Nucleic Acid Research: web server issue
E' on line la nuova issue di NAR interamente dedicata ai sistemi web based per la bioinformatica. Questi i paper più interessanti:
-Joanne A. Fox, Scott McMillan, and B. F. Francis Ouellette Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory [Abstract]
-José M. Fernández, Robert Hoffmann, and Alfonso Valencia iHOP web services [Abstract]
-Ramón Díaz-Uriarte, Andreu Alibés, Edward R. Morrissey, Andrés Cañada, Oscar M. Rueda, and Mariana L. Neves Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite [Abstract]
-Lucía Conde, David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, and Joaquín Dopazo ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling [Abstract]
-Hubert Rehrauer, Stefan Zoller, and Ralph Schlapbach MAGMA: analysis of two-channel microarrays made easy [Abstract]
-Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, and Joaquín Dopazo FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments [Abstract]
-Nicolas Goffard and Georg Weiller PathExpress: a web-based tool to identify relevant pathways in gene expression data [Abstract]
- Christina Backes, Andreas Keller, Jan Kuentzer, Benny Kneissl, Nicole Comtesse, Yasser A. Elnakady, Rolf Müller, Eckart Meese, and Hans-Peter Lenhof GeneTrail—advanced gene set enrichment analysis [Abstract]
-Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, and Jaak Vilo g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments [Abstract]
-Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, and Rolf Backofen BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data [Abstract]
Etichette: Bioinformatics
1 Commenti:
Thought I’d drop some info onto this post: here at the Technical University in Dresden, Germany, we do a lot of work with arrayCGH analysis on tumor and clinical genetics samples. We’ve taken an open-source LAMP tool called “arrayCGHbase”, fixed a ton of bugs and added a bunch of features (basically made it more stable, simultaneous multi-user-enabled, and easier to install), and have extended it’s use of several R packages, including
CBS
CLAC
GLAD
MANOR
This is in addition to several built-in in tools like lineviews, karyotype views, chromosome views, scatterplots, and other ways of looking at your experiment data.
The upshot is that if you want a single tool that gives you access to all these tools (and more as we add them), we think our application is pretty nice to use. We’re currently scaling it up to handle Agilent 244k chips, and that’s going pretty well so far.
By the way, it’s completely free and we like to support other labs using it. We include comprehensive but easy-to-follow instructions for getting the underlying tools set up (Apache, PHP, MySql), and we’re glad to work online with you to get things started. We run on both Mac and Windows.
Did I mention it’s completely free?
Drop us a line at acgh_base “at” cultureset.com and we will get you started…
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