Hi Emil, We are in the process of integrating GenePattern (http://www.broad.mit.edu/cancer/software/genepattern/) with BASE 2, and once we have a solution working we'll be happy to place it in the public domain.
GenePattern supports all the things you are asking for below, and we like for the same reasons that you liked BASE1. At the moment we have got as far as running things from GP rather than from within BASE2. I have written a BASE client that can run as a GP module (and can be integrated into workflows with R/Perl/Matlab modules, including Bioconductor) and that takes the user's login credentials as well as an experiment name as parameters. It then gets either raw data or pointers to file locations (in the case of Affy data) out of BASE and passes this to the next module (in our case a Bioconductor script that normalizes the data). We are doing things this way (rather than using the BASE analysis tools) because we are working with statisticians who like to write their own routines. We also want to look into turning this the other way round -- write a BASE2 plugin that gets some data out and then connects to GP, probably through a web service client, but we haven't started on this yet. I am happy to share any code that I have got so far, but it will probably be a good few weeks before we have a BASE plugin for GP (we have got quite a few other things on the go apart from BASE). I should also add that it is really easy to share preconfigured GP workflow modules (written in any of the supported languages) - they really just plug and play. Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm ============================= > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Emil Lundberg > Sent: 26 March 2007 22:34 > To: BASE ML > Subject: Re: [base] Questions on Reporter IDs > > > I have a few follow up questions and comments about plugins...I am > > trying to get MGH plugins from BASE2 working. Unfortunately I am > > not having much luck (see ticket http://base.thep.lu.se/ticket/511). > > So my questions are: > > > > 1) Which plugins have been successfully tested in > > Base1PluginExecuter (just so I can rule out it's not me!)? > > 2) Do you require some help testing Base1PluginExecuter? I am happy > > to help here to get this working for the common good and also I > > have a several custom plugins I have written in R and perl (and > > other plugins used in BASE 1.2) that I would really like to use on > > the data in BASE. Also I can't really move all my users of BASE 1.2 > > across to BASE2 until I get these working, since they use these > > as part of their daily analysis. > > 3) What are the plans to support non-Java plugins (via development > > of Base1PluginExecuter or otherwise) given that R and perl are very > > popular languages in bioinformatics and for arrays most serious > > analysis is done using R? > > > > I know you guys have a lot of work on and are doing fantastic job > > with BASE2, but being able to easily add analysis routines in *any > > language* and allow users to run them integrated in the web > > interface was one of the 'killer' aspects of BASE 1.2... > > Just to give you some feedback on our experience with B1PE, we have > tested it with most of the the BASE 1 plug-ins developed at the LCB, > and after some initial web server issues, we have found that it works > really well. 2-channel data only, naturally. We're in a similar > situation analysis-wise (although we're also looking at using BASE 2 > for Affy data), so the naturally empty state of BASE 2 analysis > functionality, we're really happy there is a B1PE. > > We second your plea for R/Perl/Bioconductor connectivity; it's > currently in BASE 2.4 (no date set), as are a lot of other nice > features - all in due time, I suppose... One alternative for the > impatient would be to write a plugin (perhaps based on something like > B1PE) yourself. > > To the BASE developers: is it feasible for an external developer to > help out with a ticket like R/BioC connectivity? If so, let us know! > > > best, > > /Emil Lundberg, LCB-DWH > http://www.lcb.uu.se/lcbdw.php > > > ------------------------------------------------------------------------ - > Take Surveys. Earn Cash. 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