Add your own track on chado-based GBrowse
|
View:
New views
20 Messages
—
Rating Filter:
Alert me
|
| < Prev | 1 - 2 | Next > |
 |
Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
Hi,
Does the chado-based GBrowse support uploaded tracts? One of our ousers claimed that he cannot load his data tract. Following instruction, I tried to do it again. It seems that It doesn't work. Thank you Hee |
|
|
Re: Add your own track on chado-based GBrowse
by Lincoln Stein-3
::
Rate this Message:
Is there an error in the apache error log?
Lincoln On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote:
-- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
Hi Lincoln
There is an error. [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use of uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse line 2925., referer: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ Hee
|
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
my OS is Ubuntu
GBrowse is 1.68 Thank you. Hee
|
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
I think this used to work, but now I get this message:
Can't locate object method "rel2abs" via package "Bio::DB::Das::Chado::Segment" at /usr/local/lib/perl/5.8.8/Bio/Graphics/Browser.pm line 3072, <F> line 12. I'll look into a fix and get it up on cpan as soon as I can. Scott On Thu, May 28, 2009 at 3:14 PM, Lincoln Stein <lincoln.stein@...> wrote: > Is there an error in the apache error log? > > Lincoln > > On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >> >> Hi, >> >> Does the chado-based GBrowse support uploaded tracts? >> One of our ousers claimed that he cannot load his data tract. >> Following instruction, I tried to do it again. >> It seems that It doesn't work. >> >> Thank you >> >> Hee >> -- >> View this message in context: >> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >> >> >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > -- > Lincoln D. Stein > Director, Informatics and Biocomputing Platform > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa <Renata.Musa@...> > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. > Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
Hi Heekim,
I'm putting together a new release of Bio::DB::Das::Chado that will be uploaded to cpan today and it usually takes a few days to propagate out to mirrors. If you want, you can modify your copy of Bio::DB::Das::Chado::Segment with a very simple fix. Add this subroutine to Segment.pm: sub rel2abs { shift; return @_; } and that should fix it. Otherwise, when version 0.22 propagates out to your favorite cpan mirror you can get it then. Scott On Thu, May 28, 2009 at 3:47 PM, Scott Cain <scott@...> wrote: > I think this used to work, but now I get this message: > > Can't locate object method "rel2abs" via package > "Bio::DB::Das::Chado::Segment" at > /usr/local/lib/perl/5.8.8/Bio/Graphics/Browser.pm line 3072, <F> line > 12. > > I'll look into a fix and get it up on cpan as soon as I can. > > Scott > > > On Thu, May 28, 2009 at 3:14 PM, Lincoln Stein <lincoln.stein@...> wrote: >> Is there an error in the apache error log? >> >> Lincoln >> >> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >>> >>> Hi, >>> >>> Does the chado-based GBrowse support uploaded tracts? >>> One of our ousers claimed that he cannot load his data tract. >>> Following instruction, I tried to do it again. >>> It seems that It doesn't work. >>> >>> Thank you >>> >>> Hee >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> >> >> -- >> Lincoln D. Stein >> Director, Informatics and Biocomputing Platform >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa <Renata.Musa@...> >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
Scott,
I added the code that you sent me into /usr/local/lib/perl/5.8.8/Bio/DB/Das/Chado/Segment.pm. : sub asString { : : sub rel2abs { shift; return @_; } 1; However, I still have the same error message. Hee
|
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
This is my sample datafile to load.
[expression] glyph = xyplot graph_type=boxes fgcolor = black bgcolor = red height=100 min_score=0 max_score=110 label=1 key=Expression Level reference=AAJJ01000609 expression liver 10000..12000 score=10 expression liver 12001..19999 score=50 expression liver 20000..25000 score=100 expression kidney 10000..12000 score=80 expression kidney 12001..19999 score=10 expression kidney 20000..25000 score=100 Thank you
|
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
Hi Heekim,
Can you tell us what line 2925 of your instance of gbrowse is? I don't have that version installed, so it is a little difficult to debug. Scott On Thu, May 28, 2009 at 3:28 PM, heekim <heekim@...> wrote: > > Hi Lincoln > > There is an error. > [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use of > uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse line 2925., > referer: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ > > Hee > > > Lincoln Stein-3 wrote: >> >> Is there an error in the apache error log? >> >> Lincoln >> >> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >> >>> >>> Hi, >>> >>> Does the chado-based GBrowse support uploaded tracts? >>> One of our ousers claimed that he cannot load his data tract. >>> Following instruction, I tried to do it again. >>> It seems that It doesn't work. >>> >>> Thank you >>> >>> Hee >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> Lincoln D. Stein >> Director, Informatics and Biocomputing Platform >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa <Renata.Musa@...> >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23768430.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
