Hi Marcela,<br><br>I'm happy to enter the glyphs into Bio::Graphics. I just need to know which ones to enter; I understand there have been many revisions recently and I am confused about which ones work.<br><br>Lincoln<br>
<br><div class="gmail_quote">On Fri, May 22, 2009 at 12:13 PM, Marcela K Tello-Ruiz via RT <span dir="ltr"><<a href="mailto:help@hapmap.org">help@hapmap.org</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;">
<div class="im">Hi Dave et al,<br>
<br>
All the code we developed for use <a href="http://hapmap.org" target="_blank">hapmap.org</a> is freely available and for<br>
public distribution, looks like we lagged behind in contributing the LD<br>
plot related glyphs to Bio::Graphics and would be happy to catch up.<br>
<br>
There is one thing I need to clarify. The current version of the LD plot<br>
plugin is using a new glyph, called the <a href="http://myreverseplot.pm" target="_blank">myreverseplot.pm</a>, which was<br>
originally created by Lincoln. None of our plugins is using <a href="http://ld_plot.pm" target="_blank">ld_plot.pm</a><br>
right now, whose author was also Lincoln.<br>
<br>
Lincoln - Would you be willing to enter the LD plot glyphs into<br>
Bio::Graphics or should we go ahead and do it on your behalf?<br>
<br>
Thanks,<br>
<br>
Marcela<br>
<br>
<br>
<br>
> [<a href="mailto:help@gmod.org">help@gmod.org</a> - Thu May 21 16:55:30 2009]:<br>
><br>
</div><div><div></div><div class="h5">> Hi Yuri, (and Marcela, Lincoln, and Scott)<br>
><br>
> I wouldn't send out the link to the talk just yet. The technology for<br>
> displaying NGS data in GBrowse has greatly improved in the last month<br>
> or so, and I'll post a new talk (or two) in mid-June.<br>
><br>
> I'm not sure what the best way to get ld_plot into the Bio::Graphics<br>
> CVS repository is. I think ld_plot is currently controlled by the<br>
> HapMap project.<br>
><br>
> Marcela, would HapMap be willing to contribute ld_plot to<br>
> Bio::Graphics?<br>
><br>
> Yuri, if HapMap agrees to contribute, then you will need to convince<br>
> Lincoln and/or Scott that your updates should also go in.<br>
><br>
> Thanks,<br>
><br>
> Dave C.<br>
><br>
><br>
> Was this helpful? Let us know at<br>
> <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
><br>
> Learn more about GMOD at:<br>
> SMBE:<br>
> <a href="http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27" target="_blank">http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27</a><br>
> Arthropod Genomics: <a href="http://www.k-state.edu/agc/symp2009/seminar.html" target="_blank">http://www.k-state.edu/agc/symp2009/seminar.html</a><br>
> AGA Next Gen Seq in Non-Models:<br>
> <a href="http://www.regonline.com/Nextgeneration" target="_blank">http://www.regonline.com/Nextgeneration</a><br>
><br>
><br>
><br>
> 2009/5/20 Yuri Titov Bendaña <<a href="mailto:ybendana@gmail.com">ybendana@gmail.com</a>>:<br>
> > Hi Dave,<br>
> ><br>
> > Thanks for the link! I hadn't seen this presentation posted, it has<br>
> > good information, would you like me to forward your email to the<br>
> list?<br>
> ><br>
> > By the way, I sent a message to the list yesterday about an updated<br>
> > ld_plot glyph I created, did you receive it? What's the best way to<br>
> > send code contributions?<br>
> ><br>
> > yuri<br>
> ><br>
> > On Wed, May 20, 2009 at 9:58 AM, Dave Clements, GMOD Help Desk<br>
> > <<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>> wrote:<br>
> >> Hi Yuri,<br>
> >><br>
> >> I did. Some of it is in a talk I gave at an NGS meeting in April.<br>
> See<br>
> >> <a href="http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf" target="_blank">http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf</a><br>
> >><br>
> >> However, I'm going to give updated versions of that talk in June<br>
> using<br>
> >> GBrowse 2.0 and the new SAMtools (SAM/BAM format) GBrowse adaptor.<br>
> >> So, that talk will change quite a bit. Once I'm back from the<br>
