gusdev-rad-issues — Send issues relating to the RAD componenet here

[Gusdev-rad-issues] RAD3 Process Tables deprecation

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

Here at CBIL we have decided to deprecate the usage of the tables 
RAD3.Process*** and to utilize instead a new view of 
RAD3.AnalysisResultImp to store the results of a series of 
DataTransformation protocols. The Analysis tables were created 
subsequently to the Process tables and have a more mature layout, which 
should facilitate queries. They were originally created to store 
down-stream analysis results (e.g. for differential expression or 
clustering) but they are also suitable for pre-processing result storage.
The following describes what we are implementing:

1. We have created a RAD3.ProtocolStep table to identify protocols 
consisting of an ordered series of (sub) protocols. Every protocol of the 
latter form is linked through RAD3.ProtocolStep to its components. Its 
type will be "transformation_protocol_series" 
(DataTransformationProtocolType).

2. We'll create a linking table RAD3.StudyAnalysis to facilitate queries.

3. We'll create a new view of RAD3.AnalysisResultImp, called 
RAD3.DataTransformationResult, which will store all results from a series 
of preprocessing steps obtained from protocols with type 
DataTransformationProtocolType. This will be a simple view with just 
5 relevant attributes: table_id, row_id (pointing to the spot or to the 
probeset on the array; a soft link), and 
float_value/int_value/string_value 
(which will be what's now currently stored in RAD3.ProcessResult.value).

4. When a series of processing steps is used, we will only store the 
results from the *final* step and the corresponding protocol will be of 
type "transformation_protocol_series".

5. For processes which are simple normalizations of a given quantification 
(or of a pair of quantifications for 2-channel data), the input to the 
analysis will be a LogicalGroup consisting just of that quantification 
(resp. pair of quantifications). For processes which involve averaging 
across quantifications the input LogicalGroup will contain 2 or more 
quantifications

6. In terms of plugins, the current AnalysisResultLoader in the 
GUS/RAD cvs repository at Sanger will do. 
(Enhancements or auxiliary plugins might be written for the specific case 
in which the analysis is an up-stream (=low level=processing) one. So this 
plugin will do the job that the ProcessResultLoader was doing for the 
Process tables.)

Elisabetta

[Gusdev-rad-issues] new version of GenePixStudyModuleILoader plugin now available

[Shailesh D. <sv...@pc...>]

as announced before, updates similar to the MAS5StudyModuleILoader 
plugin were made to the GenePixStudyModuleILoader as well.

an updated version of the plugin, the associated sample config file, and 
documentation is now available in via the sanger cvs. please update your 
copies accordingly.

Multiple changes:

- Method changes:
   1. The plugin had memory problems due to the very large number of
   objects created and stored before submission. This is now changed, the
   plugin creates and submits each assay.

- Enhancements:
   1. Users may include/exlude trailing slashes '/' for file paths.
   2. Users can now specify an extension for gpr files in the config file.


------------------------------------------------
  SHAILESH DATE, Postdoctoral Fellow
  1423 Blockley Hall, Center for Bioinformatics,
  423 Guardian Dr., University of Pennsylvania,
  Philadelphia, PA 19104
  Phone: 215-746-7020 | FAX: 215-573-3111
------------------------------------------------

[Gusdev-rad-issues] new version of MAS5StudyModuleILoader plugin now available

[Shailesh D. <sv...@pc...>]

an updated version the MAS5StudyModuleILoader plugin, the associated 
sample config file, and documentation is now available in via the sanger 
cvs. please update your copies accordingly.

Multiple changes:

- Method changes:
   1. The plugin had memory problems due to the very large number of
   objects created and stored before submission. This is now changed, the
   plugin creates and submits each assay.

- Bug fixes:
   1. Bug related to date/time modification (12pm was not being
   represented).

- Enhancements:
   1. Users may/may not use trailing slashes '/' for file paths.
   2. Users can now specify file extensions for each type of file: EXP,
   RPT, CEL, DAT and Metrics files

similar changes are being planned for GenePixStudyModuleILoader plugin, 
and will be announced in due time.

------------------------------------------------
  SHAILESH DATE, Postdoctoral Fellow
  1423 Blockley Hall, Center for Bioinformatics,
  423 Guardian Dr., University of Pennsylvania,
  Philadelphia, PA 19104
  Phone: 215-746-7020 | FAX: 215-573-3111
------------------------------------------------

Re: [Gusdev-rad-issues] Error loading data using ArrayResultLoader

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

Sucheta,
from the Sanger cvs:
http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/RAD/plugin/perl/?cvsroot=GUS&f=h

Elisabetta

---

On Mon, 15 Nov 2004, Sucheta Tripathy wrote:

> Hello,
>
> Can some one please point me to the site, where I get the newest version
> of RAD plugins. I guess I have older version.
>
> I did not get it in CBIL repository.
>
> Thanks
>
> Sucheta
>
>
>
>> Hi, Sucheta,
>> Attached is the testing dataset I used to run the plugin, basically I used
>> the exact same header as yours and put one line of data and run it using
>> the same command line as yours.
>>
>> The plugin runs OK. I can almostly conclude that something is wrong with
>> your data file.
>>
>> BTW,  you never use these two options together "--debug --commit", for it
>> doesn't make sense. Normally you run the plugin  without  the "--commit"
>> mode to make sure everything is right. then you run it  using "--commit"
>> mode. "--debug" mode is for debugging purpose.
>>
>> The following steps demonstrate the good pratice of using plugin:
>>
>> 1. run it with small test.dat w/o --commit
>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3
>> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
>> AffymetrixMAS5
>>
>> 2. if there is problem, add the --debug option
>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3
>> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
>> AffymetrixMAS5 --debug > & log
>>
>> 3. probolem solved, use real.dat and --commit option
>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file real.dat --array_id
>> 3 --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
>> AffymetrixMAS5 --commit > & log
>>
>>
>> ---junmin
>>
>>
>>
>> On Mon, 15 Nov 2004, Elisabetta Manduchi wrote:
>>
>>>
>>> Hi Sucheta,
>>> I'm cc-ing Junmin on this, since he wrote the plugin, so he should be
>>> able to
>>> pin down the problem.
>>> Elisabetta
>>>
>>>
>>> ---
>>>
>>> On Mon, 15 Nov 2004, Sucheta Tripathy wrote:
>>>
>>>>
>>>>
>>>> Hi Elissabetta,
>>>>
>>>> I am trying to upload data using the ArrayResultLoader plugin and
>>>> following are my command line parameters
>>>>
>>>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file <path> --array_id 3
>>>> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>>>> --quantification_id 3 --er_subclass_view AffymetrixCEL
>>>> --cr_subclass_view
>>>> AffymetrixMAS5 --debug --commit >& result_loader.err
>>>>
>>>>
>>>> And my data file has the following heeader:
>>>>
>>>> x_position y_position mean stdv name detection signal detection_p_value
>>>> data        data       data  data  data  data   data   data
>>>>
>>>> All separated by tab.
>>>>
>>>> But I get an error like this:
>>>>
>>>> Missing header x_position which is required to upload data into file.
>>>>
>>>> Although I have the x_position defined in the header.
>>>>
>>>> Am doing something wrong here. I have all the pre-requisites done.
>>>>
>>>> Thanks
>>>>
>>>> Sucheta
>>>
>
>
> -- 
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
>

