[hapmap.org #5047] Re: [Gmod-help] Re: NGS in GGB

Fri May 22 12:13:13 EDT 2009

Hi Dave et al,

All the code we developed for use hapmap.org is freely available and for
public distribution, looks like we lagged behind in contributing the LD
plot related glyphs to Bio::Graphics and would be happy to catch up.

There is one thing I need to clarify. The current version of the LD plot
plugin is using a new glyph, called the myreverseplot.pm, which was
originally created by Lincoln. None of our plugins is using ld_plot.pm
right now, whose author was also Lincoln. 

Lincoln - Would you be willing to enter the LD plot glyphs into
Bio::Graphics or should we go ahead and do it on your behalf?

Thanks,

Marcela

> [help at gmod.org - Thu May 21 16:55:30 2009]:
> 
> Hi Yuri, (and Marcela, Lincoln, and Scott)
> 
> I wouldn't send out the link to the talk just yet.  The technology for
> displaying NGS data in GBrowse has greatly improved in the last month
> or so, and I'll post a new talk (or two) in mid-June.
> 
> I'm not sure what the best way to get ld_plot into the Bio::Graphics
> CVS repository is.  I think ld_plot is currently controlled by the
> HapMap project.
> 
> Marcela, would HapMap be willing to contribute ld_plot to
> Bio::Graphics?
> 
> Yuri, if HapMap agrees to contribute, then you will need to convince
> Lincoln and/or Scott that your updates should also go in.
> 
> Thanks,
> 
> Dave C.
> 
> 
> Was this helpful?  Let us know at
> http://gmod.org/wiki/Help_Desk_Feedback
> 
> Learn more about GMOD at:
>   SMBE:
> http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>   AGA Next Gen Seq in Non-Models:
> http://www.regonline.com/Nextgeneration
> 
> 
> 
> 2009/5/20 Yuri Titov Bendaña <ybendana at gmail.com>:
> > Hi Dave,
> >
> > Thanks for the link!  I hadn't seen this presentation posted, it has
> > good information, would you like me to forward your email to the
> list?
> >
> > By the way, I sent a message to the list yesterday about an updated
> > ld_plot glyph I created, did you receive it?  What's the best way to
> > send code contributions?
> >
> > yuri
> >
> > On Wed, May 20, 2009 at 9:58 AM, Dave Clements, GMOD Help Desk
> > <gmodhelp at googlemail.com> wrote:
> >> Hi Yuri,
> >>
> >> I did.  Some of it is in a talk I gave at an NGS meeting in April.
> See
> >>  http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf
> >>
> >> However, I'm going to give updated versions of that talk in June
> using
> >> GBrowse 2.0 and the new SAMtools (SAM/BAM format) GBrowse adaptor.
> >> So, that talk will change quite a bit.  Once I'm back from the
> talks
> >> (mid-June), I'll convert the content to a web page.
> >>
> >> Dave C.
> >>
> >>
> >>
> >> Was this helpful?  Let us know at
> http://gmod.org/wiki/Help_Desk_Feedback
> >>
> >> Learn more about GMOD at:
> >>  SMBE:
> http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> >>  Arthropod Genomics: http://www.k-
> state.edu/agc/symp2009/seminar.html
> >>  AGA Next Gen Seq in Non-Models:
> http://www.regonline.com/Nextgeneration
> >>
> >>
> >>
> >> On Tue, May 19, 2009 at 12:14 PM,  <ybendana at gmail.com> wrote:
> >>> Dave,
> >>>
> >>> Did you ever get any feedback regarding Gbrowse implementations
> for visualizing NGS data?
> >>>
> >>> thanks,
> >>>
> >>> yuri
> >>>
> >>> Dave Clements, GMOD Help Desk wrote:
> >>>>
> >>>> Erick, Bernd,
> >>>>
> >>>> This came up in this week's GMOD teleconference, in a long thread
> on
> >>>> the JBrowse list last week, and I'm giving a talk about using
> GMOD for
> >>>> next generation sequencing data in a couple of weeks.  So, the
> >>>> question is timely.  :-)  Lets see if we can keep the discussion
> >>>> going:
> >>>>
> >>>> I'd say that GMOD has ideas on this but I would hesitate to call
> them
> >>>> plans at this point.  Read on.
> >>>>
> >>>> I think this breaks into two broad areas:
> >>>>
> >>>> 1. Coping with the volume of data
> >>>>
> >>>> If your users want to see each individual read then that can be a
> lot
> >>>> of features in your database.  It's possible that we'll need to
> >>>> develop some new techniques to make that tractable as datasets
> grow.
> >>>> Lincoln suggested possibly using a distributed peer-to-peer model
> like
> >>>> torrent.  This approach would presumably build on work in recent
> years
> >>>> to extend GBrowse to support data sharing and user-uploadable
