Dasty2, an Ajax protein DAS client.

Proteomics Services Team, European Bioinformatics Institute, EMBL, Hinxton, Cambridge CB10 1SD, UK.
Bioinformatics (Impact Factor: 4.62). 10/2008; 24(18):2119-21. DOI: 10.1093/bioinformatics/btn387
Source: PubMed

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

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    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; 2:4.
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    ABSTRACT: MOTIVATION: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification. AVAILABILITY: Dasty3 is an open-source tool freely available at under the terms of the GNU General public license. Source and documentation can be found at CONTACT:
    Bioinformatics 07/2011; 27(18):2616-7. · 4.62 Impact Factor
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    ABSTRACT: EpiC is a web resource for choosing epitopes for use in antibody based experiments. It integrates a suite of tools to identify the subsequence of a target protein that a binder interacts with. Where the binder is an antibody this subsequence is termed an epitope, i.e. the region of a protein that an antibody specifically recognises. EpiC is part of the Europe-wide project ProteomeBinders, thats aims to develop a resource of binding molecules for the entire Human Proteome. EpiC has a simple interactive web interface that provides experimentalists with an integrated suite of bioinformatic tools and annotation information. Crucially this neither requires the user to download any specialist software nor develop scripting tools. Given the diversity of applications for affinity reagents, it is important that the resource provides relevant information dependent on the type of experiment being carried out. It is important to note that researchers often require multiple different binders for one protein and different binders for use in different experiments. EpiC achieves access to these wide range of tools using state of the art methods of data integration. Webservices and REST interfaces such as the Distributed Annotation System are used to deliver the information to the user. These ensure that the latest versions of the analysis software and annotation are displayed to the user, relieving the user of the need to keep up to date with the latest databases and software.
    Data Integration in the Life Sciences, 6th International Workshop, DILS 2009, Manchester, UK, July 20-22, 2009. Proceedings; 01/2009

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