共查询到20条相似文献,搜索用时 203 毫秒
1.
Roberto?H?Higa Roberto?C?Togawa Arnaldo?J?Montagner Juliana?CF?Palandrani Igor?KS?Okimoto Paula?R?Kuser Michel?EB?Yamagishi Adauto?L?Mancini Goran?Neshich
Background
The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user. 相似文献2.
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Jürgen Hartler Gerhard G Thallinger Gernot Stocker Alexander Sturn Thomas R Burkard Erik Körner Robert Rader Andreas Schmidt Karl Mechtler Zlatko Trajanoski 《BMC bioinformatics》2007,8(1):197
Background
The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches. 相似文献4.
Kathleen Y. Wolin Dori M. Steinberg Ilana B. Lane Sandy Askew Mary L. Greaney Graham A. Colditz Gary G. Bennett 《PloS one》2015,10(10)
Background
While eHealth approaches hold promise for improving the reach and cost-effectiveness of behavior change interventions, they have been challenged by declining participant engagement over time, particularly for self-monitoring behaviors. These are significant concerns in the context of chronic disease prevention and management where durable effects are important for driving meaningful changes.Purpose
“Be Fit, Be Well” was an eHealth weight loss intervention that allowed participants to self-select a self-monitoring modality (web or interactive voice response (IVR)). Participants could change their modality. As such, this study provides a unique opportunity to examine the effects of intervention modality choice and changing modalities on intervention engagement and outcomes.Methods
Intervention participants, who were recruited from community health centers, (n = 180) were expected to self-monitor health behaviors weekly over the course of the 24-month intervention. We examined trends in intervention engagement by modality (web, IVR, or changed modality) among participants in the intervention arm.Results
The majority (61%) of participants chose IVR self-monitoring, while 39% chose web. 56% of those who selected web monitoring changed to IVR during the study versus no change in those who initially selected IVR. Self-monitoring declined in both modalities, but completion rates were higher in those who selected IVR. There were no associations between self-monitoring modality and weight or blood pressure outcomes.Conclusions
This is the first study to compare web and IVR self-monitoring in an eHealth intervention where participants could select and change their self-monitoring modality. IVR shows promise for achieving consistent engagement. 相似文献5.
Background
Once a new genome is sequenced, one of the important questions is to determine the presence and absence of biological pathways. Analysis of biological pathways in a genome is a complicated task since a number of biological entities are involved in pathways and biological pathways in different organisms are not identical. Computational pathway identification and analysis thus involves a number of computational tools and databases and typically done in comparison with pathways in other organisms. This computational requirement is much beyond the capability of biologists, so information systems for reconstructing, annotating, and analyzing biological pathways are much needed. We introduce a new comparative pathway analysis workbench, ComPath, which integrates various resources and computational tools using an interactive spreadsheet-style web interface for reliable pathway analyses. 相似文献6.
Background
Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. 相似文献7.
Damian DG Gessler Gary S Schiltz Greg D May Shulamit Avraham Christopher D Town David Grant Rex T Nelson 《BMC bioinformatics》2009,10(1):309-21
Background
SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies. 相似文献8.
Barbara Lazzari Andrea Caprera Alessandro Cestaro Ivan Merelli Marcello Del Corvo Paolo Fontana Luciano Milanesi Riccardo Velasco Alessandra Stella 《BMC plant biology》2009,9(1):82
Background
Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of putative microRNA genes and of their targets, and collected the most reliable microRNA predictions in a web database. The application is available at . 相似文献9.
Catherine C Beauheim Farrell Wymore Michael Nitzberg Zachariah K Zachariah Heng Jin JH Pate Skene Catherine A Ball Gavin Sherlock 《BMC bioinformatics》2007,8(1):338
Background
Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. 相似文献10.
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Background
With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in online variation databases and provide important clues to the cause of diseases and potential side effects or resistance to drugs. However, the data presentation techniques employed by most of these databases make them difficult to use and understand. 相似文献12.
Background
Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees.Methodology/Principal Findings
We introduce TreeVector, a Scalable Vector Graphics–and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print.Conclusions/Significance
TreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user''s own web server. It has already been deployed on two recognized and widely used database Web sites. 相似文献13.
Brandon Peters Charles Moad Eunseog Youn Kris Buffington Randy Heiland Sean Mooney 《BMC structural biology》2006,6(1):4-8
Background
Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. 相似文献14.
Background
Predicting metabolic sites is important in the drug discovery process to aid in rapid compound optimisation. No interactive tool exists and most of the useful tools are quite expensive. 相似文献15.
Samuel Arvidsson Miroslaw Kwasniewski Diego Mauricio Riaño-Pachón Bernd Mueller-Roeber 《BMC bioinformatics》2008,9(1):465
Background
Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. 相似文献16.
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Background
Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will allow more complex and fine-scale inferences about population history than ever before; however, new methods are needed to test complex hypotheses.Results
This article presents popRange, a forward genetic simulator, which incorporates large-scale genetic data with stochastic spatially and temporally explicit demographic and selective models. Features such as spatially and temporally variable selection coefficients and demography are incorporated in a highly flexible manner. popRange is implemented as an R package and presented with an example simulation exploring a selected allele’s trajectory in multiple subpopulations.Conclusions
popRange allows researchers to evaluate and test complex scenarios by simulating large-scale data with complicated demographic and selective features. popRange is available for download at http://cran.r-project.org/web/packages/popRange/index.html.18.
Background
Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine. 相似文献19.
Background
Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. 相似文献20.