it is in sub tableize,
# checks if this is about to rendered and if it is set the correct row/columns lengths if ( defined $categorytable{$category} ) { <---------------------- here is line 2925 @column_labels=@{$categorytable{$category}{row_labels}}; @row_labels=@{$categorytable{$category}{col_labels}}; $rows =$#row_labels+1; $columns =$#column_labels+1; } Thank you Hee
|
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
What happens if you add a category to the track definition in the
upload? Like this: [expression] glyph = xyplot graph_type=boxes fgcolor = black bgcolor = red height=100 min_score=0 max_score=110 label=1 key=Expression Level category=upload Scott On Thu, May 28, 2009 at 4:56 PM, heekim <heekim@...> wrote: > > it is in sub tableize, > > # checks if this is about to rendered and if it is set the correct > row/columns lengths > if ( defined $categorytable{$category} ) { > <---------------------- here is line 2925 > @column_labels=@{$categorytable{$category}{row_labels}}; > @row_labels=@{$categorytable{$category}{col_labels}}; > $rows =$#row_labels+1; > $columns =$#column_labels+1; > } > > Thank you > Hee > > Scott Cain-4 wrote: >> >> Hi Heekim, >> >> Can you tell us what line 2925 of your instance of gbrowse is? I >> don't have that version installed, so it is a little difficult to >> debug. >> >> Scott >> >> >> On Thu, May 28, 2009 at 3:28 PM, heekim <heekim@...> wrote: >>> >>> Hi Lincoln >>> >>> There is an error. >>> [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use of >>> uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse line >>> 2925., >>> referer: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ >>> >>> Hee >>> >>> >>> Lincoln Stein-3 wrote: >>>> >>>> Is there an error in the apache error log? >>>> >>>> Lincoln >>>> >>>> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >>>> >>>>> >>>>> Hi, >>>>> >>>>> Does the chado-based GBrowse support uploaded tracts? >>>>> One of our ousers claimed that he cannot load his data tract. >>>>> Following instruction, I tried to do it again. >>>>> It seems that It doesn't work. >>>>> >>>>> Thank you >>>>> >>>>> Hee >>>>> -- >>>>> View this message in context: >>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>> is a gathering of tech-side developers & brand creativity >>>>> professionals. >>>>> Meet >>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>> Barbarian >>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse@... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Director, Informatics and Biocomputing Platform >>>> Ontario Institute for Cancer Research >>>> 101 College St., Suite 800 >>>> Toronto, ON, Canada M5G0A3 >>>> 416 673-8514 >>>> Assistant: Renata Musa <Renata.Musa@...> >>>> >>>> ------------------------------------------------------------------------------ >>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>> is a gathering of tech-side developers & brand creativity professionals. >>>> Meet >>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>> Barbarian >>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23768430.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23769972.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
I got still the same error.
Hee
|
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
Hi Heekim,
I'm getting the feeling the category thing is a red herring. There's nothing else in the error log? Scott On Thu, May 28, 2009 at 5:05 PM, heekim <heekim@...> wrote: > > I got still the same error. > > Hee > > Scott Cain-4 wrote: >> >> What happens if you add a category to the track definition in the >> upload? Like this: >> >> [expression] >> glyph = xyplot >> graph_type=boxes >> fgcolor = black >> bgcolor = red >> height=100 >> min_score=0 >> max_score=110 >> label=1 >> key=Expression Level >> category=upload >> >> >> Scott >> >> >> On Thu, May 28, 2009 at 4:56 PM, heekim <heekim@...> wrote: >>> >>> it is in sub tableize, >>> >>> # checks if this is about to rendered and if it is set the correct >>> row/columns lengths >>> if ( defined $categorytable{$category} ) { >>> <---------------------- here is line 2925 >>> @column_labels=@{$categorytable{$category}{row_labels}}; >>> @row_labels=@{$categorytable{$category}{col_labels}}; >>> $rows =$#row_labels+1; >>> $columns =$#column_labels+1; >>> } >>> >>> Thank you >>> Hee >>> >>> Scott Cain-4 wrote: >>>> >>>> Hi Heekim, >>>> >>>> Can you tell us what line 2925 of your instance of gbrowse is? I >>>> don't have that version installed, so it is a little difficult to >>>> debug. >>>> >>>> Scott >>>> >>>> >>>> On Thu, May 28, 2009 at 3:28 PM, heekim <heekim@...> wrote: >>>>> >>>>> Hi Lincoln >>>>> >>>>> There is an error. >>>>> [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use of >>>>> uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse line >>>>> 2925., >>>>> referer: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ >>>>> >>>>> Hee >>>>> >>>>> >>>>> Lincoln Stein-3 wrote: >>>>>> >>>>>> Is there an error in the apache error log? >>>>>> >>>>>> Lincoln >>>>>> >>>>>> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >>>>>> >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Does the chado-based GBrowse support uploaded tracts? >>>>>>> One of our ousers claimed that he cannot load his data tract. >>>>>>> Following instruction, I tried to do it again. >>>>>>> It seems that It doesn't work. >>>>>>> >>>>>>> Thank you >>>>>>> >>>>>>> Hee >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>> professionals. >>>>>>> Meet >>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>> & >>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>> Barbarian >>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse@... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Lincoln D. Stein >>>>>> Director, Informatics and Biocomputing Platform >>>>>> Ontario Institute for Cancer Research >>>>>> 101 College St., Suite 800 >>>>>> Toronto, ON, Canada M5G0A3 >>>>>> 416 673-8514 >>>>>> Assistant: Renata Musa <Renata.Musa@...> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>> is a gathering of tech-side developers & brand creativity >>>>>> professionals. >>>>>> Meet >>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>> Barbarian >>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse@... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23768430.html >>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>> is a gathering of tech-side developers & brand creativity >>>>> professionals. >>>>> Meet >>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>> Barbarian >>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse@... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>>> ------------------------------------------------------------------------------ >>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>> is a gathering of tech-side developers & brand creativity professionals. >>>> Meet >>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>> Barbarian >>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23769972.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770120.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
in this time, I got an error like:
[Thu May 28 16:15:34 2009] [error] [client 85.177.47.107] Use of uninitialized value in pattern match (m//) at /usr/local/lib/perl/5.8.8/Bio/DB/Das/Chado.pm line 706, <FILE> line 109., referer: http://beetlebase.org/cgi-bin/gbrowse_details/BeetleBase3.gff3?name=TC000925;class=gene%3ACurated;ref=ChLG2;start=10353648;end=10374620;feature_id=323307 I don't have others than this. I am not sure if you accessed to it. Hee Shin
|
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
Hi Hee Shin,
Since there have been a lot of changes to the Chado adaptor since GBrowse 1.68 came out, could you try updating your Chado adaptor from cpan? If you don't get version 0.22 you'll need to add the fix to Segment.pm that mentioned a few emails back. Scott On Thu, May 28, 2009 at 5:39 PM, heekim <heekim@...> wrote: > > in this time, I got an error like: > [Thu May 28 16:15:34 2009] [error] [client 85.177.47.107] Use of > uninitialized value in pattern match (m//) at > /usr/local/lib/perl/5.8.8/Bio/DB/Das/Chado.pm line 706, <FILE> line 109., > referer: > http://beetlebase.org/cgi-bin/gbrowse_details/BeetleBase3.gff3?name=TC000925;class=gene%3ACurated;ref=ChLG2;start=10353648;end=10374620;feature_id=323307 > > I don't have others than this. > I am not sure if you accessed to it. > > Hee Shin > > > Scott Cain-4 wrote: >> >> Hi Heekim, >> >> I'm getting the feeling the category thing is a red herring. There's >> nothing else in the error log? >> >> Scott >> >> >> On Thu, May 28, 2009 at 5:05 PM, heekim <heekim@...> wrote: >>> >>> I got still the same error. >>> >>> Hee >>> >>> Scott Cain-4 wrote: >>>> >>>> What happens if you add a category to the track definition in the >>>> upload? Like this: >>>> >>>> [expression] >>>> glyph = xyplot >>>> graph_type=boxes >>>> fgcolor = black >>>> bgcolor = red >>>> height=100 >>>> min_score=0 >>>> max_score=110 >>>> label=1 >>>> key=Expression Level >>>> category=upload >>>> >>>> >>>> Scott >>>> >>>> >>>> On Thu, May 28, 2009 at 4:56 PM, heekim <heekim@...> wrote: >>>>> >>>>> it is in sub tableize, >>>>> >>>>> # checks if this is about to rendered and if it is set the correct >>>>> row/columns lengths >>>>> if ( defined $categorytable{$category} ) { >>>>> <---------------------- here is line 2925 >>>>> @column_labels=@{$categorytable{$category}{row_labels}}; >>>>> @row_labels=@{$categorytable{$category}{col_labels}}; >>>>> $rows =$#row_labels+1; >>>>> $columns =$#column_labels+1; >>>>> } >>>>> >>>>> Thank you >>>>> Hee >>>>> >>>>> Scott Cain-4 wrote: >>>>>> >>>>>> Hi Heekim, >>>>>> >>>>>> Can you tell us what line 2925 of your instance of gbrowse is? I >>>>>> don't have that version installed, so it is a little difficult to >>>>>> debug. >>>>>> >>>>>> Scott >>>>>> >>>>>> >>>>>> On Thu, May 28, 2009 at 3:28 PM, heekim <heekim@...> wrote: >>>>>>> >>>>>>> Hi Lincoln >>>>>>> >>>>>>> There is an error. >>>>>>> [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use of >>>>>>> uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse line >>>>>>> 2925., >>>>>>> referer: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ >>>>>>> >>>>>>> Hee >>>>>>> >>>>>>> >>>>>>> Lincoln Stein-3 wrote: >>>>>>>> >>>>>>>> Is there an error in the apache error log? >>>>>>>> >>>>>>>> Lincoln >>>>>>>> >>>>>>>> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Does the chado-based GBrowse support uploaded tracts? >>>>>>>>> One of our ousers claimed that he cannot load his data tract. >>>>>>>>> Following instruction, I tried to do it again. >>>>>>>>> It seems that It doesn't work. >>>>>>>>> >>>>>>>>> Thank you >>>>>>>>> >>>>>>>>> Hee >>>>>>>>> -- >>>>>>>>> View this message in context: >>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>> CaT >>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>> professionals. >>>>>>>>> Meet >>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>> Processing, >>>>>>>>> & >>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>> Barbarian >>>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>>> _______________________________________________ >>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>> Gmod-gbrowse@... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Lincoln D. Stein >>>>>>>> Director, Informatics and Biocomputing Platform >>>>>>>> Ontario Institute for Cancer Research >>>>>>>> 101 College St., Suite 800 >>>>>>>> Toronto, ON, Canada M5G0A3 >>>>>>>> 416 673-8514 >>>>>>>> Assistant: Renata Musa <Renata.Musa@...> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>> professionals. >>>>>>>> Meet >>>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>>> & >>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>> Barbarian >>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>> _______________________________________________ >>>>>>>> Gmod-gbrowse mailing list >>>>>>>> Gmod-gbrowse@... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23768430.html >>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>> professionals. >>>>>>> Meet >>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>> & >>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>> Barbarian >>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse@... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ------------------------------------------------------------------------ >>>>>> Scott Cain, Ph. D. scott at >>>>>> scottcain >>>>>> dot net >>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>>> Ontario Institute for Cancer Research >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>> is a gathering of tech-side developers & brand creativity >>>>>> professionals. >>>>>> Meet >>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>> Barbarian >>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse@... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23769972.html >>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>> is a gathering of tech-side developers & brand creativity >>>>> professionals. >>>>> Meet >>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>> Barbarian >>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse@... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>>> ------------------------------------------------------------------------------ >>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>> is a gathering of tech-side developers & brand creativity professionals. >>>> Meet >>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>> Barbarian >>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770120.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770641.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
Scott,
I have two versions of GBrowse. One is v1.68, which is running BeetleBase. the other is v2.0, which is the newest version and is running my test server. I tried to load user-defined data in both machines. Both of them did not work. It seems to me that Chado-Based GBrowse doesn't support the function. Thank you. Hee Shin
|
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
Hi Hee Shin,
I don't currently have an instance of GBrowse2 installed but I do have GBrowse pre-1.70 and it does work with the most current release of Bio::DB::Das::Chado (version 0.22). Have you tried that version with GBrowse2? Scott On Fri, May 29, 2009 at 2:10 PM, heekim <heekim@...> wrote: > > Scott, > > I have two versions of GBrowse. One is v1.68, which is running BeetleBase. > the other is v2.0, which is the newest version and is running my test > server. > > I tried to load user-defined data in both machines. > Both of them did not work. > > It seems to me that Chado-Based GBrowse doesn't support the function. > Thank you. > > Hee Shin > > > Scott Cain-4 wrote: >> >> Hi Hee Shin, >> >> Since there have been a lot of changes to the Chado adaptor since >> GBrowse 1.68 came out, could you try updating your Chado adaptor from >> cpan? If you don't get version 0.22 you'll need to add the fix to >> Segment.pm that mentioned a few emails back. >> >> Scott >> >> >> On Thu, May 28, 2009 at 5:39 PM, heekim <heekim@...> wrote: >>> >>> in this time, I got an error like: >>> [Thu May 28 16:15:34 2009] [error] [client 85.177.47.107] Use of >>> uninitialized value in pattern match (m//) at >>> /usr/local/lib/perl/5.8.8/Bio/DB/Das/Chado.pm line 706, <FILE> line 109., >>> referer: >>> http://beetlebase.org/cgi-bin/gbrowse_details/BeetleBase3.gff3?name=TC000925;class=gene%3ACurated;ref=ChLG2;start=10353648;end=10374620;feature_id=323307 >>> >>> I don't have others than this. >>> I am not sure if you accessed to it. >>> >>> Hee Shin >>> >>> >>> Scott Cain-4 wrote: >>>> >>>> Hi Heekim, >>>> >>>> I'm getting the feeling the category thing is a red herring. There's >>>> nothing else in the error log? >>>> >>>> Scott >>>> >>>> >>>> On Thu, May 28, 2009 at 5:05 PM, heekim <heekim@...> wrote: >>>>> >>>>> I got still the same error. >>>>> >>>>> Hee >>>>> >>>>> Scott Cain-4 wrote: >>>>>> >>>>>> What happens if you add a category to the track definition in the >>>>>> upload? Like this: >>>>>> >>>>>> [expression] >>>>>> glyph = xyplot >>>>>> graph_type=boxes >>>>>> fgcolor = black >>>>>> bgcolor = red >>>>>> height=100 >>>>>> min_score=0 >>>>>> max_score=110 >>>>>> label=1 >>>>>> key=Expression Level >>>>>> category=upload >>>>>> >>>>>> >>>>>> Scott >>>>>> >>>>>> >>>>>> On Thu, May 28, 2009 at 4:56 PM, heekim <heekim@...