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

[Brad Chapman]

Dan and Markus;
Interesting discussion, especially as a developer on another of the more
general biological AMIs: CloudBioLinux (http://cloudbiolinux.org).

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

This all makes good sense. There is definitely a need for both
specialized and generalized AMIs.

On the other side, I also think there is lots of room for working
collaboratively on these. The approach we've taken in CloudBioLinux
is to produce an automated framework that is used to build the
images:

https://github.com/chapmanb/cloudbiolinux

with packages and libraries specified in configuration files. For
instance here is R/Bioconductor configuration file (with lots taken
from your list of packages):

https://github.com/chapmanb/cloudbiolinux/blob/master/config/r-libs.yaml

This framework makes it easy to keep rolling new updates to stay
current, and also allows deployment to multiple types of virtual machines.
For instance, the latest AMI has 2.12 since it was made just before
the latest R release, but the VirtualBox image has 2.13 since we did
it last Friday.

On the practical side, this also handles a lot of the worries you
mentioned. It's EBS backed and contains Rgraphviz and plenty more
ready to go.

Our hope is this could save you time with building images by
automating a lot of the installation, allowing you to focus on the
higher level additions that are harder to automate and make your
custom AMIs so useful.

>From our point of view, it would be great to have the Bioconductor
team involved. This would contribute back to making the general
AMI more stable and useful, in addition to it just being fun
to work together. We've also been trying to convince Pjotr and the
BioNode folks to collaborate; I'm planning to roll a Debian image 
for them.

Thanks for the Bioconductor AMI. It's really great to see more
people working in this area,
Brad