Re: [Gusdev-rad-issues] Error loading data using ArrayResultLoader

[Sucheta T. <su...@vb...>]

Hello,

Can some one please point me to the site, where I get the newest version
of RAD plugins. I guess I have older version.

I did not get it in CBIL repository.

Thanks

Sucheta



> Hi, Sucheta,
> Attached is the testing dataset I used to run the plugin, basically I used
> the exact same header as yours and put one line of data and run it using
> the same command line as yours.
>
> The plugin runs OK. I can almostly conclude that something is wrong with
> your data file.
>
> BTW,  you never use these two options together "--debug --commit", for it
> doesn't make sense. Normally you run the plugin  without  the "--commit"
> mode to make sure everything is right. then you run it  using "--commit"
> mode. "--debug" mode is for debugging purpose.
>
> The following steps demonstrate the good pratice of using plugin:
>
> 1. run it with small test.dat w/o --commit
> ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3
> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
> AffymetrixMAS5
>
> 2. if there is problem, add the --debug option
> ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3
> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
> AffymetrixMAS5 --debug > & log
>
> 3. probolem solved, use real.dat and --commit option
> ga GUS::RAD::Plugin::ArrayResultLoader --data_file real.dat --array_id
> 3 --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
> AffymetrixMAS5 --commit > & log
>
>
> ---junmin
>
>
>
> On Mon, 15 Nov 2004, Elisabetta Manduchi wrote:
>
>>
>> Hi Sucheta,
>> I'm cc-ing Junmin on this, since he wrote the plugin, so he should be
>> able to
>> pin down the problem.
>> Elisabetta
>>
>>
>> ---
>>
>> On Mon, 15 Nov 2004, Sucheta Tripathy wrote:
>>
>>>
>>>
>>> Hi Elissabetta,
>>>
>>> I am trying to upload data using the ArrayResultLoader plugin and
>>> following are my command line parameters
>>>
>>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file <path> --array_id 3
>>> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>>> --quantification_id 3 --er_subclass_view AffymetrixCEL
>>> --cr_subclass_view
>>> AffymetrixMAS5 --debug --commit >& result_loader.err
>>>
>>>
>>> And my data file has the following heeader:
>>>
>>> x_position y_position mean stdv name detection signal detection_p_value
>>> data        data       data  data  data  data   data   data
>>>
>>> All separated by tab.
>>>
>>> But I get an error like this:
>>>
>>> Missing header x_position which is required to upload data into file.
>>>
>>> Although I have the x_position defined in the header.
>>>
>>> Am doing something wrong here. I have all the pre-requisites done.
>>>
>>> Thanks
>>>
>>> Sucheta
>>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-rad-issues] Error loading data using ArrayResultLoader

[Junmin L. <ju...@pc...>]

Hi, Sucheta,
Attached is the testing dataset I used to run the plugin, basically I used 
the exact same header as yours and put one line of data and run it using 
the same command line as yours.

The plugin runs OK. I can almostly conclude that something is wrong with 
your data file.

BTW,  you never use these two options together "--debug --commit", for it 
doesn't make sense. Normally you run the plugin  without  the "--commit" 
mode to make sure everything is right. then you run it  using "--commit" 
mode. "--debug" mode is for debugging purpose.

The following steps demonstrate the good pratice of using plugin:

1. run it with small test.dat w/o --commit
ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3 
--e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily 
--quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view 
AffymetrixMAS5

2. if there is problem, add the --debug option
ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3 
--e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily 
--quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view 
AffymetrixMAS5 --debug > & log

3. probolem solved, use real.dat and --commit option
ga GUS::RAD::Plugin::ArrayResultLoader --data_file real.dat --array_id 
3 --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily 
--quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view 
AffymetrixMAS5 --commit > & log


---junmin



On Mon, 15 Nov 2004, Elisabetta Manduchi wrote:

>
> Hi Sucheta,
> I'm cc-ing Junmin on this, since he wrote the plugin, so he should be able to 
> pin down the problem.
> Elisabetta
>
>
> ---
>
> On Mon, 15 Nov 2004, Sucheta Tripathy wrote:
>
>> 
>> 
>> Hi Elissabetta,
>> 
>> I am trying to upload data using the ArrayResultLoader plugin and
>> following are my command line parameters
>> 
>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file <path> --array_id 3
>> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
>> AffymetrixMAS5 --debug --commit >& result_loader.err
>> 
>> 
>> And my data file has the following heeader:
>> 
>> x_position y_position mean stdv name detection signal detection_p_value
>> data        data       data  data  data  data   data   data
>> 
>> All separated by tab.
>> 
>> But I get an error like this:
>> 
>> Missing header x_position which is required to upload data into file.
>> 
>> Although I have the x_position defined in the header.
>> 
>> Am doing something wrong here. I have all the pre-requisites done.
>> 
>> Thanks
>> 
>> Sucheta
>

Re: [Gusdev-rad-issues] Error loading data using ArrayResultLoader

[Junmin L. <ju...@pc...>]

Hi, Sucheta,
Looks like the plugin didn't read the header line correctly. The problem 
can be due to either the wrong format of the file or bug in the plugin.
  Can you send me the data file?