> tracks.
> >>>>
> >>>> If your users don't care about individual tracks then the problem
> >>>> becomes more tractable because you would only show
> summary/consensus
> >>>> data in GBrowse.  Of course you still have to generate that
> >>>> summary/consensus data, but that is outside of GBrowse.  I
> suspect
> >>>> that over time, typical use cases will drift toward
> summary/consensus.
> >>>>  (When reference assemblies were new, people also cared a lot
> about
> >>>> the individual reads.)
> >>>>
> >>>> 2. Visualizing information that you couldn't gather without NGS.
> >>>>
> >>>> Next generation sequencing allows us to ask a whole slew of new
> >>>> questions, most of which, I'd bet, haven't even been thought of
> yet.
> >>>> What can you discover when you have data from 1000 or 10,000
> >>>> individuals?  Thinking a few years out, what can you do when you
> have
> >>>> complete genomes from that many individuals?  I have no idea how
> to
> >>>> deal with this because I have no idea what these questions will
> be.
> >>>>
> >>>>
> >>>> For my part, I have a goal of documenting how to use GMOD for
> next
> >>>> generation sequence data.  The PAG 2009 poster Erick referred to
> was a
> >>>> start on that.  I'll also be giving a talk on this in two weeks.
> By
> >>>> mid-year I aim to have that poster and that talk translated into
> pages
> >>>> on the GMOD wiki.
> >>>>
> >>>> TO HELP ME WITH THAT (and with the presentation in two weeks), I
> HAVE
> >>>> A REQUEST of anyone on this list who is using GBrowse to show NGS
> >>>> data:  Can you send me (and/or this list) a link to your GBrowse
> >>>> instance(s), preferably along with a short description of what
> NGS
> >>>> data it is showing and how you show it.  I'd like to give people
> at
> >>>> the workshop a feel for a wide range of possibilities, and it
> will
> >>>> help me with the doc.
> >>>>
> >>>> Thanks for reading this far, :-)
> >>>>
> >>>> Dave C
> >>>> GMOD Help Desk
> >>>>
> >>>> Was this helpful?  Let us know at
> http://gmod.org/wiki/Help_Desk_Feedback
> >>>>
> >>>> On Thu, Mar 12, 2009 at 7:52 AM, Bernd Jagla
> <bernd.jagla at pasteur.fr>
> >>>> wrote:
> >>>>> I am currently setting up GBrowser GBrowser_karyotype to work
> with our
> >>>>> NGS/Solexa data. As I am just working on this for a few days I
> am very
> >>>>> much
> >>>>> open for discussions.
> >>>>> Right now I am trying to understand the GFF3 format to convert
> the FASTQ
> >>>>> files for later import into a MySQL database.
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Bernd
> >>>>>
> >>>>>
> >>>>>
> >>>>> -----Original Message-----
> >>>>> From: Erick Antezana [mailto:erant at psb.vib-ugent.be]
> >>>>> Sent: Thursday, March 12, 2009 3:43 PM
> >>>>> To: gmod-gbrowse at lists.sourceforge.net
> >>>>> Subject: [Gmod-gbrowse] NGS in GGB
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>>  I have seen that teh GMOD team presented a poster at the last
> PAG
> >>>>> meeting
> >>>>> (http://gmod.org/w/images/6/6a/PAG2009NextGenSeqPoster.pdf).
> Also, I
> >>>>> found that GBrowse is successfully exploited for visualisation
> (e.g.
> >>>>> http://lalitponnala.googlepages.com/CHIposter.pdf)... I was
> wondering
> >>>>> about the future development plans of GGB in that regard (to
> deal with
> >>>>> NextGenSeq data)?
> >>>>>
> >>>>> thanks for the info,
> >>>>> Erick
> >>>>>
> >>>>>
> >>>>>
>
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> >>>>>
> >>>>>
> >>>>>
>
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> >>>>>
> >>>>
> >>>>
>
------------------------------------------------------------------------------
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> Builder(TM) are
> >>>> powering Web 2.0 with engaging, cross-platform capabilities.
> Quickly and
> >>>> easily build your RIAs with Flex Builder, the Eclipse(TM)based
> development
> >>>> software that enables intelligent coding and step-through
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> >>>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> >>>> _______________________________________________
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> >>>>
> >>>>
> >>> Quoted from:  http://www.nabble.com/NGS-in-GGB-
> tp22477878p22568894.html
> >>>
> >>>
> >>
> >
> 
> 
> 
-- 
Marcela K. Tello-Ruiz
HapMap Data Coordination Center
Cold Spring Harbor Laboratory