> wrote: >>>>>>> >>>>>>> it is in sub tableize, >>>>>>> >>>>>>> # checks if this is about to rendered and if it is set the correct >>>>>>> row/columns lengths >>>>>>> if ( defined $categorytable{$category} ) { >>>>>>> <---------------------- here is line 2925 >>>>>>> @column_labels=@{$categorytable{$category}{row_labels}}; >>>>>>> @row_labels=@{$categorytable{$category}{col_labels}}; >>>>>>> $rows =$#row_labels+1; >>>>>>> $columns =$#column_labels+1; >>>>>>> } >>>>>>> >>>>>>> Thank you >>>>>>> Hee >>>>>>> >>>>>>> Scott Cain-4 wrote: >>>>>>>> >>>>>>>> Hi Heekim, >>>>>>>> >>>>>>>> Can you tell us what line 2925 of your instance of gbrowse is? I >>>>>>>> don't have that version installed, so it is a little difficult to >>>>>>>> debug. >>>>>>>> >>>>>>>> Scott >>>>>>>> >>>>>>>> >>>>>>>> On Thu, May 28, 2009 at 3:28 PM, heekim <heekim@...> wrote: >>>>>>>>> >>>>>>>>> Hi Lincoln >>>>>>>>> >>>>>>>>> There is an error. >>>>>>>>> [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use of >>>>>>>>> uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse >>>>>>>>> line >>>>>>>>> 2925., >>>>>>>>> referer: >>>>>>>>> http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ >>>>>>>>> >>>>>>>>> Hee >>>>>>>>> >>>>>>>>> >>>>>>>>> Lincoln Stein-3 wrote: >>>>>>>>>> >>>>>>>>>> Is there an error in the apache error log? >>>>>>>>>> >>>>>>>>>> Lincoln >>>>>>>>>> >>>>>>>>>> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Does the chado-based GBrowse support uploaded tracts? >>>>>>>>>>> One of our ousers claimed that he cannot load his data tract. >>>>>>>>>>> Following instruction, I tried to do it again. >>>>>>>>>>> It seems that It doesn't work. >>>>>>>>>>> >>>>>>>>>>> Thank you >>>>>>>>>>> >>>>>>>>>>> Hee >>>>>>>>>>> -- >>>>>>>>>>> View this message in context: >>>>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>>>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>>> CaT >>>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>>> professionals. >>>>>>>>>>> Meet >>>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>>> Processing, >>>>>>>>>>> & >>>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>>>> Barbarian >>>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Lincoln D. Stein >>>>>>>>>> Director, Informatics and Biocomputing Platform >>>>>>>>>> Ontario Institute for Cancer Research >>>>>>>>>> 101 College St., Suite 800 >>>>>>>>>> Toronto, ON, Canada M5G0A3 >>>>>>>>>> 416 673-8514 >>>>>>>>>> Assistant: Renata Musa <Renata.Musa@...> >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>> CaT >>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>> professionals. >>>>>>>>>> Meet >>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>> Processing, >>>>>>>>>> & >>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>>> Barbarian >>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>> _______________________________________________ >>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> View this message in context: >>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23768430.html >>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>> CaT >>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>> professionals. >>>>>>>>> Meet >>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>> Processing, >>>>>>>>> & >>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>> Barbarian >>>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>>> _______________________________________________ >>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>> Gmod-gbrowse@... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> Scott Cain, Ph. D. scott at >>>>>>>> scottcain >>>>>>>> dot net >>>>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>>>>> Ontario Institute for Cancer Research >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>> professionals. >>>>>>>> Meet >>>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>>> & >>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>> Barbarian >>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>> _______________________________________________ >>>>>>>> Gmod-gbrowse mailing list >>>>>>>> Gmod-gbrowse@... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23769972.html >>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>> professionals. >>>>>>> Meet >>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>> & >>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>> Barbarian >>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse@... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ------------------------------------------------------------------------ >>>>>> Scott Cain, Ph. D. scott at >>>>>> scottcain >>>>>> dot net >>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>>> Ontario Institute for Cancer Research >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>> is a gathering of tech-side developers & brand creativity >>>>>> professionals. >>>>>> Meet >>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>> Barbarian >>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse@... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770120.html >>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>> is a gathering of tech-side developers & brand creativity >>>>> professionals. >>>>> Meet >>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>> Barbarian >>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse@... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>>> ------------------------------------------------------------------------------ >>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>> is a gathering of tech-side developers & brand creativity professionals. >>>> Meet >>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>> Barbarian >>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770641.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23784718.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by heekim