--junmin


On Mon, 15 Nov 2004, Elisabetta Manduchi wrote:

>
> Hi Sucheta,
> I'm cc-ing Junmin on this, since he wrote the plugin, so he should be able to 
> pin down the problem.
> Elisabetta
>
>
> ---
>
> On Mon, 15 Nov 2004, Sucheta Tripathy wrote:
>
>> 
>> 
>> Hi Elissabetta,
>> 
>> I am trying to upload data using the ArrayResultLoader plugin and
>> following are my command line parameters
>> 
>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file <path> --array_id 3
>> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
>> AffymetrixMAS5 --debug --commit >& result_loader.err
>> 
>> 
>> And my data file has the following heeader:
>> 
>> x_position y_position mean stdv name detection signal detection_p_value
>> data        data       data  data  data  data   data   data
>> 
>> All separated by tab.
>> 
>> But I get an error like this:
>> 
>> Missing header x_position which is required to upload data into file.
>> 
>> Although I have the x_position defined in the header.
>> 
>> Am doing something wrong here. I have all the pre-requisites done.
>> 
>> Thanks
>> 
>> Sucheta
>

[Gusdev-rad-issues] Re: [Gusdev-gusdev] prerequisites for RAD ArrayLoader

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

Kevin,

> So, for instance, in an array load data file I got from CBIL 
> (HG-U133A.forRAD.txt), the ext_db_rel_id column is 2 for all rows, where 2 
> refers to a release id in CBIL's database that indirectly links to an 
> SRES.ExternalDatabase record that might represent GenBank?  (Is it Genbank, 
> in this case?) And the source_id column might contain the accession number of 
> a Genbank sequence (e.g. U48705) to which this probe row is related?

Yes, it's Genbank.

> Our GUS instance does not have GenBank loaded yet.

What do you mean by loaded? You do not have to have the actual data from 
Genbank in your database. You only need to have one entry in 
SRes.ExternalDatabase denoting the Genbank database and then one or more 
entries in SRes.ExternalDatabaseRelease pointing to the latter. (In our 
instance we only keep one general ExternalDatabaseRelease entry for 
Genbank.)

> Is it OK just to put in a placeholder record for GenBank in 
> SRES.ExternalDatabase and then replace '2' 
> with whatever our release id winds up being in the corresponding 
> SRES.ExternalDatabaseRelease record?

Yes, that's what you need to do.
Elisabetta

Re: [Gusdev-rad-issues] Error loading data using ArrayResultLoader

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

Hi Sucheta,
I'm cc-ing Junmin on this, since he wrote the plugin, so he should be able 
to pin down the problem.
Elisabetta


---

On Mon, 15 Nov 2004, Sucheta Tripathy wrote:

>
>
> Hi Elissabetta,
>
> I am trying to upload data using the ArrayResultLoader plugin and
> following are my command line parameters
>
> ga GUS::RAD::Plugin::ArrayResultLoader --data_file <path> --array_id 3
> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
> AffymetrixMAS5 --debug --commit >& result_loader.err
>
>
> And my data file has the following heeader:
>
> x_position y_position mean stdv name detection signal detection_p_value
> data        data       data  data  data  data   data   data
>
> All separated by tab.
>
> But I get an error like this:
>
> Missing header x_position which is required to upload data into file.
>
> Although I have the x_position defined in the header.
>
> Am doing something wrong here. I have all the pre-requisites done.
>
> Thanks
>
> Sucheta

[Gusdev-rad-issues] Re: [Gusdev-gusdev] prerequisites for RAD ArrayLoader

[Kevin M. <mu...@ge...>]

On Nov 15, 2004, at 12:54 PM, Elisabetta Manduchi wrote:
> yes you'll need to have the relevant entry in 
> SRes.ExternalDatabaseRelease if you want to enter 
> (external_database_release_id, source_id) in any given GUS table and 
> you create this in the order you outline.

Pardon my thickness.

So, for instance, in an array load data file I got from CBIL 
(HG-U133A.forRAD.txt), the ext_db_rel_id column is 2 for all rows, 
where 2 refers to a release id in CBIL's database that indirectly links 
to an SRES.ExternalDatabase record that might represent GenBank?  (Is 
it Genbank, in this case?) And the source_id column might contain the 
accession number of  a Genbank sequence (e.g. U48705) to which this 
probe row is related?

Our GUS instance does not have GenBank loaded yet.  Is it OK just to 
put in a placeholder record for GenBank in SRES.ExternalDatabase and 
then replace '2' with whatever our release id winds up being in the 
corresponding SRES.ExternalDatabaseRelease record?

Thanks,
Kevin Murphy

[Gusdev-rad-issues] Error loading data using ArrayResultLoader

[Sucheta T. <su...@vb...>]

Hi Elissabetta,

I am trying to upload data using the ArrayResultLoader plugin and
following are my command line parameters

ga GUS::RAD::Plugin::ArrayResultLoader --data_file <path> --array_id 3
--e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
--quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
AffymetrixMAS5 --debug --commit >& result_loader.err


And my data file has the following heeader:

x_position y_position mean stdv name detection signal detection_p_value
data        data       data  data  data  data   data   data

All separated by tab.

But I get an error like this:

Missing header x_position which is required to upload data into file.

Although I have the x_position defined in the header.

Am doing something wrong here. I have all the pre-requisites done.

