On Tue, Sep 27, 2011 at 1:51 AM, Nicklas Nordborg <nick...@thep.lu.se> wrote: > 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.
That all sounds fantastic, and is really useful for our planning. You guys rock! cheers, Bob. > > /Nicklas > > ------------------------------------------------------------------------------ > 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. > http://p.sf.net/sfu/splunk-d2dcopy1 > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net > ------------------------------------------------------------------------------ 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. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
