共查询到20条相似文献,搜索用时 15 毫秒
1.
Wei Tan Ravi Madduri Alexandra Nenadic Stian Soiland-Reyes Dinanath Sulakhe Ian Foster Carole A Goble 《BMC bioinformatics》2010,11(1):542
Background
In biological and medical domain, the use of web services made the data and computation functionality accessible in a unified manner, which helped automate the data pipeline that was previously performed manually. Workflow technology is widely used in the orchestration of multiple services to facilitate in-silico research. Cancer Biomedical Informatics Grid (caBIG) is an information network enabling the sharing of cancer research related resources and caGrid is its underlying service-based computation infrastructure. CaBIG requires that services are composed and orchestrated in a given sequence to realize data pipelines, which are often called scientific workflows. 相似文献2.
3.
Background
Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. 相似文献4.
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5.
Background
Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort. 相似文献6.
Background
The relationship between disease susceptibility and genetic variation is complex, and many different types of data are relevant. We describe a web resource and database that provides and integrates as much information as possible on disease/gene relationships at the molecular level. 相似文献7.
Background
With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent results of the exploratory analysis on the web in an easy-to-comprehend form and to facilitate convenient information retrieval. 相似文献8.
Background
Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. 相似文献9.
Kevin Garwood Christopher Garwood Cornelia Hedeler Tony Griffiths Neil Swainston Stephen G Oliver Norman W Paton 《BMC bioinformatics》2006,7(1):532-14
Background
The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. 相似文献10.
Sheng-An Lee Chen-Hsiung Chan Tzu-Chi Chen Chia-Ying Yang Kuo-Chuan Huang Chi-Hung Tsai Jin-Mei Lai Feng-Sheng Wang Cheng-Yan Kao Chi-Ying F Huang 《BMC bioinformatics》2009,10(1):114-11
Background
Protein-protein interactions (PPIs) are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools. 相似文献11.
Anne Parker Eugene Bragin Simon Brent Bethan Pritchard James A Smith Stephen Trevanion 《BMC bioinformatics》2010,11(1):239
Background
The Ensembl web site has provided access to genomic information for almost 10 years. During this time the amount of data available through Ensembl has grown dramatically. At the same time, the World Wide Web itself has become a dramatically more important component of the scientific workflow and the way that scientists share and access data and scientific information. 相似文献12.
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13.
Background
Brucellaspecies are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Sequences of fourBrucellagenomes have been published, and variousBrucellagene and genome data and analysis resources exist. A web gateway to integrate these resources will greatly facilitateBrucellaresearch.Brucellagenome data in current databases is largely derived from computational analysis without experimental validation typically found in peer-reviewed publications. It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation. It is further hypothesized that literature-basedBrucellagene annotation would increase understanding of complicatedBrucellapathogenesis mechanisms. 相似文献14.
Amol Carl Shetty Prashanth Athri Kajari Mondal Vanessa L Horner Karyn Meltz Steinberg Viren Patel Tamara Caspary David J Cutler Michael E Zwick 《BMC bioinformatics》2010,11(1):471
Background
The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research. 相似文献15.
Background
Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products. 相似文献16.
Background
Scientists striving to unlock mysteries within complex biological systems face myriad barriers in effectively integrating available information to enhance their understanding. While experimental techniques and available data sources are rapidly evolving, useful information is dispersed across a variety of sources, and sources of the same information often do not use the same format or nomenclature. To harness these expanding resources, scientists need tools that bridge nomenclature differences and allow them to integrate, organize, and evaluate the quality of information without extensive computation. 相似文献17.
Coral kin aggregations exhibit mixed allogeneic reactions and enhanced fitness during early ontogeny
Background
Aggregated settlement of kin larvae in sessile marine invertebrates may result in a complex array of compatible and incompatible allogeneic responses within each assemblage. Each such aggregate can, therefore, be considered as a distinct self-organizing biological entity representing adaptations that have evolved to maximize the potential benefits of gregarious settlement. However, only sparse information exists on the selective forces and ecological consequences of allogeneic coalescence. 相似文献18.
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19.
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