Thanks

Sucheta





-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

[Gusdev-rad-issues] Re: [Gusdev-gusdev] prerequisites for RAD ArrayLoader

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

Kevin,
yes you'll need to have the relevant entry in SRes.ExternalDatabaseRelease 
if you want to enter (external_database_release_id, source_id) in any 
given GUS table and you create this in the order you outline.
For the specific case of the ArrayLoader, this pair of fields is present 
both in RAD3.Array and in views of RAD3.ElementImp and 
RAD3.CompositeElementImp.
An example of an external_database for a RAD3.Array entry might be 
ArrayExpress, if you want to indicate an identifier (through source_id) 
for the same array in another database. In our instance of RAD our arrays 
are typically pointed to an ArrayExpress array (if they are also in there) 
or to nothing, but of course you can point to anything you like.
In views of ElementImp and CompositeElementImp the external database is 
typically important as it enables to identify what the element or 
composite element on the array represent. Examples of databases that are 
of relevance here might be GenBank, IMAGE, etc. For the same array 
different elements (composite elements) on that array might point to 
different databases. For examples, for some of the non-commercial arrays 
stored in our instance of RAD, some of the spots on that array are 
identified through an image clone id, others through a GenBank, etc. 
depending on available information.
The source_id always refer to the main identifier in the db pointed to by 
external database id, which identifies the specific entry. For example it 
would be the accession_num for GenBank, the image clone_id for IMAGE, etc. 
Elisabetta
P.S. When you send emails to the GUS list that are of particular 
interest to RAD, could you please also cc the rad-issues source forge 
list, here copied? If you have not subscribed to the latter, I recommend 
you do.

---

On Mon, 15 Nov 2004, Kevin Murphy wrote:

> When loading a new array using GUS/RAD/Plugin/ArrayLoader.pm, what are the 
> database prerequisites for the external_database_release_id and source_id 
> columns in the input data file?
>
> Are you supposed to create an SRES.ExternalDatabase record with, e.g. a 
> 'name' column value of 'FooArray123', then create a corresponding 
> SRES.ExternalDatabaseRelease record, and use that 
> external_database_release_id in the data file?
>
> And what of the source_id column?
>
> Thanks,
> Kevin Murphy
>
>
>
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[Gusdev-rad-issues] CBIL RAD cvs repository now public

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

Hi all,
apologies if you receive this message twice, you might be in more than one 
mailing list.
This is to let you know that the CBIL RAD cvs repository is now public 
(read-only) and available at http://cvs.cbil.upenn.edu

Some important clarifications:

1. The RAD plugins described at 
http://www.cbil.upenn.edu/RAD/php/RAD-installation.php? and
documented at http://www.gusdb.org/documentation/plugins/
are NOT those in this repository, but they are contained  (and have been 
available all along) in the Sanger Center GUS/RAD cvs repository 
http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/RAD/?cvsroot=GUS&f=h
*These are the ones you want to use.* The plugins contained in the CBIL 
RAD repository are either deprecated or specific of our instance.

2. The utility of having the CBIL RAD repository available though is that 
you can get from there the most recent code for the StudyAnnotator and for 
MR_T as well as for the RAD Querier.
So the relevant directories and files in 
http://cvs.cbil.upenn.edu/cgi-bin/cvsweb.cgi/RAD/
are build.xml, StudyAnnotator, Querier and MR_T.
(You should mostly ignore the directories DataLoad and config.)

Elisabetta

[Gusdev-rad-issues] Re: [Gusdev-gusdev] important correction Re: RAD schema

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

Hi Sucheta,
the old configuration files (those in the CBIL RAD repository which 
will be public soon) are a mix of files for older versions of the 
plugins, now deprecated, or for plugins that are specific of our instance 
of RAD. I recommend not to use these. You can get the most recent plugins 
from the Sanger CVS, from the GUS/RAD repository and I recommend you use 
these together with the accompanying sample config files in the same 
repository.
As for Affy data, MAS5 is not the only view we have. We also have 
RMAexpress, MOID, and (this is the most recent in the RAD schema) 
ProbeProfiler. More views of CompositeElementResultImp can be created as 
needed. Same story for ElementResultImp. Also, these are a tables that 
accomodate results straight out of a given quantification software. In 
RAD there are other sets of tables to accomodate other processing steps 
(including ad hoc normalizations) that are done by a user subsequently 
(the Process tables) and also tables to accomodate down stream analysis 
results (the Analysis tables). I should mention that we are 
planning to soon just use the Analysis tables also for processing results 
and to deprecate the Process tables, as the former are more mature in 
their design.
Elisabetta
P.S. I'm cc-ing the gus-rad-issue mailing list. I don't recall if you 
subscribed to this, I would recommend you do and also it would help if you 
could cc this list when you have RAD questions, so we can keep an archive.

---

On Tue, 9 Nov 2004, Sucheta Tripathy wrote:

