Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.

High-performance Web servers are essential to meet the growing demands of the Internet and large-scale intranets. Satisfying these demands requires a thorough understanding of key factors affecting Web server performance. This paper presents empirical analysis illustrating how dynamic and static adaptivity can enhance Web server performance. Two research contributions support this conclusion. First, the paper presents results from a comprehensive empirical study of Web servers (such as Apache, Netscape Enterprise, PHTTPD, Zeus, and JAWS) over high-speed ATM networks. This study illustrates their relative performance and precisely pinpoints the server design choices that cause performance bottlenecks. Once network and disk I/O overheads are reduced to negligible constant factors, the main determinants of Web server performance are its protocol processing path and concurrency strategy. Moreover no single strategy performs optimally for all load conditions and traffic types. Second, we describe the design techniques and optimizations used to develop JAWS, our high-performance adaptive Web server. JAWS is an object-oriented Web server that was explicitly designed to alleviate the performance bottlenecks we identified in existing Web servers. The performance optimizations used in JAWS include adaptive prespawned threading, fixed headers, cached date processing, and file caching. In addition, JAWS uses a novel software architecture that substantially improves its portability and flexibility, relative to other Web servers.