> talks<br>
> >> (mid-June), I'll convert the content to a web page.<br>
> >><br>
> >> Dave C.<br>
> >><br>
> >><br>
> >><br>
> >> Was this helpful? Let us know at<br>
> <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
> >><br>
> >> Learn more about GMOD at:<br>
> >> SMBE:<br>
> <a href="http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27" target="_blank">http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27</a><br>
> >> Arthropod Genomics: <a href="http://www.k-" target="_blank">http://www.k-</a><br>
> <a href="http://state.edu/agc/symp2009/seminar.html" target="_blank">state.edu/agc/symp2009/seminar.html</a><br>
> >> AGA Next Gen Seq in Non-Models:<br>
> <a href="http://www.regonline.com/Nextgeneration" target="_blank">http://www.regonline.com/Nextgeneration</a><br>
> >><br>
> >><br>
> >><br>
> >> On Tue, May 19, 2009 at 12:14 PM, <<a href="mailto:ybendana@gmail.com">ybendana@gmail.com</a>> wrote:<br>
> >>> Dave,<br>
> >>><br>
> >>> Did you ever get any feedback regarding Gbrowse implementations<br>
> for visualizing NGS data?<br>
> >>><br>
> >>> thanks,<br>
> >>><br>
> >>> yuri<br>
> >>><br>
> >>> Dave Clements, GMOD Help Desk wrote:<br>
> >>>><br>
> >>>> Erick, Bernd,<br>
> >>>><br>
> >>>> This came up in this week's GMOD teleconference, in a long thread<br>
> on<br>
> >>>> the JBrowse list last week, and I'm giving a talk about using<br>
> GMOD for<br>
> >>>> next generation sequencing data in a couple of weeks. So, the<br>
> >>>> question is timely. :-) Lets see if we can keep the discussion<br>
> >>>> going:<br>
> >>>><br>
> >>>> I'd say that GMOD has ideas on this but I would hesitate to call<br>
> them<br>
> >>>> plans at this point. Read on.<br>
> >>>><br>
> >>>> I think this breaks into two broad areas:<br>
> >>>><br>
> >>>> 1. Coping with the volume of data<br>
> >>>><br>
> >>>> If your users want to see each individual read then that can be a<br>
> lot<br>
> >>>> of features in your database. It's possible that we'll need to<br>
> >>>> develop some new techniques to make that tractable as datasets<br>
> grow.<br>
> >>>> Lincoln suggested possibly using a distributed peer-to-peer model<br>
> like<br>
> >>>> torrent. This approach would presumably build on work in recent<br>
> years<br>
> >>>> to extend GBrowse to support data sharing and user-uploadable<br>
> tracks.<br>
> >>>><br>
> >>>> If your users don't care about individual tracks then the problem<br>
> >>>> becomes more tractable because you would only show<br>
> summary/consensus<br>
> >>>> data in GBrowse. Of course you still have to generate that<br>
> >>>> summary/consensus data, but that is outside of GBrowse. I<br>
> suspect<br>
> >>>> that over time, typical use cases will drift toward<br>
> summary/consensus.<br>
> >>>> (When reference assemblies were new, people also cared a lot<br>
> about<br>
> >>>> the individual reads.)<br>
> >>>><br>
> >>>> 2. Visualizing information that you couldn't gather without NGS.<br>
> >>>><br>
> >>>> Next generation sequencing allows us to ask a whole slew of new<br>
> >>>> questions, most of which, I'd bet, haven't even been thought of<br>
> yet.<br>
> >>>> What can you discover when you have data from 1000 or 10,000<br>
> >>>> individuals? Thinking a few years out, what can you do when you<br>
> have<br>
> >>>> complete genomes from that many individuals? I have no idea how<br>
> to<br>
> >>>> deal with this because I have no idea what these questions will<br>
> be.<br>
> >>>><br>
> >>>><br>
> >>>> For my part, I have a goal of documenting how to use GMOD for<br>
> next<br>
> >>>> generation sequence data. The PAG 2009 poster Erick referred to<br>
> was a<br>
> >>>> start on that. I'll also be giving a talk on this in two weeks.<br>
> By<br>
> >>>> mid-year I aim to have that poster and that talk translated into<br>
> pages<br>
> >>>> on the GMOD wiki.<br>
> >>>><br>
> >>>> TO HELP ME WITH THAT (and with the presentation in two weeks), I<br>