> Hi Elisabetta,
>
> Thanks for yor reply. When you say old configuration file does it mean the
> config files for the older versions of plugins? In that case actually we
> have not updated our RAD plugins lately, so I was wondering if there will
> be a conflict of new cfg files with older plugins.
>
> Regarding the data files we are not sure which views to use, I guesss we
> need to study them more carefully before deciding which one is suitable
> for each plugin.
>
> I am not sure what you use, but we have several issues in using MAS5 for
> normalization, so we may go with other methods, and I don't know if there
> are views to support all these different methods.
>
> Anyway, regarding the choices of views I will get back to you soon, so
> that you can tell us which data files to use.
>
> _sucheta
>
>>
>> Sorry, I guess I didn't make myself clear.
>> The new configuration files are those in the Sanger cvs repository, in the
>> GUS/RAD/config folder. These are already available.
>> The ones that are old are those that are contained in the *CBIL RAD cvs
>> repository*, which is the repository not yet available. (When available,
>> this repository will be useful for other things, but the config files in
>> it are obsolete or not of general application outside of CBIL instances.)
>> Regarding the datafiles, the samples will vary according to the plugin and
>> the view that is used. If you tell me which exact plugin(s) you have in
>> mind and what view(s) you are going to load into (e.g. ArrayResultLoader
>> plugin with AffymetrixMAS5 view), I'll select a subset of data
>> files to send you as samples. We have so many data files that it would
>> be overwhelming to send you all kinds and it might be more efficient to
>> just send you those for views and plugins you will actually be using.
>> Note: for the special case of the BatchResultLoader plugin, the data
>> files are just those out of the relevant software and the work is in
>> building an appropriate xml file, samples of which are in the Sanger
>> repository.
>> Elisabetta
>>
>> ---
>>
>> On Mon, 8 Nov 2004, Sucheta Tripathy wrote:
>>
>>> Hi Elisabetta,
>>>
>>> Since you said the existing cfg files in the repository are old and
>>> should
>>> not be used, I guess here I am confused, where do I look for the new cfg
>>> files.
>>>
>>> Also it will be great if you could provide us small sample data files or
>>> tell us where we find them. The pointers provided in the plugins often
>>> tell
>>> " The file contains the values for attributes in ElementResultImp,
>>> CompositeResultElementImp". Which is kind of unclear about the exact
>>> format.
>>>
>>> Thanks a lot.
>>>
>>> Sucheta
>>>
>>> At 03:49 PM 11/8/2004 -0500, you wrote:
>>>
>>>> Sorry,
>>>> **important correction** regarding sample cfg files. Ignore my the
>>>> second
>>>> to last comment on the CBIL RAD cvs for config files in my previous
>>>> email. The CBIL RAD repository will be made indeed public and will
>>>> contain other useful things, like the latest StudyAnnotator code, etc.
>>>> But the sample cfg files are stored at **the Sanger GUS cvs** in the
>>>> repository GUS/RAD/config and *already available* (there are config
>>>> files
>>>> in the CBIL RAD repository I cited below, but those are old and should
>>>> not be used.) Again, the documentation of each plugin should point to
>>>> the
>>>> location of its sample config file *within the Sanger GUS cvs
>>>> repository*.
>>>> Sorry for the confusion on this point, I got mixed up on our various
>>>> cvs
>>>> repositories...
>>>>
>>>> Elisabetta
>>>>
>>>> ---
>>>>
>>>> On Mon, 8 Nov 2004, Elisabetta Manduchi wrote:
>>>>
>>>>>
>>>>> Hi Sucheta,
>>>>> first a reminder, also for the benefit of others in the cc of this
>>>>> email, that general information on the RAD pipeline and on how to set
>>>>> RAD up is at http://www.cbil.upenn.edu/RAD/php/RAD-installation.php?
>>>>> In terms of the RAD schema, I'm not sure of exactly what you are
>>>>> looking
>>>>> for. RAD is part of GUS, so you if you install the GUS schema
>>>>> (instructions at http://www.gusdb.org/documentation.html) you'll have
>>>>> the RAD schema as well. I believe that the plans are to make available
>>>>> the next release of the schema (3.5?) in the next few weeks.
>>>>> The documentation for the RAD schema is contained in that of the GUS
>>>>> schema at http://www.gusdb.org/cgi-bin/schemaBrowser.
>>>>> All RAD plugins are available from the Sanger CVS and documentation
>>>>> can
>>>>> also be viewed at: http://www.gusdb.org/documentation/plugins.
>>>>> In terms of sample files, configuration sample files for most of the
>>>>> plugins are currently stored in the CBIL RAD cvs repository. This
>>>>> repository will be made public (read-only) very shortly, possibly even
>>>>> tomorrow, and will be added to the repositories currently viewable at
>>>>> http://cvs.cbil.upenn.edu. So, if you check back at this website in a
>>>>> few days you should see our RAD repository. All available sample files
>>>>> (mostly samples of cfg files) are in the directory /DataLoad/config/
>>>>> of
>>>>> this repository and the name of the relevant cfg sample file for each
>>>>> plugin is are specified in the plugin's documentation.
>>>>> We don't currently store sample data files in cvs, but the format is
>>>>> typically explained in the plugin doc and if you need any further
>>>>> clarification feel free to contact us with the specifics of the plugin
>>>>> you are interested in and we can provide additional info and examples.
>>>>> Hope this helps,
>>>>> Elisabetta
>>>>>
>>>>> ---
>>>>>
>>>>> On Mon, 8 Nov 2004, Sucheta Tripathy wrote:
>>>>>
>>>>>> Hi Elisabetta,
>>>>>> How are you? It was nice visiting you all at CBIL.
>>>>>> I have one group here working on a pipeline to upload data to the RAD
>>>>>> module. For that I was wondering if you can point us a place, where
>>>>>> we
>>>>>> get the RAD schema and also sample data files for all the plugins for
>>>>>> RAD.
>>>>>> That will be a great help.
>>>>>> Thanks in advance.
>>>>>> Have a great day.
>>>>>> Sucheta
>>>>>>
>>>>>> At 11:47 AM 9/15/2003 -0400, Elisabetta Manduchi wrote:
>>>>>>
>>>>>>> I've cvs committed a change to GUS/PluginMgr/lib/perl/Plugin.pm,
>>>>>>> suggested
>>>>>>> by Steve, to fix a problem occurring when registering a new plugin
>>>>>>> written
>>>>>>> using the most recent documentation features.
>>>>>>> Elisabetta
>>>>>>>
>>>>>>> -------------------------------------------------------
>>>>>>> This sf.net email is sponsored by:ThinkGeek
>>>>>>> Welcome to geek heaven.
>>>>>>> http://thinkgeek.com/sf
>>>>>>> _______________________________________________
>>>>>>> Gusdev-gusdev mailing list
>>>>>>> Gus...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by:
>>>> Sybase ASE Linux Express Edition - download now for FREE
>>>> LinuxWorld Reader's Choice Award Winner for best database on Linux.
>>>> http://ads.osdn.com/?ad_id=5588&alloc_id=12065&op=click
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>
>
> -- 
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
>

