Features:
======

    * Gene expression data normalization, preprocessing, and imputation.
    * Analysis of differential gene expression
    * Search for molecular signatures, with survival and (planned) class data.
    * Search for class prediction and survival prediction models using gene/protein expression data.
    * (planned) Analysis of tissue array data.
    * Analisys of aCGH data including calling gains and losses, estimating copy number changes, and (planned) joint analysis of aCGH and expression data.
    * Functional annotation of analyses results.
    * Distributed computing using MPI, (planned) UPC and (planned) Grid.

Status:
=====

Asterias is fully functional. It is working and publicly available from the main Asterias site. Some of the tools have been running since September 2005 and the latest tools have been publicly accessible since January 2006. During the month of May 2006 Asterias had about 300 hundred usages (these are true usage counts, not webalizer hits), excluding IDConverter, which itself had about 1100 usages during this period.

Who:
===

All of Asterias developers are, as of today, from the Statistical Computing Team at the Spanish National Cancer Research Center. (You can see names and links to individual developers from the specific applications). Expanding this list of developers depends on your joining the project!

Using Asterias:
=========

You don't need to install anything. Just go to the application(s) that interest you.

Installing Asterias:
===========

The code is available for download. Right now, except for the R packages, installing the rest of the code still involves a fair amount of manual work, like changing IPs, LAM/MPI settings, etc. The Pylons installer should make that easier, once it is fully functional. You will, for now, definitely need something like the files provided in "Asterias Common", and then whichever applications you are interested in. Some additional information is provided here: http://bioinformatics.org/asterias/wiki/Main/DownloadPage

Downloading Asterias:
=============

We use Bazaar for version control. To get the code of, say, genesrf do (after installing Bazaar):

      bzr get http://bazaar.launchpad.net/~rdiaz02/genesrf/main

(in same cases you might also do:
      bzr get http://bazaar.launchpad.net/~rdiaz02/genesrf/main-bnf
)

or, if you want to download from Bioinformatics.org

      bzr get http://bioinformatics.org/asterias/bzr/genesrf

You get the idea. If you want another application, just change the corresponding name. (All two --or three, if bnf exists--- should give you the exact same thing; but we've had problems with firewalls and some server's downtime; so if one of the options doesn't work, try the other).

Documentation:
==========

The "standard" R packages (ADaCGH, varSelRF, RJaCGH) have the usual documentation for R packages and some might also have vignettes. For the web-based applications there is the online help, which you can access from the application, and which you also get in full if you download the code. All applications have commented examples, etc, illustrating several features.

A few papers have been published describing some of the applications. These are the URLs:

SignS: http://www.biomedcentral.com/1471-2105/9/30
ADaCGH: http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000737
GeneSrF: http://www.biomedcentral.com/1471-2105/8/328
Asterias: http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_2/W75