Dasty2, an Ajax protein DAS client
ABSTRACT Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS). AVAILABILITY: Dasty2 is an open source tool freely available under the terms of the Apache License 2.0, publicly available at http://www.ebi.ac.uk/dasty/.
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Article: Dasty2, an Ajax protein DAS client
- SourceAvailable from: Alberto Labarga
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- "To accomplish this, participants chose the distributed annotation system (DAS ) protocol to gather sequence annotations from distant servers and implemented a DAS layer for FESD II and DBTSS. As a tangible outcome, participants developed TFBS prediction systems that compute the enrichment of the TFBS for a list of genes or proteins, and present the results using an Ajax DAS viewer . The components of this system are shown in Figure 3. "
ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.Journal of Biomedical Semantics 08/2011; 2(1):4. DOI:10.1186/2041-1480-2-4 · 2.26 Impact Factor
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- "Protein-oriented clients usually offer a wide range of representation possibilities (3D structure, interactions graph, alignments) and most of them are stand-alone applications –. A notable exception is Dasty , a web-based protein-oriented client that creates an interactive and visually attractive representation of protein data in the browser without relying on the newest web technologies. It uses series of specially styled and positioned HTML div elements to create the graphical representation of the features and a Java applet to show the 3D structure of the protein. "
ABSTRACT: The Distributed Annotation System (DAS) offers a standard protocol for sharing and integrating annotations on biological sequences. There are more than 1000 DAS sources available and the number is steadily increasing. Clients are an essential part of the DAS system and integrate data from several independent sources in order to create a useful representation to the user. While web-based DAS clients exist, most of them do not have direct interaction capabilities such as dragging and zooming with the mouse. Here we present GenExp, a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser. Thanks to client-side rendering most position changes do not need a network request to the server and so responses to zooming and panning are almost immediate. In GenExp it is possible to explore the genome intuitively moving it with the mouse just like geographical map applications. Additionally, in GenExp it is possible to have more than one data viewer at the same time and to save the current state of the application to revisit it later on. GenExp is a new interactive web-based client for DAS and addresses some of the short-comings of the existing clients. It uses client-side data rendering techniques resulting in easier genome browsing and exploration. GenExp is open source under the GPL license and it is freely available at http://gralggen.lsi.upc.edu/recerca/genexp.PLoS ONE 07/2011; 6(7):e21270. DOI:10.1371/journal.pone.0021270 · 3.23 Impact Factor
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- "In addition, the UniProt web site provides access to the Dasty2 web client (36) for visualizing protein sequence feature information from more than 40 DAS servers. Dasty2 integrates and merges sequence annotations from multiple sources and also displays sequence details and other information such as publications and protein structures when available. "
ABSTRACT: The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/Database The Journal of Biological Databases and Curation 03/2011; 2011:bar009. DOI:10.1093/database/bar009 · 3.37 Impact Factor