[Gusdev-rad-issues] Re: RAD schema

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

Hi Sucheta,
first a reminder, also for the benefit of others in the cc of this email, 
that general information on the RAD pipeline and on how to set RAD up is 
at http://www.cbil.upenn.edu/RAD/php/RAD-installation.php?
In terms of the RAD schema, I'm not sure of exactly what you are looking 
for. RAD is part of GUS, so you if you install the GUS schema 
(instructions at http://www.gusdb.org/documentation.html) you'll have the 
RAD schema as well. I believe that the plans are to make available the 
next release of the schema (3.5?) in the next few weeks.
The documentation for the RAD schema is contained in that of the GUS 
schema at http://www.gusdb.org/cgi-bin/schemaBrowser.
All RAD plugins are available from the Sanger CVS and documentation can 
also be viewed at: http://www.gusdb.org/documentation/plugins.
In terms of sample files, configuration sample files for most of the 
plugins are currently stored in the CBIL RAD cvs repository. This 
repository will be made public (read-only) very shortly, possibly even 
tomorrow, and will be added to the repositories currently viewable at
http://cvs.cbil.upenn.edu. So, if you check back at this website in a few 
days you should see our RAD repository. All available sample files (mostly 
samples of cfg files) are in the directory /DataLoad/config/ of this 
repository and the name of the relevant cfg sample file for each plugin 
is  are specified in the plugin's documentation.
We don't currently store sample data files in cvs, but the format is 
typically explained in the plugin doc and if you need any further 
clarification feel free to contact us with the specifics of the plugin you 
are interested in and we can provide additional info and examples.
Hope this helps,
Elisabetta

---

On Mon, 8 Nov 2004, Sucheta Tripathy wrote:

> Hi Elisabetta,
>
> How are you? It was nice visiting you all at CBIL.
>
> I have one group here working on a pipeline to upload data to the RAD 
> module. For that I was wondering if you can point us a place, where we get 
> the RAD schema and also sample data files for all the plugins for RAD.
>
> That will be a great help.
>
> Thanks in advance.
>
> Have a great day.
>
> Sucheta
>
>
> At 11:47 AM 9/15/2003 -0400, Elisabetta Manduchi wrote:
>
>> I've cvs committed a change to GUS/PluginMgr/lib/perl/Plugin.pm, 
>> suggested
>> by Steve, to fix a problem occurring when registering a new plugin 
>> written
>> using the most recent documentation features.
>> Elisabetta
>> 
>> 
>> 
>> -------------------------------------------------------
>> This sf.net email is sponsored by:ThinkGeek
>> Welcome to geek heaven.
>> http://thinkgeek.com/sf
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-rad-issues] important correction Re: RAD schema

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

Sorry,
**important correction** regarding sample cfg files. Ignore my the 
second to last comment on the CBIL RAD cvs for config files in my 
previous email. The CBIL RAD repository will be made indeed public and 
will contain other useful things, like the latest StudyAnnotator code, 
etc.
But the sample cfg files are stored at **the Sanger GUS cvs** in the 
repository GUS/RAD/config and *already available* (there are config files 
in the CBIL RAD repository I cited below, but those are old and should 
not be used.) Again, the documentation of each plugin should point to the 
location of its sample config file *within the Sanger GUS cvs repository*.
Sorry for the confusion on this point, I got mixed up on our various cvs 
repositories...

Elisabetta

---

On Mon, 8 Nov 2004, Elisabetta Manduchi wrote:

>
> Hi Sucheta,
> first a reminder, also for the benefit of others in the cc of this email, 
> that general information on the RAD pipeline and on how to set RAD up is at 
> http://www.cbil.upenn.edu/RAD/php/RAD-installation.php?
> In terms of the RAD schema, I'm not sure of exactly what you are looking 
> for. RAD is part of GUS, so you if you install the GUS schema (instructions 
> at http://www.gusdb.org/documentation.html) you'll have the RAD schema as 
> well. I believe that the plans are to make available the next release of 
> the schema (3.5?) in the next few weeks.
> The documentation for the RAD schema is contained in that of the GUS schema 
> at http://www.gusdb.org/cgi-bin/schemaBrowser.
> All RAD plugins are available from the Sanger CVS and documentation can 
> also be viewed at: http://www.gusdb.org/documentation/plugins.
> In terms of sample files, configuration sample files for most of the 
> plugins are currently stored in the CBIL RAD cvs repository. This 
> repository will be made public (read-only) very shortly, possibly even 
> tomorrow, and will be added to the repositories currently viewable at
> http://cvs.cbil.upenn.edu. So, if you check back at this website in a few 
> days you should see our RAD repository. All available sample files (mostly 
> samples of cfg files) are in the directory /DataLoad/config/ of this 
> repository and the name of the relevant cfg sample file for each plugin is 
> are specified in the plugin's documentation.
> We don't currently store sample data files in cvs, but the format is 
> typically explained in the plugin doc and if you need any further 
> clarification feel free to contact us with the specifics of the plugin you 
> are interested in and we can provide additional info and examples.
> Hope this helps,
> Elisabetta
>
> ---
>
> On Mon, 8 Nov 2004, Sucheta Tripathy wrote:
>
>> Hi Elisabetta,
>> 
>> How are you? It was nice visiting you all at CBIL.
>> 
>> I have one group here working on a pipeline to upload data to the RAD 
>> module. For that I was wondering if you can point us a place, where we 
>> get the RAD schema and also sample data files for all the plugins for 
>> RAD.
>> 
>> That will be a great help.
>> 
>> Thanks in advance.
>> 
>> Have a great day.
>> 
>> Sucheta
>> 
>> 
>> At 11:47 AM 9/15/2003 -0400, Elisabetta Manduchi wrote:
>> 
>>> I've cvs committed a change to GUS/PluginMgr/lib/perl/Plugin.pm, 
>>> suggested
>>> by Steve, to fix a problem occurring when registering a new plugin 
>>> written
>>> using the most recent documentation features.
>>> Elisabetta
>>> 
>>> 
>>> 
>>> -------------------------------------------------------
>>> This sf.net email is sponsored by:ThinkGeek
>>> Welcome to geek heaven.
>>> http://thinkgeek.com/sf
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> 
>

[Gusdev-rad-issues] Re: Questions (MIKE please note)

[Michael S. <msa...@pc...>]

Hi Urska,

To address your first issue:  As Elisabetta said, RAD is a subcomponent 
of GUS, which requires a Unix-like operating system to run.  It's known 
to work with Linux (which we use and recommend), but also Mac OS X and 
Solaris (both are less tested...).  Oracle need not be on the same 
system as the GUS application components (and I wouldn't recommend it), 
and thus Oracle could be on Linux, Mac OS X, etc (although again, we 
recommend Linux where it has the most testing).

