Hi,

On 2010-10-18 20.35, Adam Halstead wrote:
> Thanks for your response Jari.
> I understand support for next generation sequencing data is currently being
> developed by the BASE developers - is there a beta version we can look at?
> Do you need help developing this functionality? What kind of effort would be
> involved here?

There is no beta version. The sequencing support specification is still 
being drafted. That work is unfortunately currently halted due to other 
non-BASE related work. However, we expect to continue with specification 
work soon again. Hopefully we can present our ideas in the coming weeks. 
Then we will have an understanding of the effort involved and we happily 
accept help in developing the functionality. The first step would be 
input and feedback to the sequencing specifications when we release them.

The current BASE development timeline is that we are finalizing the next 
2.16 milestone. We were hoping to have what we call plate events in that 
release but it did not work out. The next milestone 2.17 will focus on 
solving/implementing plate events such that it supports our in-house 
needs for biomaterial tracking and processing.

The milestone after 2.17 will be to introduce sequencing support in 
BASE. We expect this to happen during spring 2011. You may notice that I 
did not say 2.18 here since we will also look into having the sequencing 
support as an addon like the Illumina plugins package 
(http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina). However, I 
expect that we need changes to the BASE core even if we go for the addon 
option.


> For your in-house sequencing data, are you using BASE to manage it?

Yes and no and we will. I'll start by explaining from the more negative 
no and finish with a positive yes.

The no is related to that in the specific project we have not generated 
data as a part of the project. We are still developing and testing 
sequencing protocols and setting up new hardware for the project.

We will store all sequencing data in BASE ... or at least information 
and references to where the raw sequencing data is stored. Our current 
thinking is that since we are already storing all sequencing raw (and 
processed) files in a file server serving our HiSeq we will not move 
these into the BASE file system. That said, I think this will be a use 
case for the sequencing specification.

Yes, we are already using BASE to store and track biomaterial 
information related to the project. We are already doing laborative work 
on our material (currently more than 500 samples) and track the 
processing information about the material. When BASE supports sequencing 
data and we actually produce sequences we will add that information to BASE.


> Our time-line is that we need to build an omics data warehouse solution by
> year end .

BASE will not support sequencing data as we want it to do before spring 
next year as outlined above. However, BASE can be used to store any data 
including sequencing data already today but you need to adapt to the 
microarray language and procedure. It is doable, we have done that as a 
excercise, but we prefer to add more sequencing specific support for our 
sequencing projects.


Cheers,

Jari

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