On 2011-09-26 22:19, Bob MacCallum wrote:
> Hi Nicklas et al,
> I've been scanning the 3.0 alfa documentation and have seen how
> biomaterials are handled with respect next gen (with the new library
> type).
> However, I can't see how raw data and analysis works.  Do the concepts
> of reporters and array designs still apply? I'm happy to install and
> play but first I would greatly appreciate a few sentences of
> explanation.  Apologies if I missed this previously on the mailing
> list.

I don't think you missed anything because that part is not implemented 
in the alpha release. The ongoing work more or less follows the ideas 
that you posted in http://base.thep.lu.se/ticket/1153 a few years ago. 
For 1) we are providing a GTF importer that creates a "virtual" array 
design referencing the genes/transcripts that is of interest.

3a is the main choice so far. Everything done outside BASE can however 
be tracked and intermediate result files can be uploaded and stored. The 
"derived bioassay" item replaces "scan" and it is now also possible to 
have multiple steps of derived bioassays before a raw bioassay is 
created. In theory, it would be possible to implement BASE plug-ins to 
do the analysis here also, but in practice it is not so easy because of 
the large amount of data that is generated and the processing time 
required to analyze it. I don't know much about the details here, but in 
the end Cufflinks (http://cufflinks.cbcb.umd.edu/) is generating one 
output file per sample containing a count (fpkm) that should be usable 
as the expression level. This can be imported as a raw bioassay.

We have some ideas to create a specialized kind of "job agent" that 
follows a scripted path of analysis programs to run and then report to 
BASE what has been done and upload some of the results files. We have 
not started on this yet and there is no real time plan either. I guess 
it will be rather site-specific to begin with, since much depend on 
details about file storage areas, computational clusters, etc.

We'll keep the "Generic" platform for microarray experiments and add a 
new platform for sequencing experiments, but that's mostly cosmetics and 
a way for plug-ins to hide/show themselves depending on the context.

Hope this answers some of your questions. We'll try to release a new 
version (beta?) in about two weeks if we can get the desired 
functionality in place.


All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
The BASE general discussion mailing list
unsubscribe: send a mail with subject "unsubscribe" to

Reply via email to