[BioC] BioC in the cloud (was Re: [Bioc-devel] Bioconductor 2.8 is released)

[Dan Tenenbaum]

Hi Markus,

On Fri, Apr 15, 2011 at 1:24 PM, Markus Schmidberger
<markus.schmidberger at mytum.de> wrote:
>
>   Hi,
>   it is great to have R and BioC in the cloud! Is there any reason to provide
>   your own image from the BioC core team?
>   Check this: [1]http://www.wurlug.org/wurlug/index.php/BioNode
>   Great group, great support, ...
>   Best
>   Markus
>
> References
>
>   1. http://www.wurlug.org/wurlug/index.php/BioNode
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> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>

Thanks for your question. I'll try and answer.

We want to keep our cloud support focused tightly on Bioconductor. We
aim to provide a new AMI with each new Bioconductor release.

Our AMI has many important Bioconductor packages already installed,
both software packages (particularly focused on sequencing tasks) and
annotation packages.

If other groups want to integrate Bioconductor into AMIs that they
release, we welcome that and will do what we can to help, but our AMI
should be considered the only "officially supported" one. We may like
what other groups have done, but even if we work with them, we can't
completely control what they do with Bioconductor.

Our goals with this AMI are not just to provide Bioconductor in the
cloud, but to try and enable use cases that are 1) particularly useful
in the cloud, and 2) perhaps somewhat tricky for individual users to
set up, or 3) both. To this end, we make it easy to do things like:
set up an MPI cluster in the cloud, to run Rgraphviz, and to make it
easy to run R in a web browser using RStudio Server.

I took a quick look at BioNode. Their most recent AMI is running R
2.11.1 and it doesn't appear that they have too many Bioconductor
packages installed.  I did not test extensively to see if the use
cases I mention above are made easy with their AMI, because none of
that is very important if the version of R and Bioconductor that's
available is not current.

Incidentally, the BioNode AMI is an S3-backed (instance store) AMI
which takes several minutes to load. The Bioconductor AMI is
EBS-backed which means instances will be available in a few seconds.

I hope this answers your question.
Dan