::
Rate this Message:
Scott,
I downloaded Bio-DB-Das-Chado-0.22 and then do the followings, perl ./Build -> sudo ./Build -> sudo ./Build test -> sudo ./Build install. There was no error. But I couldn't get the user defined track in the GB. I also checked the error log file for Apache, I had the same error message that i reported in the earlier thread. Thank you Hee Shin
|
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
Hi Hee Shin,
Can you tell me what version of Bioperl you are using with your production (1.68) system? I'll try to reproduce it. Scott On Fri, May 29, 2009 at 4:59 PM, heekim <heekim@...> wrote: > > Scott, > > I downloaded Bio-DB-Das-Chado-0.22 and then do the followings, perl ./Build > -> sudo ./Build -> sudo ./Build test -> sudo ./Build install. > There was no error. > > But I couldn't get the user defined track in the GB. > I also checked the error log file for Apache, I had the same error message > that i reported in the earlier thread. > > Thank you > > Hee Shin > > > Scott Cain-4 wrote: >> >> Hi Hee Shin, >> >> I don't currently have an instance of GBrowse2 installed but I do have >> GBrowse pre-1.70 and it does work with the most current release of >> Bio::DB::Das::Chado (version 0.22). Have you tried that version with >> GBrowse2? >> >> Scott >> >> On Fri, May 29, 2009 at 2:10 PM, heekim <heekim@...> wrote: >>> >>> Scott, >>> >>> I have two versions of GBrowse. One is v1.68, which is running >>> BeetleBase. >>> the other is v2.0, which is the newest version and is running my test >>> server. >>> >>> I tried to load user-defined data in both machines. >>> Both of them did not work. >>> >>> It seems to me that Chado-Based GBrowse doesn't support the function. >>> Thank you. >>> >>> Hee Shin >>> >>> >>> Scott Cain-4 wrote: >>>> >>>> Hi Hee Shin, >>>> >>>> Since there have been a lot of changes to the Chado adaptor since >>>> GBrowse 1.68 came out, could you try updating your Chado adaptor from >>>> cpan? If you don't get version 0.22 you'll need to add the fix to >>>> Segment.pm that mentioned a few emails back. >>>> >>>> Scott >>>> >>>> >>>> On Thu, May 28, 2009 at 5:39 PM, heekim <heekim@...> wrote: >>>>> >>>>> in this time, I got an error like: >>>>> [Thu May 28 16:15:34 2009] [error] [client 85.177.47.107] Use of >>>>> uninitialized value in pattern match (m//) at >>>>> /usr/local/lib/perl/5.8.8/Bio/DB/Das/Chado.pm line 706, <FILE> line >>>>> 109., >>>>> referer: >>>>> http://beetlebase.org/cgi-bin/gbrowse_details/BeetleBase3.gff3?name=TC000925;class=gene%3ACurated;ref=ChLG2;start=10353648;end=10374620;feature_id=323307 >>>>> >>>>> I don't have others than this. >>>>> I am not sure if you accessed to it. >>>>> >>>>> Hee Shin >>>>> >>>>> >>>>> Scott Cain-4 wrote: >>>>>> >>>>>> Hi Heekim, >>>>>> >>>>>> I'm getting the feeling the category thing is a red herring. There's >>>>>> nothing else in the error log? >>>>>> >>>>>> Scott >>>>>> >>>>>> >>>>>> On Thu, May 28, 2009 at 5:05 PM, heekim <heekim@...> wrote: >>>>>>> >>>>>>> I got still the same error. >>>>>>> >>>>>>> Hee >>>>>>> >>>>>>> Scott Cain-4 wrote: >>>>>>>> >>>>>>>> What happens if you add a category to the track definition in the >>>>>>>> upload? Like this: >>>>>>>> >>>>>>>> [expression] >>>>>>>> glyph = xyplot >>>>>>>> graph_type=boxes >>>>>>>> fgcolor = black >>>>>>>> bgcolor = red >>>>>>>> height=100 >>>>>>>> min_score=0 >>>>>>>> max_score=110 >>>>>>>> label=1 >>>>>>>> key=Expression Level >>>>>>>> category=upload >>>>>>>> >>>>>>>> >>>>>>>> Scott >>>>>>>> >>>>>>>> >>>>>>>> On Thu, May 28, 2009 at 4:56 PM, heekim <heekim@...> wrote: >>>>>>>>> >>>>>>>>> it is in sub tableize, >>>>>>>>> >>>>>>>>> # checks if this is about to rendered and if it is set the correct >>>>>>>>> row/columns lengths >>>>>>>>> if ( defined $categorytable{$category} ) { >>>>>>>>> <---------------------- here is line 2925 >>>>>>>>> @column_labels=@{$categorytable{$category}{row_labels}}; >>>>>>>>> @row_labels=@{$categorytable{$category}{col_labels}}; >>>>>>>>> $rows =$#row_labels+1; >>>>>>>>> $columns =$#column_labels+1; >>>>>>>>> } >>>>>>>>> >>>>>>>>> Thank you >>>>>>>>> Hee >>>>>>>>> >>>>>>>>> Scott Cain-4 wrote: >>>>>>>>>> >>>>>>>>>> Hi Heekim, >>>>>>>>>> >>>>>>>>>> Can you tell us what line 2925 of your instance of gbrowse is? I >>>>>>>>>> don't have that version installed, so it is a little difficult to >>>>>>>>>> debug. >>>>>>>>>> >>>>>>>>>> Scott >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, May 28, 2009 at 3:28 PM, heekim <heekim@...