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. /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 email@example.com unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net