To address your third issue:  This is an issue you'll have to address 
with Oracle.  My understanding is that Oracle provides *evaluation* 
copies available for download on their website, but they are *not* free 
for non-commercial use.  Here at Penn, we a have a site-license for 
Oracle, which I'm sure the University pays for.  Ultimately, only Oracle 
can answer licensing questions about Oracle software.

If you don't have access to Oracle, and cost is an issue, you may be 
interested in the PostgreSQL compatible version of GUS, which should be 
released in the coming months.

Thanks,

Mike


Elisabetta Manduchi wrote:
> 
> Hi Urska,
> thanks for your interest in RAD.
> RAD is part of GUS which here is installed on Linux. But our dba Mike 
> Saffitz, here cc-ed, is the best person to respond to your questions 
> regarding installation and Oracle.
> In GUS we have a system of attaching to each individual row in each 
> table information on user, group, project and read/write permissions, so 
> one could have fine control up to row-by-row if desired.
> In our instance we typically apply control on a larger level, i.e. at 
> the study level (RAD3.Study) and we have a web interface that queries 
> RADs and shows publicly only those studies whose other_read is set to 1 
> (and everything relative to that study, from hybs info to final 
> quantified results is visible) and which shows the private studies only 
> upon logging in. Again, this is how we use our instance of the system, 
> but the system is flexible enough to allow control as fine as desired.
> Elisabetta
> P.S. We have a sourcefourge mailing list for RAD, which I have cc-ed in 
> my reply. You might want to subscribe to it and it would be helpful if 
> for any RAD related question you could email to that list.
> 
> ---
> 
> On Thu, 14 Oct 2004, Urska Cvek wrote:
> 
>> Hello,
>>
>> I have discovered your RAD database of microarray and non-microarray 
>> experiments. I would like to use it, but I have been trying to figure 
>> out some answers as to how exactly this works:
>>
>> - RAD is implemented on top of GUS - where is GUS installed and where 
>> is RAD installed? Are they running of a single Linux/UNIX server, or 
>> are they installed on a Windows server?
>>
>> - I need to provide different levels of user access, for example, 
>> access to only public data to certain users, and access to all data 
>> for other users (like the administrators or investigators). Do you 
>> have that implemented as well?
>>
>> - My last question is wrt Oracle - I visited the Oracle web page and 
>> as it looks like I can download and install Oracle 9i for free. Am I 
>> correct (I am at an educational institution and this would be a 
>> non-commercial database) or do I have to have a different version of 
>> Oracle that is not free?
>>
>> Thank you,
>>
>> Urska Cvek
>> Assistant Professor
>> LSUS

[Gusdev-rad-issues] Re: Questions (MIKE please note)

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

Hi Urska,
thanks for your interest in RAD.
RAD is part of GUS which here is installed on Linux. But our dba Mike 
Saffitz, here cc-ed, is the best person to respond to your questions 
regarding installation and Oracle.
In GUS we have a system of attaching to each individual row in each table 
information on user, group, project and read/write permissions, so one 
could have fine control up to row-by-row if desired.
In our instance we typically apply control on a larger level, i.e. at the 
study level (RAD3.Study) and we have a web interface that queries RADs and 
shows publicly only those studies whose other_read is set to 1 (and 
everything relative to that study, from hybs info to final quantified 
results is visible) and which shows the private studies only upon logging 
in. Again, this is how we use our instance of the system, but the system 
is flexible enough to allow control as fine as desired.
Elisabetta
P.S. We have a sourcefourge mailing list for RAD, which I have cc-ed in my 
reply. You might want to subscribe to it and it would be helpful if for 
any RAD related question you could email to that list.

---

On Thu, 14 Oct 2004, Urska Cvek wrote:

> Hello,
>
> I have discovered your RAD database of microarray and non-microarray experiments. I would like to use it, but I have been trying to figure out some answers as to how exactly this works:
>
> - RAD is implemented on top of GUS - where is GUS installed and where is RAD installed? Are they running of a single Linux/UNIX server, or are they installed on a Windows server?
>
> - I need to provide different levels of user access, for example, access to only public data to certain users, and access to all data for other users (like the administrators or investigators). Do you have that implemented as well?
>
> - My last question is wrt Oracle - I visited the Oracle web page and as it looks like I can download and install Oracle 9i for free. Am I correct (I am at an educational institution and this would be a non-commercial database) or do I have to have a different version of Oracle that is not free?
>
> Thank you,
>
> Urska Cvek
> Assistant Professor
> LSUS

[Gusdev-rad-issues] added view for RAD3.ElementResultImp

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

We are creating the following new view to accomodate QuantArray results:

CREATE VIEW RAD3.QuantArrayElementResult AS SELECT
  element_result_id,
  element_id,
  composite_element_result_id,
  quantification_id,
  subclass_view,
  foreground AS intensity,
  background,
  foreground_sd AS intensity_sdev,
  background_sd AS background_sdev,
  float1 As x_location,
  float2 AS y_location,
  float3 AS diameter,
  float4 AS area,
  float5 AS footprint,
  float6 AS circularity,
  float7 AS spot_uniformity,
  float8 AS bkg_uniformity,
  float9 AS sn_ratio,
  float10 AS confidence,
  tinyint1 AS diameter_filter
  tinyint2 AS area_filter,
  tinyint3 AS footprint_filter,
  smallint1 AS circularity_filter,
  smallint2 AS spot_uniformity_filter,
  smallint3 AS bkg_uniformity_filter,
  int1 AS sn_ratio_filter,
  int2 AS replicate_filter,
  int3   AS ignore_filter,
  modification_date,
  user_read,
  user_write,
  group_read,
  group_write,
  other_read,
  other_write,
  row_user_id,
  row_group_id,
  row_project_id,
  row_alg_invocation_id
FROM ElementResultImp
WHERE subclass_view = 'QuantArrayElementResult' WITH CHECK OPTION;
--

