Hi all, I need your opinion about using R-Rapache to build a knowlegde base to bioinformatics field. I have copious amount of genotype information (some few million records) and would like to store it in MySQL database. Then, using RMySQL connector I would like to use it for further analysis using R over a web interface. The web interface which I am thnking off, just does not serve the purose of statistical analysis, it should also serve as displaying data in grids and interactive maps etc on web interface. I had thought of doing the same using python-MySQLdb to store data and then R-rpy for further statistical analysis. But as R is now directly made to work on web I am very much excited about RApache project. Very recently I was introducing Rapache project and concept of building knowledge base using Rapache-R-MySQL combination to our team memebrs, Unfortunately few memebers were not that happy with using R directly in middle tier. There were serious comments about R that it is slow and generating plots on the fly wont be too fast. there was also discussion about maturity of RMySQL database connector, i mean fastness of querying MySQL will vary significantly with RMySQL when campared to MySQLdb connector? It would be nice if you give me a detailed opinion on this. Thanking you all in anticipation. Regards, mlsc [[alternative HTML version deleted]]
Hi, I am not sure about your data structure, but if you do not alter those often from third-party programs, then storing the information in R's native file formats (like RData) might give you some performance boost against always querying MySQL. Of course this depends on data structure and volume. Also, checking out some NoSQL techniques (like CouchDB or redis) might be a good idea for a web service - if your data is not profiting from relational database structure. Well, you need some benchmarks here. About plots: I would not say that the base graphics library (or even lattice) would be slow, although ggplot2 has some issues. So IMHO it depends on what type of plots would you generate, but I would say there would be no serious performance issues. After all: I think going the direct R way is great option :) Best, Gergely On Mon, Feb 6, 2012 at 07:36, MLSC <mlscmahe@gmail.com> wrote:> Hi all, > > I need your opinion about using R-Rapache to build a knowlegde base to > bioinformatics field. > > I have copious amount of genotype information (some few million records) > and would like to store it in MySQL database. Then, using RMySQL connector > I would like to use it for further analysis using R over a web interface. > The web interface which I am thnking off, just does not serve the purose of > statistical analysis, it should also serve as displaying data in grids and > interactive maps etc on web interface. > > I had thought of doing the same using python-MySQLdb to store data and > then R-rpy for further statistical analysis. But as R is now directly made > to work on web I am very much excited about RApache project. Very recently > I was introducing Rapache project and concept of building knowledge base > using Rapache-R-MySQL combination to our team memebrs, Unfortunately few > memebers were not that happy with using R directly in middle tier. There > were serious comments about R that it is slow and generating plots on the > fly wont be too fast. there was also discussion about maturity of RMySQL > database connector, i mean fastness of querying MySQL will vary > significantly with RMySQL when campared to MySQLdb connector? > > It would be nice if you give me a detailed opinion on this. > > Thanking you all in anticipation. > > Regards, > mlsc > > -- > You received this message because you are subscribed to the Google Groups > "rapache" group. > To post to this group, send email to rapache@googlegroups.com. > To unsubscribe from this group, send email to > rapache+unsubscribe@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/rapache?hl=en. >[[alternative HTML version deleted]]
Have you tried Bioconductor (www.bioconductor.org <http://www.bioconductor.org/>)? Spencer On 2/5/2012 10:36 PM, MLSC wrote:> Hi all, > > I need your opinion about using R-Rapache to build a knowlegde base to > bioinformatics field. > > I have copious amount of genotype information (some few million records) > and would like to store it in MySQL database. Then, using RMySQL connector > I would like to use it for further analysis using R over a web interface. > The web interface which I am thnking off, just does not serve the purose of > statistical analysis, it should also serve as displaying data in grids and > interactive maps etc on web interface. > > I had thought of doing the same using python-MySQLdb to store data and then > R-rpy for further statistical analysis. But as R is now directly made to > work on web I am very much excited about RApache project. Very recently I > was introducing Rapache project and concept of building knowledge base > using Rapache-R-MySQL combination to our team memebrs, Unfortunately few > memebers were not that happy with using R directly in middle tier. There > were serious comments about R that it is slow and generating plots on the > fly wont be too fast. there was also discussion about maturity of RMySQL > database connector, i mean fastness of querying MySQL will vary > significantly with RMySQL when campared to MySQLdb connector? > > It would be nice if you give me a detailed opinion on this. > > Thanking you all in anticipation. > > Regards, > mlsc > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web:www.structuremonitoring.com -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web: www.structuremonitoring.com [[alternative HTML version deleted]]