21872273
The Protein Information Resource (PIR)
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Sequence Database (JIPID). The expanded PIR WWW site allows sequence similarity and text searching of the Protein Sequence Database and auxiliary databases. Several new web-based search engines combine searches of sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. New capabilities for searching the PIR sequence databases include annotation-sorted search, domain search, combined global and domain search, and interactive text searches. The PIR-International databases and search tools are accessible on the PIR WWW site at http://pir.georgetown.edu and at the MIPS WWW site at http://www. mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP.
205231250
The Universal Protein Resource (UniProt)
The ability to store and interconnect all available information on proteins is crucial to modern biological research. Accordingly, the Universal Protein Resource (UniProt) plays an increasingly important role by providing a stable, comprehensive, freely accessible central resource on protein sequences and functional annotation. UniProt is produced by the UniProt Consortium, formed in 2002 by the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt web site and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of three major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase and the UniProt Reference Clusters. An additional component consisting of metagenomic and environmental sequences has recently been added to UniProt to ensure availability of such sequences in a timely fashion. UniProt is updated and distributed on a bi-weekly basis and can be accessed online for searches or download at .
7795322
The Protein Information Resource
The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range. Family classification is used for sensitive identification, consistent annotation, and detection of annotation errors. The superfamily curation defines signature domain architecture and categorizes memberships to improve automated classification. To increase the amount of experimental annotation, the PIR has developed a bibliography system for literature searching, mapping, and user submission, and has conducted retrospective attribution of citations for experimental features. PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information. PIR-NREF provides a timely and comprehensive collection of protein sequences, currently consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB. The PIR web site (http://pir.georgetown.edu) connects data analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and text searches, and sorting and visual exploration of search results. The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files.
490124
Modeling Psychological Refractory Period (PRP) and Practice Effect on PRP with Queuing Networks and Reinforcement Learning Algorithms
PRP (Psychological Refractory Period) is a basic but important form of human information processing in dual-task situations. This article describes a queuing network model of PRP that successfully modeled PRP without the need of setting up complex lock/unlock performance strategies employed in the EPIC model of PRP or drawing complex scheduling charts employed in the ACT-R/PM model of PRP. Further, by integrating queuing networks with reinforcement learning algorithms, the queuing network model successfully simulated practice effect on PRP, which has not been modeled in existing PRP models. The current research indicates that depending on an individual’s degree of practice, cognition can be either serial or parallel at the level of production or response selection. Extensions of queuing network model in modeling other tasks and its easiness in modeling concurrent tasks in practice are also discussed.
463160
A Rule-Based Circuit Representation for Automated CMOS Design and Verification
A novel rule-based circuit representation is proposed to describe the connectivities of CMOS circuits at the transistor level. The unique feature of the rule-based representation is its ability to automate CMOS circuit design and verification. A precise symbolic description of the functionality of a transistor-level circuit can be derived based on a set of production rules in linear time. Automated synthesis and verification of CMOS logic circuits are demonstrated.
11048111
Modified Chinese remainder theorem and its application to proxy signatures
Chinese Remainder Theorem has been used for hundreds of years and has been applied to many domains such as integers and polynomials. An assumption made is that the component moduli are pairwise co-prime. In this paper, first we remove this assumption; then we give an algorithm to find whether a given system of congruent equations has a solution, and if so, how to find the solution in an efficient manner. Further we apply the modified Chinese Remainder Theorem to design proxy signatures.
17356448
Web Directory Integration Using Conditional Random Fields
The purpose of integrating web directories is to transfer instances from a source to a target directory. Unlike conventional text categorization, in directory integration, there is extra information about the source directory that can be used to improve the classification accuracy. Many approaches exploit the measured similarity between two corresponding classes to enhance traditional text classifiers. These methods perform well if the topics of two classes are very similar, but they could lead to misclassification if the topics are dissimilar. We propose a directory integration approach based on the conditional random fields (CRFs) model, and model the integration process using a finite-state model. The advantage of using CRFs is that the transition features naturally include information about the relations between classes. Our results show that CRFs outperform conventional text classifiers. In addition, CRFs allow us to apply complex features to integrate the information about the contents of class and their labels. The performance of our approach can be improved by applying these features, especially for instances whose source and target classes are moderately similar
6100465
A distributed connection manager interface for web services on IBM SP systems
In essence, the World Wide Web is a worldwide string of computer databases using a common information retrieval architecture. With the increasing popularity of the World Wide Web, more and more functions have been added to retrieve not only documents written in HTML (Hypertext Markup Language), but also those in other forms through the Common Gateway Interface (CGI), by constructing HTML documents dynamically. Dynamic construction of HTML documents for handling information such as digital libraries is slow and requires much more computer power. A significant performance bottleneck is the initialization and setup phase for a CGI process to gain access to the system containing the data. In this paper we describe the design and implementation of a Connection Manager Interface on IBM SP systems. The Connection Manager provides cliette processes to serve CGI requests and eliminates such bottlenecks. An IBM SP system is used for this emerging area to show that our design and implementation is flexible enough to take advantage of the High-Performance Switch in an IBM SP system. We trace and monitor this scalable Web services using UTE (Unified Trace Environment) tools, and present its performance analysis and visualization.