On 2011-11-22 09.43, Nicklas Nordborg wrote:
> On 2011-11-21 21:32, Nantel Andre wrote:
>> We don't have any "regular" users yet since we are still figuring out
>> how it works. I am doing everything from my administrator account.
> Have you created a file format configuration for the files you are
> using? This is done in Administrate ->  Plug-ins&  Extensions ->  Plug-in
> configurations. Create a new configuration for the 'Raw data importer'
> plug-in and use the 'Test with file' function to get regular
> expressions, etc. correct.
>> Anyway that's all the time I can give to this problem until later
>> this week. This whole process has been much much more difficult than
>> we expected. Please don't take this the wrong way but it might be a
>> problem for your team as well if you ever hope to expand on your user
>> base. It's not like we're new at this, we've been using microarrays
>> since 1999 but I was getting tired of sending thousands of dollars to
>> Agilent every year.
> Setting up a BASE server is not trivial. We have recently set up a new
> BASE installation for a project here and I guess we have spent several
> months just setting up lab procedures, data import procedures, and also
> made some customizations to BASE in order to further streamline the data
> entry.
> We don't have an explicit goal to get more users. We are primarily using
> BASE at our own site to solve our own "problems". The Illumina extension
> package is an example of that. Unfortunately, we don't have the
> resources to develop things targeted for other platforms than what we
> are using ourselves. This doesn't mean that BASE can't be used with
> other platforms, but in order to get the most out of BASE one need to
> invest time and maybe also resources for customization. In may
> experience at least a week would be needed for initial testing and
> prototyping and then maybe a couple of months for setting up a
> production-ready server, formalizing lab and data handling procedures,
> developing custom plug-ins and extensions, etc.

Two internal large scale uses are outlined in the BASE 3 document 

To get the most of BASE you need to dedicate resources to customize BASE 
to fit your needs and to learn what BASE can do for you.

BASE use is a process, you start small and then extend your use of BASE 
as appropriate. In our lab (well some projects not all admittedly) we 
collect all important information collected during labwork in BASE. 
Therefore BASE is an integral part when setting up labprocesses where we 
make minor changes to lab work where needed and create customizations in 
BASE that fit our needs. The illumina extension was mentioned by 
Nicklas, but the reggie extension, 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie is the tool most 
appreciated by lab personnel. We track a lot of information about our 
samples and use the biomaterial LIMS extensively and reggie streamlines 
data input but also makes crosschecks and catches errors in data entry. 
Currently, we are working on defining our sequencing procedure in the 
lab and mirroring it in BASE.

Our larger projects span over long time (years) and handles large sample 
sets. These projects use BASE to get organized, reduce errors, collect 
information that normally ends up in labbooks, to be able to share data, 
and as a analysis platform. And we have noticed improvements in labwork 
too :)

Of course, our extensive BASE engagement is made easier because our PIs 
and funding agencies understand the benefits from organization and 
sharing of data/information.

However, I want to emphasises, BASE is also usable for smaller groups 
and projects. One can ignore biomaterial and array LIMS, and directly 
create raw bioassays. Collect these into an experiment and head on to do 
analysis - The README for the affymetrix plug-in 
(http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix) outlines what 
needs to be done to get started with basically an empty BASE. The steps 
are general and can be adopted for other platforms.



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