> wrote: >>>>>>>>>>> >>>>>>>>>>> Hi Lincoln >>>>>>>>>>> >>>>>>>>>>> There is an error. >>>>>>>>>>> [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use >>>>>>>>>>> of >>>>>>>>>>> uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse >>>>>>>>>>> line >>>>>>>>>>> 2925., >>>>>>>>>>> referer: >>>>>>>>>>> http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ >>>>>>>>>>> >>>>>>>>>>> Hee >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Lincoln Stein-3 wrote: >>>>>>>>>>>> >>>>>>>>>>>> Is there an error in the apache error log? >>>>>>>>>>>> >>>>>>>>>>>> Lincoln >>>>>>>>>>>> >>>>>>>>>>>> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> Does the chado-based GBrowse support uploaded tracts? >>>>>>>>>>>>> One of our ousers claimed that he cannot load his data tract. >>>>>>>>>>>>> Following instruction, I tried to do it again. >>>>>>>>>>>>> It seems that It doesn't work. >>>>>>>>>>>>> >>>>>>>>>>>>> Thank you >>>>>>>>>>>>> >>>>>>>>>>>>> Hee >>>>>>>>>>>>> -- >>>>>>>>>>>>> View this message in context: >>>>>>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>>>>>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, >>>>>>>>>>>>> NYC. >>>>>>>>>>>>> CaT >>>>>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>>>>> professionals. >>>>>>>>>>>>> Meet >>>>>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>>>>> Processing, >>>>>>>>>>>>> & >>>>>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights >>>>>>>>>>>>> like >>>>>>>>>>>>> Barbarian >>>>>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Lincoln D. Stein >>>>>>>>>>>> Director, Informatics and Biocomputing Platform >>>>>>>>>>>> Ontario Institute for Cancer Research >>>>>>>>>>>> 101 College St., Suite 800 >>>>>>>>>>>> Toronto, ON, Canada M5G0A3 >>>>>>>>>>>> 416 673-8514 >>>>>>>>>>>> Assistant: Renata Musa <Renata.Musa@...> >>>>>>>>>>>> >>>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>>>> CaT >>>>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>>>> professionals. >>>>>>>>>>>> Meet >>>>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>>>> Processing, >>>>>>>>>>>> & >>>>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights >>>>>>>>>>>> like >>>>>>>>>>>> Barbarian >>>>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> View this message in context: >>>>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23768430.html >>>>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>>> CaT >>>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>>> professionals. >>>>>>>>>>> Meet >>>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>>> Processing, >>>>>>>>>>> & >>>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>>>> Barbarian >>>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>> Scott Cain, Ph. D. scott at >>>>>>>>>> scottcain >>>>>>>>>> dot net >>>>>>>>>> GMOD Coordinator (http://gmod.org/) >>>>>>>>>> 216-392-3087 >>>>>>>>>> Ontario Institute for Cancer Research >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>> CaT >>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>> professionals. >>>>>>>>>> Meet >>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>> Processing, >>>>>>>>>> & >>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>>> Barbarian >>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>> _______________________________________________ >>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> View this message in context: >>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23769972.html >>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>> CaT >>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>> professionals. >>>>>>>>> Meet >>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>> Processing, >>>>>>>>> & >>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>> Barbarian >>>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>>> _______________________________________________ >>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>> Gmod-gbrowse@... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> Scott Cain, Ph. D. scott at >>>>>>>> scottcain >>>>>>>> dot net >>>>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>>>>> Ontario Institute for Cancer Research >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>> professionals. >>>>>>>> Meet >>>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>>> & >>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>> Barbarian >>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>> _______________________________________________ >>>>>>>> Gmod-gbrowse mailing list >>>>>>>> Gmod-gbrowse@... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770120.html >>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>> professionals. >>>>>>> Meet >>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>> & >>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>> Barbarian >>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse@... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ------------------------------------------------------------------------ >>>>>> Scott Cain, Ph. D. scott at >>>>>> scottcain >>>>>> dot net >>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>>> Ontario Institute for Cancer Research >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>> is a gathering of tech-side developers & brand creativity >>>>>> professionals. >>>>>> Meet >>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>> Barbarian >>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse@... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770641.html >>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>> is a gathering of tech-side developers & brand creativity >>>>> professionals. >>>>> Meet >>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>> Barbarian >>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse@... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>>> ------------------------------------------------------------------------------ >>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>> is a gathering of tech-side developers & brand creativity professionals. >>>> Meet >>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>> Barbarian >>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23784718.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23786967.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Add your own track on chado-based GBrowse
