Re: [Gusdev-gusdev] how to upload dataset of 'RAD' and 'DoTS' ? many thanks in advance!

[Elisabetta M. <man...@pc...>]

Dear Sam,
regarding your question on RAD data loading:

> sorry for the long error information. in a word, I
> don't know how can I upload 'RAD' data even though I
> found there several plugins for uploading 'RAD'
> dataset. besides, I don't know if I should use
> 'ArrayLoader' plugin to upload dataset download from
> the following webpage:
> http://www.cbil.upenn.edu/RAD3/php/download.php#study5
> because I saw there are totally six differents plugins
> in 'RAD'. I don't know which plugin should upload
> which data, in fact, I just find the above link about
> RAD dataset. and I don't know if there are some other
> datasets that can be downloaded from the website.

the RAD pipeline for how data should be loaded is summarized at the 
bottom of this email.
NOTE 1: We are currently working on a plugin that will enable batch 
loading for step 6. 
NOTE 2: The RAD Study-Annotator is available from a tarball that includes 
a README file and various dumps (see 
http://www.cbil.upenn.edu/RAD/RAD-installation.htm) and proper usage of 
the forms is described in a suite of tutorials at 
https://www.cbil.upenn.edu/RAD/tutorial/index.html.
NOTE 3: individual plugin documentation is at the gusdb website.
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RAD Data Loading Pipeline (as of October 2003)

1. Array is loaded via ArrayLoader.pm, if not already in RAD.
2. User creates a new Study in RAD using the appropriate Study form in 
the StudyAnnotator.
3. Images and quantified data files are provided via CD or ftp. These 
files are archived on in appropriate directories for the study of 
interest.
4. A file on our web server mapping studies to their uris for images and 
quantified data is updated, with the info for this study. This file is 
subsequently used in the StudyAnnotator to link acquisitions and 
quantifications to the archived files.
5. Annotation for this study is done via the StudyAnnotator.
6. The quantified data are loaded into RAD via ArrayResultLoader.pm, 
after appropriate parsing.
7. At this point, if available, files with preprocessed (e.g. 
normalized, averaged, etc.) data can be loaded in RAD via (possibly 
repeated uses of) ProcessedResultLoader.pm.
8. If available, analysis result files are loaded via 
AnalysisResultLoader.pm. New views of RAD3::AnalysisResultImp can be 
created to accomodate new analysis protocols.
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