Hi Ross, Thank you for the offer, it's a bit complicated for me. My users are bioinformaticians who are doing a lot of microarray analysis and meta-analysis and they need many of the public tools available that I see on GenePattern GenePattern seems to have many tools and visualizers around microarray analysis, pathway and network inferencing, etc. Galaxy seems to have many tools and visualizers around next-gen sequencing, genomic analysis, and public server integration, etc. I've written quite a few tools for Galaxy for other purposes and love how easy it is to develop against and how flexible it is to your needs. You can really do some elegant stuff and it is accomodating. GenePattern I find to be much more rigid in what you can do and how you have to develop against it. If I could only have the Galaxy development platform with the GenePattern and Galaxy tools! :( -Leandro On Wed, Jul 21, 2010 at 1:24 PM, Ross <ross.lazarus@gmail.com> wrote:

I have wrappers for a couple of popular bioconductor packages. Not yet ready for production use, but happy to talk if you're interested?

On Wed, Jul 21, 2010 at 7:09 PM, Leandro Hermida <softdev@leandrohermida.com> wrote:

...

Hello,

Are there publicly available tools in Galaxy for microarray data analysis, visualization, etc?  Or is this kind of GenePattern's space and you want to stay separate? :)

best, Leandro _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Hi there, I saw this.... I can't wait :) will make life much more "integrated" On Wed, Jul 21, 2010 at 4:29 PM, Oliver Hofmann <ohofmann@hsph.harvard.edu> wrote:

Leandro,

that's hopefully on it's way (http://www.genomespace.org/).

Cheers,

   Oliver

On 21 Jul 2010, at 10:13, Leandro Hermida wrote:

...

Hi Ross,

Thank you for the offer, it's a bit complicated for me.  My users are bioinformaticians who are doing a lot of microarray analysis and meta-analysis and they need many of the public tools available that I see on GenePattern

GenePattern seems to have many tools and visualizers around microarray analysis, pathway and network inferencing, etc. Galaxy seems to have many tools and visualizers around next-gen sequencing, genomic analysis, and public server integration, etc.

I've written quite a few tools for Galaxy for other purposes and love how easy it is to develop against and how flexible it is to your needs.  You can really do some elegant stuff and it is accomodating. GenePattern I find to be much more rigid in what you can do and how you have to develop against it.

If I could only have the Galaxy development platform with the GenePattern and Galaxy tools! :(

-Leandro

On Wed, Jul 21, 2010 at 1:24 PM, Ross <ross.lazarus@gmail.com> wrote:

...

I have wrappers for a couple of popular bioconductor packages. Not yet ready for production use, but happy to talk if you're interested?

On Wed, Jul 21, 2010 at 7:09 PM, Leandro Hermida <softdev@leandrohermida.com> wrote:

...

Hello,

Are there publicly available tools in Galaxy for microarray data analysis, visualization, etc?  Or is this kind of GenePattern's space and you want to stay separate? :)

best, Leandro _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

-- Research Scientist    Department of Biostatistics Associate Director    Bioinformatics Core                      Harvard School of Public Health Skype: ohofmann       Phone: +1 (617) 365 0984