I have implemented the incorporation of Illumina data into our BASE system,
along with a raw data importer. Our version requires that the
gene_profile.csv be split up into separate files, which we have done with an
R script. This can also be done manually in excel, or feasibly in a BASE
script.
Nicklas, how do I share the plugin configurations with others?
Jeremy
UCLA Department of Neurology
On 2/5/07, Nicklas Nordborg <[EMAIL PROTECTED]> wrote:
Emil Lundberg wrote:
> Hi all,
>
> Our site will likely wish to store Illumina array data in BASE 2 in the
> near future. Sifting through the mailing list archive, this seems indeed
> possible (based on the post below, from july '06).
>
> My question is has anyone implemented this already (Reha Y.?) and is
> willing to share the specifications and/or will this find its way into
> BASE 2 proper some day?
If somebody is willing to implement it. Right now we have to focus on
other things. We can put it into the standard BASE distribution if
someone:
* comes up with a <raw-data-type> definition for the Illumina Chip
* provides one or more plugin configurations for importing the data files
For an example of the existing plugin configurations see:
http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
/Nicklas
>
>
> regards,
>
> /Emil
>
> ________________________________
> Emil Lundberg / Sysadm
> Linnaeus Centre for Bioinformatics
> Uppsala University
>
>
>> Reha Yildirimman wrote:
>> > Hello,
>> >
>> > using Base2 we are trying to implement the Illumina Chip design.
>> In order
>> > to use the raw data files describing coordinates and intensities
>> of probes
>> > there is a need to define a new raw data type besides the given ones
>> > (affymetrix,agilent,spotfinder,...).
>> >
>> > Is this already implemented, is there a way around the "data
>> type" problem
>> > or am I looking at the wrong spot in base2 ?
>>
>> Yes, you can add raw data types to Base2. You have to find and modify
>> the file 'raw-data-types.xml'. It should be located in the
>> <basedir>/www/WEB-INF/classes directory.
>>
>> Add a tag <raw-data-type> for the Illumina Chip for example:
>>
>> <raw-data-type
>> id="illumina"
>> channels="2"
>> name="Illumina"
>> table="RawDataIllumina"
>> >
>>
>> Then add as many <property> tags as you need. The last step is to run
>> the <basedir>/bin/updatedb.sh script to create the new table.
>>
>> /Nicklas
>
>
>
>
>
> ------------------------------------------------------------------------
>
>
-------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services,
security?
> Get stuff done quickly with pre-integrated technology to make your job
easier.
> Download IBM WebSphere Application Server v.1.0.1 based on Apache
Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> The BASE general discussion mailing list
> basedb-users@lists.sourceforge.net
> unsubscribe: send a mail with subject "unsubscribe" to
> [EMAIL PROTECTED]
-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job
easier.
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier.
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