> HAVE<br>
> >>>> A REQUEST of anyone on this list who is using GBrowse to show NGS<br>
> >>>> data: Can you send me (and/or this list) a link to your GBrowse<br>
> >>>> instance(s), preferably along with a short description of what<br>
> NGS<br>
> >>>> data it is showing and how you show it. I'd like to give people<br>
> at<br>
> >>>> the workshop a feel for a wide range of possibilities, and it<br>
> will<br>
> >>>> help me with the doc.<br>
> >>>><br>
> >>>> Thanks for reading this far, :-)<br>
> >>>><br>
> >>>> Dave C<br>
> >>>> GMOD Help Desk<br>
> >>>><br>
> >>>> Was this helpful? Let us know at<br>
> <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
> >>>><br>
> >>>> On Thu, Mar 12, 2009 at 7:52 AM, Bernd Jagla<br>
> <<a href="mailto:bernd.jagla@pasteur.fr">bernd.jagla@pasteur.fr</a>><br>
> >>>> wrote:<br>
> >>>>> I am currently setting up GBrowser GBrowser_karyotype to work<br>
> with our<br>
> >>>>> NGS/Solexa data. As I am just working on this for a few days I<br>
> am very<br>
> >>>>> much<br>
> >>>>> open for discussions.<br>
> >>>>> Right now I am trying to understand the GFF3 format to convert<br>
> the FASTQ<br>
> >>>>> files for later import into a MySQL database.<br>
> >>>>><br>
> >>>>> Best,<br>
> >>>>><br>
> >>>>> Bernd<br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>> -----Original Message-----<br>
> >>>>> From: Erick Antezana [mailto:<a href="mailto:erant@psb.vib-ugent.be">erant@psb.vib-ugent.be</a>]<br>
> >>>>> Sent: Thursday, March 12, 2009 3:43 PM<br>
> >>>>> To: <a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a><br>
> >>>>> Subject: [Gmod-gbrowse] NGS in GGB<br>
> >>>>><br>
> >>>>> Hi,<br>
> >>>>><br>
> >>>>> I have seen that teh GMOD team presented a poster at the last<br>
> PAG<br>
> >>>>> meeting<br>
> >>>>> (<a href="http://gmod.org/w/images/6/6a/PAG2009NextGenSeqPoster.pdf" target="_blank">http://gmod.org/w/images/6/6a/PAG2009NextGenSeqPoster.pdf</a>).<br>
> Also, I<br>
> >>>>> found that GBrowse is successfully exploited for visualisation<br>
> (e.g.<br>
> >>>>> <a href="http://lalitponnala.googlepages.com/CHIposter.pdf%29." target="_blank">http://lalitponnala.googlepages.com/CHIposter.pdf).</a>.. I was<br>
> wondering<br>
> >>>>> about the future development plans of GGB in that regard (to<br>
> deal with<br>
> >>>>> NextGenSeq data)?<br>
> >>>>><br>
> >>>>> thanks for the info,<br>
> >>>>> Erick<br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
><br>
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> >>>>> _______________________________________________<br>
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> >>>><br>
> >>>><br>
><br>
------------------------------------------------------------------------------<br>
> >>>> Apps built with the Adobe(R) Flex(R) framework and Flex<br>
> Builder(TM) are<br>
> >>>> powering Web 2.0 with engaging, cross-platform capabilities.<br>
> Quickly and<br>
> >>>> easily build your RIAs with Flex Builder, the Eclipse(TM)based<br>
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> >>>> software that enables intelligent coding and step-through<br>
> debugging.<br>
> >>>> Download the free 60 day trial. <a href="http://p.sf.net/sfu/www-adobe-com" target="_blank">http://p.sf.net/sfu/www-adobe-com</a><br>
> >>>> _______________________________________________<br>
> >>>> Gmod-gbrowse mailing list<br>
> >>>> <a href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</a><br>
> >>>> <a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><br>
> >>>><br>
> >>>><br>
> >>> Quoted from: <a href="http://www.nabble.com/NGS-in-GGB-" target="_blank">http://www.nabble.com/NGS-in-GGB-</a><br>
> tp22477878p22568894.html<br>
> >>><br>
> >>><br>
> >><br>
> ><br>
><br>
><br>
><br>
</div></div><div><div></div><div class="h5">--<br>
Marcela K. Tello-Ruiz<br>
HapMap Data Coordination Center<br>
Cold Spring Harbor Laboratory<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>