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 ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
