Hi Jeff,<br><br><div class="gmail_quote">On Wed, Sep 16, 2009 at 8:49 AM, Jeff Bowes <span dir="ltr"><<a href="mailto:bowes@ucalgary.ca">bowes@ucalgary.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Scott, Dave<br>
<br>
About your suggestion to Kevin that we move to GBrowse 2.0.:<br>
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1) Is there a best practice for the user it should be installed under, do you usually give GBrowse its own user?, This was not clear in the install Wiki.<br></blockquote><div> <br>The default practice is to use the web server user. I hesitate to call this a best practice, though. I think it is just easier to set up.<br>
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2) I'm a little leery about using Beta software in production. How solid is Gbrowse 2.0 ?<br></blockquote><div><br>I haven't played with it extensively since mid-summer. It still had some issues then. However, I would get it, and test it with your data and see how it runs.<br>
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3) Who is using it in production now?<br></blockquote><div> <br>There are several power users out there who are using it in production, including CBRG at Oxford and Bayer CropScience (see <a href="http://gmod.org/wiki/August_2009_GMOD_Meeting">http://gmod.org/wiki/August_2009_GMOD_Meeting</a> for more on them), and modENCODE.<br>
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4) When is the expected release date for gbrowse 2.0<br></blockquote><div><br>I'm not touching that one. :-) <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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5) If we install Gbrowse 2.0 beta what would be the process for installing fixes and the updating to the final release version. (Will it be pain-free?!)<br></blockquote><div><br>I have not heard anything about major changes coming to GBrowse 2 between now and release. I think all expected work is bug fixes.<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Currently we run Gbrowse using the Chado adpator. At the time we did this I only new of us and dictybase that were doing this. Like, dicty to make this work we had to rewrite a number of queries to speed it up. This makes it a pain to keep up with upgrades. Additionally, the methylation data Kevin mentioned would require 46 million feature entries- I'm not sure the Chado adaptor can handle this. So I am thinking we should move to having Gbrowse have its own data store and batch updates from chado.So my questions are:<br>
</blockquote><div> <br>46 million feature entries! What does the methylation data look like? If it can represented in a wiggle_xyplot then this will greatly reduce the volume of the data. The CBRG uses wiggle_xyplot very successfully to show a lot of methylation data.<br>
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1) Do you agree that we should move away from the Chado adaptor<br></blockquote><div><br>Yes.<br></div><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2) What is the fastest back end data store choice for Gbrowse<br></blockquote><div> <br>The preferred choice is SeqFeature::Store. It is slow to load though. I think that at browser time, SeqFeature::Store in MySQL (with it's none to bright optimizer) will clearly beat Chado in DB2 (with it's darn good optimizer).<br>
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3) Is the process for keeping it up to data to just do batch GFF3 exports from chado and import them into GBrowse?<br></blockquote><div> <br>Yes, but ...<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
4) For whatever data store you recommend, is it possible to make incremental updates to it or do updates have to pretty much work as blow away and replace it.<br></blockquote><div> <br>... I don't believe that SeqFeature::Store lends itself to incremental updates. I would create a parallel database and switch the config file once it is done being created.<br>
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5) Any other advice about this?<br></blockquote><div> <br>No , but, do you have to deal with reference sequence updates? MAKER has now added a functionality to move annotations from one version to the next. <br><br>Hope all is well, and give my regards to Erik,<br>
<br>Dave C.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks very much,<br>
<br>
Jeff<br>
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Kevin Snyder wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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------------------------------------------------------------------------<br>
<br>
Subject:<br>
Re: [Gmod-help] Displaying wiggle tracks<br>
From:<br>
Scott Cain <<a href="mailto:scott@scottcain.net" target="_blank">scott@scottcain.net</a>><br>
Date:<br>
Thu, 10 Sep 2009 13:02:45 -0400<br>
To:<br>
<a href="mailto:scott@scottcain.net" target="_blank">scott@scottcain.net</a><br>
<br>
To:<br>
<a href="mailto:scott@scottcain.net" target="_blank">scott@scottcain.net</a><br>
CC:<br>
Kevin Snyder <<a href="mailto:ksnyder@ucalgary.ca" target="_blank">ksnyder@ucalgary.ca</a>>, <a href="mailto:help@gmod.org" target="_blank">help@gmod.org</a><div><div></div><div class="h5"><br>
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Hi Kevin,<br>
<br>
Since you're likely doing an upgrade anyway, you might want to look at GBrowse2 (not officially released yet, but available on CPAN), as it will have many performance boosts over what you are currently using.<br>
<br>
Scott<br>
<br>
On Sep 10, 2009, at 12:31 PM, Scott Cain wrote:<br>
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<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Kevin,<br>
<br>
You won't be able to display wiggle plots without a never version of Bio::Graphics (which is no longer part of BioPerl) and a newer version of BioPerl (1.6 or better).<br>
<br>
Scott<br>
<br>
On Sep 10, 2009, at 12:22 PM, Kevin Snyder wrote:<br>
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<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
We are using a rather old version of gbrowse at the moment (1.64) along with Perl 5.8.8 and BioPerl 1.5.1. We have been give a large set of data in wiggle BED format. Will this version properly display the data in wiggle format<br>
or do we need to upgrade?<br>
<br>
Kevin Snyder<br>
Xenbase<br>
</blockquote>
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Scott Cain, Ph. D. scott at scottcain dot net<br>
GMOD Coordinator (<a href="http://gmod.org/" target="_blank">http://gmod.org/</a>) 216-392-3087<br>
Ontario Institute for Cancer Research<br>
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-----------------------------------------------------------------------<br>
Scott Cain, Ph. D. scott at scottcain dot net<br>
GMOD Coordinator (<a href="http://gmod.org/" target="_blank">http://gmod.org/</a>) 216-392-3087<br>
Ontario Institute for Cancer Research<br>
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</div></div></blockquote><font color="#888888">
<br>
-- <br>
Jeff Bowes M.Sc.<br>
Technical Director, Xenbase<br>
Department of Biological Sciences<br>
University of Calgary<br>
Calgary, Alberta T2N 1N4<br>
CANADA<br>
Tel: (403) 220-2824 Fax: (403) 284-4707<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>GMOD News: <a href="http://gmod.org/wiki/GMOD_News">http://gmod.org/wiki/GMOD_News</a><br>