Search Results (6)

BioShell is an open-source package for processing biological data, particularly focused on structural applications. The package provides parsers, data structures and algorithms for handling and analyzing macromolecular sequences, structures and sequence profiles. The most frequently used routines are accessible by a set of easy-to-use command line utilities for a Linux environment. The full functionality of the package assumes knowledge of C++ or Python to assemble an application using this software library. Since the last publication that announced the version 2.0, the package has been greatly expanded and rewritten in C++ standard 11 (C++11) to improve its modularity and efficiency. A new testing platform has been implemented to continuously test the correctness and integrity of the package. More than two hundred test programs have been published to provide simple examples that can be used as templates. This makes BioShell an easy to use library that greatly speeds up development of bioinformatics applications and web services without compromising computational efficiency. Full article

In this paper, we present a web-based decision support system (DSS)—wSADfLOR—to facilitate the access of stakeholders to tools that may contribute to enhancing forest management planning. The emphasis is on a web-based architecture and a web graphic user interface (wGUI) that may effectively support the analysis of trade-offs between ecosystem services in order to address participatory and sustainable forest management objectives. For that purpose, the wGUI provides remote access to a management information system, enabling users to analyze environmental and biometric data and topological information as well. Moreover, the wGUI provides remote access to forest simulators so that users may define and simulate prescriptions such as chronological sequences of management options and the corresponding forest ecosystem services outcomes. Remote access to management planning methods is further provided so that users may input their objectives and constraints. The wGUI delivers information about tradeoffs between ecosystem services in the form of decision maps so that users in different locations may negotiate bundles of ecosystem services as well as the plan needed to provide them. The multiple criteria programming routines provide proposals for management plans that may be assessed further, using geographical and alphanumeric information provided by the wGUI. Results for an application to a forested landscape extending to 14,388 ha are presented and discussed. This landscape provides several ecosystem services and the development of its management plan involves multiple stakeholders. Results show that the web-based architecture and the wGUI provide effective access for stakeholders to information about the forest management planning area and to decision support tools that may contribute to addressing complex multi-objective and multiple-decision-maker management planning contexts. They also highlight that the involvement and participation of stakeholders in the design of the web-based architecture contributes to assuring the quality and the usability of the system. Full article

Over the last decade new species of Protozoa have been sequenced and deposited in GenBank. Analyzing large amounts of genomic data, especially using Next Generation Sequencing (NGS), is not a trivial task, considering that researchers used to deal or focus their studies on few genes or gene families or even small genomes. To facilitate the information extraction process from genomic data, we developed a database system called ProtozoaDB that included five genomes of Protozoa in its first version. In the present study, we present a new version of ProtozoaDB called ProtozoaDB 2.0, now with the genomes of 22 pathogenic Protozoa. The system has been fully remodeled to allow for new tools and a more expanded view of data, and now includes a number of analyses such as: (i) similarities with other databases (model organisms, the Conserved Domains Database, and the Protein Data Bank); (ii) visualization of KEGG metabolic pathways; (iii) the protein structure from PDB; (iv) homology inferences; (v) the search for related publications in PubMed; (vi) superfamily classification; and (vii) phenotype inferences based on comparisons with model organisms. ProtozoaDB 2.0 supports RESTful Web Services to make data access easier. Those services were written in Ruby language using Ruby on Rails (RoR). This new version also allows a more detailed analysis of the object of study, as well as expanding the number of genomes and proteomes available to the scientific community. In our case study, a group of prenyltransferase proteinsalready described in the literature was found to be a good drug target for Trypanosomatids. Full article

Recently, mobile web services have become a more emerging topic due to popularity of smart phones and laptops. Mobile web services are becoming popular because the growth of internet speeds. Mobile web service is not only useful for particular user, but also for business purposes. It is useful for growth of a particular business. For a particular business, it is important to have the knowledge of user's interest. In M-commerce environment user's interesting web service sequence mining is also an emerging topic now a day. If a business person knows the web service accessing sequence of any user, he can plan new information for that particular user. Today, user's web service accessing sequence mining is based on type of service, visiting locations, timing and some specific constraints. The constraint may define the importance or utility of a particular web service. Here, we consider utility based constraint for particular user in M-commerce environment. We proposed an efficient approach, namely Mobile Web Service Sequence Mining to mine utility based user's interesting web service accessing sequence. Experimental results show that the proposed approach is better than previous constraint based approaches. Full article

We present KnoWDiaL, an approach for Learning and using task-relevant Knowledge from human-robot Dialog and access to the Web. KnoWDiaL assumes that there is an autonomous agent that performs tasks, as requested by humans through speech. The agent needs to “understand” the request, (i.e., to fully ground the task until it can proceed to plan for and execute it). KnoWDiaL contributes such understanding by using and updating a Knowledge Base, by dialoguing with the user, and by accessing the web. We believe that KnoWDiaL, as we present it, can be applied to general autonomous agents. However, we focus on our work with our autonomous collaborative robot, CoBot, which executes service tasks in a building, moving around and transporting objects between locations. Hence, the knowledge acquired and accessed consists of groundings of language to robot actions, and building locations, persons, and objects. KnoWDiaL handles the interpretation of voice commands, is robust regarding speech recognition errors, and is able to learn commands involving referring expressions in an open domain, (i.e., without requiring a lexicon). We present in detail the multiple components of KnoWDiaL, namely a frame-semantic parser, a probabilistic grounding model, a web-based predicate evaluator, a dialog manager, and the weighted predicate-based Knowledge Base. We illustrate the knowledge access and updates from the dialog and Web access, through detailed and complete examples. We further evaluate the correctness of the predicate instances learned into the Knowledge Base, and show the increase in dialog efficiency as a function of the number of interactions. We have extensively and successfully used KnoWDiaL in CoBot dialoguing and accessing the Web, and extract a few corresponding example sequences from captured videos. Full article

Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private ‘Workbench’ spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens. Full article