CREATE OR REPLACE VIEW Rad3ver.QuantArrayElementResultVer AS
  SELECT
  element_result_id,
  element_id,
  composite_element_result_id,
  quantification_id,
  subclass_view,
  foreground AS intensity,
  background,
  foreground_sd AS intensity_sdev,
  background_sd AS background_sdev,
  float1 As x_location,
  float2 AS y_location,
  float3 AS diameter,
  float4 AS area,
  float5 AS footprint,
  float6 AS circularity,
  float7 AS spot_uniformity,
  float8 AS bkg_uniformity,
  float9 AS sn_ratio,
  float10 AS confidence,
  tinyint1 AS diameter_filter
  tinyint2 AS area_filter,
  tinyint3 AS footprint_filter,
  smallint1 AS circularity_filter,
  smallint2 AS spot_uniformity_filter,
  smallint3 AS bkg_uniformity_filter,
  int1 AS sn_ratio_filter,
  int2 AS replicate_filter,
  int3   AS ignore_filter,
  modification_date,
  user_read,
  user_write,
  group_read,
  group_write,
  other_read,
  other_write,
  row_user_id,
  row_group_id,
  row_project_id,
  row_alg_invocation_id,
  version_alg_invocation_id,
  version_date,
  version_transaction_id
FROM RAD3ver.ElementResultImpVer WHERE subclass_view =
'QuantArrayElementResult'
WITH CHECK OPTION
--

[Gusdev-rad-issues] new plugin for RAD

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

A new plugin is now available from the Sanger cvs repository: the 
BatchArrayResultLoader. All the supporting utilds an  Documentation is 
available at 
http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-BatchArrayResultLoader.html
This plugin can be used to load *in batch* quantification results from any of 
Affymetrix MAS 4.0, Affymetrix MAS 5.0, RMAExpress, GenePix, ArrayVision into 
RAD.
Note, this plugin was previously in the CBIL cvs repository as it contains some 
hard-coded parts which are specific of our database instance. However, see the 
section 'NOTES: Warning' of the above documentation for information on how to 
modify the plugin to make it compatible with your own instance of the database.
Elisabetta

Re: [Gusdev-rad-issues] RAD graphical output

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

Hi Sucheta,
yes there are graphical outputs available illustrating the biomaterials 
and their treatments, both for a study as a whole and for individual 
assays. The attached document contains instructions on how to query the 
RAD website (see 6.d for the graphical display part). You can try them out 
and query the public studies, for which you don't need a login.
Currently we do not show the individual gene chip image files. We do 
archive the .tifs or .dat files in our fileserver and can make images 
available upon request. There is a plan to possibly display .jpegs of the 
individual chips on the query site for some or all of the assays, but it's 
not a high priority for us at the moment.
For specific inquiries about the RAD Querier code, you can contact Junmin 
Liu, here cc-ed.
Elisabetta

  ---

On Mon, 28 Jun 2004, Sucheta Tripathy wrote:

> Hi Elissabetta,
>
> I just saw your querying features in RAD website. I think most of the outputs 
> are available as text files.
> Is there some graphical outputs available?
>
> Also Do you show the individual gene chip image files?
>
> Thanks
>
> Sucheta

[Gusdev-rad-issues] RAD graphical output

[Sucheta T. <su...@vb...>]

Hi Elissabetta,

I just saw your querying features in RAD website. I think most of the 
outputs are available as text files.
Is there some graphical outputs available?

Also Do you show the individual gene chip image files?

Thanks

Sucheta

[Gusdev-rad-issues] Schema change: StudyFactorValue table

[Trish W. <wh...@pc...>]

Hi,

I would like to add the nullable attribute channel_id to the RAD table 
StudyFactorValue in order to attach a study factor value to a 
channel rather than just an assay.

Trish

[Gusdev-rad-issues] Re: ddl for RAD3

[Angel P. <an...@pc...>]

Hi Phillip,

RAD is part of the GUS system, and hence relies on some GUS tables that
are not part of the RAD schema.

You can downlaod all of the ORACLE DDL files from www.gusdb.org. The DDL
files that are specific to RAD are prefixed with "rad3-".
Very soon we are going to release a postgres version of GUS for
open-source folks.

Please send any more issues you have to the gusdev-rad-issues mailing
list (CC'd)
Cheers,
Angel




Phillip Stafford wrote:

> Do you guys have the actual "create table...." ddl for RAD?  I assume 
> the only changes from one type of database to another are the 
> datatypes.  Wouldn't someone there have the code to generate the 
> tables on a MySQL or Oracle or DB2 or SequelServer or similar database??
>
>
> Thank you;
>
>
> Phillip

[Gusdev-rad-issues] FASD project: Online survey launched

[<ben...@id...>]

Dear Open Source developer

I am doing a research project on "Fun and Software Development" in which I kindly invite you to participate.
You will find the online survey under http://fasd.ethz.ch/qsf/. The questionnaire consists of 53 questions and you will need about 15 minutes to complete it.

With the FASD project (Fun and Software Development) we want to define the motivational significance of fun when software developers decide to engage in Open Source projects. What is special about our research project is that a similar survey is planned with software developers in commercial firms. This procedure allows the immediate comparison between the involved individuals and the conditions of production of these two development models. Thus we hope to obtain substantial new insights to the phenomenon of Open Source Development.


With many thanks for your participation,
Benno Luthiger


PS:
The results of the survey will be published under http://www.isu.unizh.ch/fuehrung/blprojects/FASD/.
We have set up the mailing list fa...@we... for this study. Please see http://fasd.ethz.ch/qsf/mailinglist_en.html for registration to this mailing list.

_______________________________________________________________________

Benno Luthiger
Swiss Federal Institute of Technology Zurich
8092 Zurich

Mail: benno.luthiger(at)id.ethz.ch
_______________________________________________________________________