[BioC] Analysis Interface Projects [was Seeking collaboration for an opensource data analysisinterface project]

Gordon Smyth smyth at wehi.edu.au
Tue Sep 9 10:47:38 MEST 2003

This is probably a good time to mention on the BioC mailing list that we 
have developed a GUI interface to the limma package using the R tktcl 
library and tktcl extensions. The GUI package package is publicly available 
from http://bioinf.wehi.edu.au/limmaGUI. The package currently takes users 
from data input through data analysis to differential expression with 
two-color microarrays. It runs on most platforms that R runs on.

It would be good to keep in touch about work on R and BioC user interfaces, 
real progress seems to being made now. Are you planning to make your visual 
basic interface to R publicly available?


At 02:11 AM 9/09/2003, Park, Richard wrote:
>Hi Andrea,
>I have spent sometime trying to create microarray analysis interfaces 
>between visual basic to R/S-plus/ArrayAnalyzer. What types of platforms 
>were you thinking of using to implement this idea? I have found that 
>creating interfaces in s-plus is sort of cumbersome and hard to adapt for 
>multi-step analyses of microarray experiments.
>ArrayAnalyzer makes use of java applets through an automation server to 
>power its interfaces, but it still is in its basic forms of guiding a 
>"simple" user to differential gene expression. I have seen a big need for 
>interfaces into R. One option of creating an interface into R could be 
>using the same tools they used for some of the packages in bioconductor 
>such as affy, or making use of an automation server of such as Dcom 
>created by Thomas Baier which is similar to automation server found in 
>S-plus. It allows for communication between visual basic (ms packages: 
>i.e. excel, access) as well as perl.
>Please let me know what your ideas are, I have spent a lot of time trying 
>to figure out how to help users easily access the power in R w/o having to 
>spend the time to learn the semantics of the language. I have a basic 
>interface created in visual basic that is currently keeping track of 350+ 
>microarray experiments and a simple "point and click" interface to guide 
>the user to create any data group from any of the 350 arrays into a basic 
>analysis format (making use of tools and algorithms w/in bioconductor).
>Richard Park
>Computational Data Analyzer - Immunology and Immunogenetics
>Joslin Diabetes Center/ Harvard Medical School
>-----Original Message-----
>From: Andrea Splendiani [mailto:andrea.splendiani at unimib.it]
>Sent: Thursday, September 04, 2003 11:5 AM
>To: bioconductor at stat.math.ethz.ch
>Subject: [BioC] Seeking collaboration for an opensource data
>analysisinterface project
>We are looking for people interested in  an opensource data analysis
>software that we would like to propose as a NEXT-Adventure project (we
>are from Univ. Milano Bicocca, Italy. Dep. of Computer Science and Dep.
>of Biotechnology and Bioengineering).
>Obviously it would not make sense to replicate Bioconductor and R
>efforts (that we think are excellent), our intention is to develop
>mainly interfaces more intended to the end user, trying to make tools
>present in Bioconductor more easily accessible.
>So for this proposal we would like to have as a partner someone from
>the Bioconductor community (should be from Europe).
>If anyone is interested in knowing more about this, please send me an
>Andrea Splendiani

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