Delivering web service coordination capability to users Oinn, Tom; Addis, Matthew; Ferris, Justin ...
Proceedings of the 13th international World Wide Web conference on Alternate track papers & posters,
05/2004
Conference Proceeding
Odprti dostop
As web service technology matures there is growing interest in exploiting workflow techniques to coordinate web services. Bioinformaticians are a user community who combine web resources to perform ...in silico experiments. These users are scientists and not information technology experts they require workflow solutions that have a low cost of entry for service users and providers. Problems satisfying these requirements with current techniques led to the development of the Simple conceptual unified flow language (Scufl). Scufl is supported by the Freefluo enactment engine 1, and the Taverna editing workbench 3. The extensibility of Scufl, supported by these tools, means that workflows coordinating web services can be matched to how users view their problems. The Taverna workbench exploits the web to keep Scufl simple by retrieving detail from URIs when required, and by scavenging the web for services. Scufl and its tools are not bioinformatics specific. They can be exploited by other communities who require user-driven composition and execution of workflows coordinating web resources.
NAD+ metabolism may be linked to telomere end protection in yeast. Background Telomeres prevent the ends of eukaryotic chromosomes from being recognized as damaged DNA and protect against cancer and ...ageing. When telomere structure is perturbed, a co-ordinated series of events promote arrest of the cell cycle so that cells carrying damaged telomeres do not divide. In order to better understand the eukaryotic response to telomere damage, budding yeast strains harboring a temperature sensitive allele of an essential telomere capping gene (cdc13-1) were subjected to a transcriptomic study. Results The genome-wide response to uncapped telomeres in yeast cdc13-1 strains, which have telomere capping defects at temperatures above approximately 27DGC, was determined. Telomere uncapping in cdc13-1 strains is associated with the differential expression of over 600 transcripts. Transcripts affecting responses to DNA damage and diverse environmental stresses were statistically over-represented. BNA2, required for the biosynthesis of NAD super(+), is highly and significantly up-regulated upon telomere uncapping in cdc13-1 strains. We find that deletion of BNA2 and NPT1, which is also involved in NAD super(+ )synthesis, suppresses the temperature sensitivity of cdc13-1 strains, indicating that NAD super(+ )metabolism may be linked to telomere end protection. Conclusions Our data support the hypothesis that the response to telomere uncapping is related to, but distinct from, the response to non-telomeric double-strand breaks. The induction of environmental stress responses may be a conserved feature of the eukaryotic response to telomere damage. BNA2, which is involved in NAD super(+ )synthesis, plays previously unidentified roles in the cellular response to telomere uncapping.
The analysis of microbial genome sequences can identify protein families that provide potential drug targets for new antibiotics. With the rapid accumulation of newly sequenced genomes, this analysis ...has become a computationally intensive and data-intensive problem. This paper describes the development of a Web-service-enabled, component-based, architecture to support the large-scale comparative analysis of complete microbial genome sequences and the subsequent identification of orthologues and protein families (Microbase). The system is coordinated through the use of Web-service-based notifications and integrates distributed computing resources together with genomic databases to realize all-against-all comparisons for a large volume of genome sequences and to present the data in a computationally amenable format through a Web service interface. We demonstrate the use of the system in searching for orthologues and candidate protein families, which ultimately could lead to the identification of potential therapeutic targets.
the MIAPE Gel Electrophoresis (MIAPE-GE) guidelines specify the minimum information that should be provided when reporting the use of n-dimensional gel electrophoresis in a proteomics experiment. ...Developed through a joint effort between the gel-based analysis working group of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/) and the wider proteomics community, they constitute one part of the overall Minimum Information about a Proteomics Experiment (MIAPE) documentation system published last August in Nature Biotechnology
On the use of agents in a BioInformatics grid Moreau, L.; Miles, S.; Goble, C. ...
CCGrid 2003. 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid, 2003. Proceedings,
2003
Conference Proceeding
Odprti dostop
My Grid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help them to automate the management of such workflows ...through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of my Grid and how it will be used by the scientist. We then show how my Grid can benefit from agents technologies. We have identified three key uses of agent technologies in my Grid: user agents, able to customize and personalise data, agent communication languages offering a generic and portable communication medium, and negotiation allowing multiple distributed entities to reach service level agreements.
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