Hi Jonathan,
Thanks very much for your reply. My comments are inline below:
2009/1/12 Jonathan Warren <[email protected]>:
Hi Dan
Thanks for putting up the table - I'll add some info to it shortly.
Cheers, that would be great!
The dasregistry source code is downloadable using subversion at
http://www.derkholm.net/svn/repos/dasregistry/trunk/
You will also need a mysql instance set up. I can send you some info on
that if you wish.
Please provide as much information as possible! :-D
There are many dependencies and configurations needed- so it may take a
while to set up a fully fledged version - it may be better to experiment
with your sources using the real one - I'll help you out if you need
clarification on anything such as error messages and logs. Or is it that
you don't want to release your data to the world and only want an in
house version?
Yes. In the long run we will be making all our data publicly
available, however, for R&D purposes and leading up to publication of
the source data we would like to experiment with an in-house registry.
Also, I think it would be a convenient administrative / organizational
tool for us. i.e. to keep track of the various data sources
(experimental or otherwise) that are being developed in-house.
I think I would recomment using ensembl to connect to your sources in
the first instance - but if you want the client to sit on your
desktop/local server then maybe GBrowse (this is for genomic annotations
obvioyusly)?
Sorry for my ignorance, but can I ask if you mean that I should use
ensembl remotely (on some server 'out there') and point it at my local
reference / annotation server? The problem is again that both are
internal, with no outfacing interface. In any case, its clear that I
need to read more about ensembl, so feel free to ignore this question.
In another email you said: "You can just put the table onto biodas.org
if you wish..."
I see this point. I am never sure how 'external' wikis should interact
with Wikipedia when overlapping data is available in both. In this
case I thought I'd edit WP, but please feel free to move the table to
somewhere within biodas.org - I wasn't immediately sure where to put
it, which is partly why I picked WP.
Thanks very much for the information above,
Dan.
On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote:
Hi all,
I'm relatively new to DAS, and I have been playing with setting up a
DAS server using Dazzle. Now that I have created my reference and
annotation data sources, naturally enough I would like to start
browsing and visualizing the data. So...
Q1) Which DAS client do you recommend for a beginner working with Dazzle?
I am working in a Linux OS, and I am looking at gene predictions on a
chromosome as well as 'similarity' features between the chromosome and
several 'clones' from a closely related organism.
To organize my research into the various clients available, I created
the following page on Wikipedia:
http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients
That table is still quite rough, so please feel free to contribute
information there. I put the table into a sub-page of the DAS page so
that sites like http://www.biodas.org/ can easily 'transclude' this
information. I'm not sure if that's sensible or not yet, so let me
know what you think.
Since we are exploring the various possibilities of using DAS with our
projects, is it possible to set up a local (private) DAS registry
server? This would be useful for testing purposes, especially as we
may be initially working with unpublished data.
Q2) What steps are required for setting up a local or a secure DAS registry?
Thanks very much for any help with the above two questions.
Dan
P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange
data encoding that I don't understand? I've seen more than one page
that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss -
Should I go ahead and delete this pages?
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