This paper proposes a Java-based multi-participant 3D graphics application interface to provide 3D graphics and interactive capabilities over network. Two libraries support this interface, one is a 3D graphics library, called JavaGL, and the other is a network library, called JavaNL. The 3D graphics library is almost identical to OpenGL application interface but is written in Java to satisfy th...

BRAGI offers an efficient visual access to sequence alignment information, 3D alignments and annotated protein structure-function correlations. As a new feature we have mapped information from SWISSPROT and InterPro to individual entries of the PDB. 3D structural alignments from DALI database were converted to XML files for easy access in BRAGI. BRAGI provides interactive access to NCBI-Blast a...

UNLABELLED RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware anc...

The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RN...

PREFACE TRADOC Analysis Center (TRAC) asked the Arroyo Center to develop a framework for performing credible analysis using Distributed Interactive Simulation (DIS). This documented briefing reports on research that extends and demonstrates the credible analysis framework. The Focused Dispatch Advanced Warfighting Experiment (AWE), really a series of experiments, is used to conduct an exemplar ...

This presentation describes the architecture and engineering development of the Multi-Service Distributed Training Testbed (MDT2). It summarizes the basic principles underlying Distributed Interactive Simulation (DIS) and the major components ofMDT2. It then discusses the problem of simulator interoperability and describes some ofthe interoperability problems encountered in developing MDT2. MDT...

We describe the architecture and design for the Distributed Mission Training Integrated Threat Environment (DMTITE) system. DMTITE supports the development and deployment of different types of computer generated actors (CGAs) in large-scale Distributed Interactive Simulation (DIS) and High Level Architecture (HLA) based simulations. To address issues in software architecture, design, and protot...

Homology searches and amino acid alignments, using the Streptomyces R61 DD-peptidase/penicillin-binding protein as reference, have been applied to the beta-lactamases of classes A and C, the Oxa-2 beta-lactamase (considered as the first known member of an additional class D), the low-Mr DD-peptidases/penicillin-binding proteins (protein no. 5 of Escherichia coli and Bacillus subtilis) and penic...

We have developed Phylo-VISTA (Shah et al., 2003), an interactive software tool for analyzing multiple alignments by visualizing a similarity measure for DNA sequences of multiple species. The complexity of visual presentation is effectively organized using a framework based upon inter-species phylogenetic relationships. The phylogenetic organization supports rapid, user-guided inter-species co...

The PRINTS database of protein family 'fingerprints' is a diagnostic resource that complements the PROSITE dictionary of sites and patterns. Unlike regular expressions, fingerprints exploit groups of conserved motifs within sequence alignments to build characteristic signatures of family membership. Thus fingerprints inherently offer improved diagnostic reliability by virtue of the mutual conte...