Asterias

Asterias includes applications for the analysis of genomic (and, to a lesser extent, proteomic) data that cover from data normalization to development of prediction models for survival data. Most of our applications use parallelization (via MPI) and run on a server with 60 CPUs for computation. And most of our applications allow the user to obtain additional information about the genes (chromosomal location, PubMed ids, Gene Ontology terms, etc) by using clickable links in tables and/or figures, thus allowing for enhanced interpretability of the results.


If you would like to get involved in the development of the project, see the pages for the Asterias project at Bioinformatics.org and Launchpad. See here for a discussion of the history and differences between Asterias and Gepas.

Tnasas Pomelo II DNMAD preP GeneSrF IDClight IDconverter ADaCGH SignS Asterias PaLS

Clickable map displaying the available paths for information transfer between applications


Asterias is a genus of the Asteriidae family of starfish. As a starfish, this set of applications has several arms (tools). And as a starfish quite a bit of the "stuff" happens in a "parallelized" fashion, so we can also think of the arms of the starfish as the nodes of our computing cluster. So we used two different analogies to arrive to the name.

Download the pdf for a tutorial overview of Asterias as 1-slide-per-page or as 4-slides-per-page.


Applications:
  • DNMAD: Normalization of expression data
  • preP: Filtering, merging of replicates and imputation of missing values
  • Pomelo II: Finding differentially expressed genes related to class (via ANOVA or t), a continuous covariate (regression) or a censored continuous variable (Cox model)
  • Tnasas: Searching for models of class prediction using a variety of class prediction and gene filtering algorithms
  • GeneSrF: Searching either for minimal models for class prediction or for large subsets of genes with predictive capacity with random forests
  • SignS: Searching for molecular signatures and predictive genes with survival data
  • ADaCGH: Analysis of aCGH data for the detection of regions of genomic DNA gain or loss
  • IDconverter: Map your ids to other known public DBs
  • IDClight:Tool for conversion of single IDs through URL. Link to it from your own applications
  • PaLS: Filtering of genes/proteins according to their shared information

Site map
DNMAD IDconverter IDClight preP Tnasas Pomelo II SignS GeneSrF ADaCGH PaLS Asterias DNMAD help DNMAD tutorial IDconverter help IDClight help preP help Tnasas help Tnasas example Pomelo II help Pomelo II tutorial Pomelo II example SignS help SignS example GeneSrF help GeneSrF example ADaCGH help ADaCGH example PaLS help PaLS example

Clickable site map displaying all the Asterias applications and their documentation


(Photographic credits: the image on the top right does not belong to the genus Asterias. It is a feather star (Ptilometra australis) from the Crinoidea class, one class of the Echinodermata to which the Asteroidea belong. But it is a really beautiful picture that also conveys the "distributed/parallelized" idea. This image was taken from the Wikipedia entry for crinoids. The image for the interactive map is a modified image taken from the Wikipedia entry for Asterias, and belongs to Hans Hillewaert.).

webmaster - Last Update: 2006-12-19