Re: Clouds and NG sequencing
On 08/08/2010 09:00 PM, Andreas Tille wrote:
> Hi,
>
> On Mon, Aug 09, 2010 at 12:13:27AM +0530, PRAKHAR gaur wrote:
>>
>> I am currently working in a newly setup NGS lab. My work presently to optimize Alignment algorithms(BFAST), for memory usage.
>> Also working to create a Linux Distro for Bioinformatics, Steffen has given a lot of advise.
>> I would be interested in knowing about the work you have been doing regarding NGS.
>
> Could you please elaborate more why you need to create a Linux Distro
> for Bioinformatics?
India is sleeping at the moment, I just use the opportunity to
lay out my understanding from a couple of off-list emails.
Prakhar and his group need something they feel they can
reliably work on, something that is as close to their
perfectly tailored working environment as possible.
Prakhar's group has developed some non-trivial collection of software
packages themselves already. And there is some strong interest
in some rather lowish levels of the boot process hoping
to optimise that for speed, efficiency and ... curiosity
(I hope :o) ) .
> Why not integrating your software into Debian and
> just use Debian Med?
This is likely to happen. But there are no other Debian
people directly around him. His only interface to Debian
is us ... and the source code. For the moment, Prakhar
is exactly investigating this "why", it is thus too
early to ask and I am confident that Prakhar will come
up with a summary eventually. I personally am more
interested in the "why^{-1}", like, how can he integrate
Debian (which is the community (us) and/or the software)
into his scientific world - which again is the technology
and the people.
It may well be that why = why^-1 and that means to
package their lab's software (for a public or private
repository), which is the technical bits, and somehow
letting Prakhar realize that he has no need to fear any
unwelcome surprises when using Debian, the social bits.
The major gap that I see for the why-symmetry is the
data management. This (today) is something that the
community has not managed to share, i.e. the reason
why the local presentation of Debian needs to be more
than what is on the servers. This is why (amongst others)
Charles and I (to the degree that our time permits) are
interested in the getData (data management) and cloud
(data and compute time) efforts so much.
Many greetings
Steffen
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