Conference Paper

P2SI2-ImmunoGrid services integration: a working example of web based approach

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... The main challenge that has been faced when implementing this grid solution has been that grid clients have to be completely accessible via the command line in order for the PHP job launcher to interact with them. Solutions to this problem have been presented in [68]. ...
Conference Paper
In this paper we present the ImmunoGrid project, whose goal is to develop an immune system simulator which integrates molecular and system level models with Grid computing resources for large-scale tasks and databases. We introduce the models and the technologies used in the ImmunoGrid Simulator, showing how to use them through the ImmunoGrid web interface. The ImmunoGrid project has proved that simulators can be used in conjunction with grid technologies for drug and vaccine discovery, demonstrating that it is possible to drastically reduce the developing time of such products.
. Quantitative proteomics is a growing field where several experimentaltechniques such as those based around stable isotope labellingare reaching maturity. These advances require the parallel developmentof informatics tools to process and analyse the data, especially for highthroughputexperiments seeking to quantify large numbers of proteins.We have developed a novel algorithm for the quantitative analysis of stableisotope-based proteomics data at the peptide level. Without prior formalidentification of the peptides by MS/MS, the algorithm determinesthe mass charge ratio m/z and retention time t of stable isotope-labelledpeptide pairs and calculates their relative ratios. It supports several nonproprietaryXML input formats and requires only minimal parametertuning and runs fully automated. We have tested its performance on alow complexity peptide sample in an initial study. In comparison to amanual analysis and an automated approach using MSQuant, it performsas well or better and therefore we believe it has utility for groups wishingto perform high-throughput experiments.
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