. The latest cell phone message alerting subsystem, a case study, in NTUH proved that the DiHOSE could integrate the user required functions without much work. We concluded that both HSMS and DiHOSE can generalize and extend application demands efficiently