by Scott Cain-4
::
Rate this Message:
Hi Hee Shin,
One important thing I thought of over the weekend: when you do "sudo ./Build install" you need to add "--uninst 1", because GBrowse 1.X installed adaptors in the architecture dependent libraries, but this installer goes in the independent libraries (which is where it should have been to begin with). With out the uninst, GBrowse will continue to use the old adaptor because it comes first in the list of paths to use for perl. You can just rerun the install command: sudo ./Build install --uninst 1 Scott On Fri, May 29, 2009 at 4:59 PM, heekim <heekim@...> wrote: > > Scott, > > I downloaded Bio-DB-Das-Chado-0.22 and then do the followings, perl ./Build > -> sudo ./Build -> sudo ./Build test -> sudo ./Build install. > There was no error. > > But I couldn't get the user defined track in the GB. > I also checked the error log file for Apache, I had the same error message > that i reported in the earlier thread. > > Thank you > > Hee Shin > > > Scott Cain-4 wrote: >> >> Hi Hee Shin, >> >> I don't currently have an instance of GBrowse2 installed but I do have >> GBrowse pre-1.70 and it does work with the most current release of >> Bio::DB::Das::Chado (version 0.22). Have you tried that version with >> GBrowse2? >> >> Scott >> >> On Fri, May 29, 2009 at 2:10 PM, heekim <heekim@...> wrote: >>> >>> Scott, >>> >>> I have two versions of GBrowse. One is v1.68, which is running >>> BeetleBase. >>> the other is v2.0, which is the newest version and is running my test >>> server. >>> >>> I tried to load user-defined data in both machines. >>> Both of them did not work. >>> >>> It seems to me that Chado-Based GBrowse doesn't support the function. >>> Thank you. >>> >>> Hee Shin >>> >>> >>> Scott Cain-4 wrote: >>>> >>>> Hi Hee Shin, >>>> >>>> Since there have been a lot of changes to the Chado adaptor since >>>> GBrowse 1.68 came out, could you try updating your Chado adaptor from >>>> cpan? If you don't get version 0.22 you'll need to add the fix to >>>> Segment.pm that mentioned a few emails back. >>>> >>>> Scott >>>> >>>> >>>> On Thu, May 28, 2009 at 5:39 PM, heekim <heekim@...> wrote: >>>>> >>>>> in this time, I got an error like: >>>>> [Thu May 28 16:15:34 2009] [error] [client 85.177.47.107] Use of >>>>> uninitialized value in pattern match (m//) at >>>>> /usr/local/lib/perl/5.8.8/Bio/DB/Das/Chado.pm line 706, <FILE> line >>>>> 109., >>>>> referer: >>>>> http://beetlebase.org/cgi-bin/gbrowse_details/BeetleBase3.gff3?name=TC000925;class=gene%3ACurated;ref=ChLG2;start=10353648;end=10374620;feature_id=323307 >>>>> >>>>> I don't have others than this. >>>>> I am not sure if you accessed to it. >>>>> >>>>> Hee Shin >>>>> >>>>> >>>>> Scott Cain-4 wrote: >>>>>> >>>>>> Hi Heekim, >>>>>> >>>>>> I'm getting the feeling the category thing is a red herring. There's >>>>>> nothing else in the error log? >>>>>> >>>>>> Scott >>>>>> >>>>>> >>>>>> On Thu, May 28, 2009 at 5:05 PM, heekim <heekim@...> wrote: >>>>>>> >>>>>>> I got still the same error. >>>>>>> >>>>>>> Hee >>>>>>> >>>>>>> Scott Cain-4 wrote: >>>>>>>> >>>>>>>> What happens if you add a category to the track definition in the >>>>>>>> upload? Like this: >>>>>>>> >>>>>>>> [expression] >>>>>>>> glyph = xyplot >>>>>>>> graph_type=boxes >>>>>>>> fgcolor = black >>>>>>>> bgcolor = red >>>>>>>> height=100 >>>>>>>> min_score=0 >>>>>>>> max_score=110 >>>>>>>> label=1 >>>>>>>> key=Expression Level >>>>>>>> category=upload >>>>>>>> >>>>>>>> >>>>>>>> Scott >>>>>>>> >>>>>>>> >>>>>>>> On Thu, May 28, 2009 at 4:56 PM, heekim <heekim@...> wrote: >>>>>>>>> >>>>>>>>> it is in sub tableize, >>>>>>>>> >>>>>>>>> # checks if this is about to rendered and if it is set the correct >>>>>>>>> row/columns lengths >>>>>>>>> if ( defined $categorytable{$category} ) { >>>>>>>>> <---------------------- here is line 2925 >>>>>>>>> @column_labels=@{$categorytable{$category}{row_labels}}; >>>>>>>>> @row_labels=@{$categorytable{$category}{col_labels}}; >>>>>>>>> $rows =$#row_labels+1; >>>>>>>>> $columns =$#column_labels+1; >>>>>>>>> } >>>>>>>>> >>>>>>>>> Thank you >>>>>>>>> Hee >>>>>>>>> >>>>>>>>> Scott Cain-4 wrote: >>>>>>>>>> >>>>>>>>>> Hi Heekim, >>>>>>>>>> >>>>>>>>>> Can you tell us what line 2925 of your instance of gbrowse is? I >>>>>>>>>> don't have that version installed, so it is a little difficult to >>>>>>>>>> debug. >>>>>>>>>> >>>>>>>>>> Scott >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, May 28, 2009 at 3:28 PM, heekim <heekim@...> wrote: >>>>>>>>>>> >>>>>>>>>>> Hi Lincoln >>>>>>>>>>> >>>>>>>>>>> There is an error. >>>>>>>>>>> [Thu May 28 14:21:30 2009] [error] [client 129.130.115.205] Use >>>>>>>>>>> of >>>>>>>>>>> uninitialized value in hash element at /usr/lib/cgi-bin/gbrowse >>>>>>>>>>> line >>>>>>>>>>> 2925., >>>>>>>>>>> referer: >>>>>>>>>>> http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/ >>>>>>>>>>> >>>>>>>>>>> Hee >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Lincoln Stein-3 wrote: >>>>>>>>>>>> >>>>>>>>>>>> Is there an error in the apache error log? >>>>>>>>>>>> >>>>>>>>>>>> Lincoln >>>>>>>>>>>> >>>>>>>>>>>> On Thu, May 28, 2009 at 2:52 PM, heekim <heekim@...> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> Does the chado-based GBrowse support uploaded tracts? >>>>>>>>>>>>> One of our ousers claimed that he cannot load his data tract. >>>>>>>>>>>>> Following instruction, I tried to do it again. >>>>>>>>>>>>> It seems that It doesn't work. >>>>>>>>>>>>> >>>>>>>>>>>>> Thank you >>>>>>>>>>>>> >>>>>>>>>>>>> Hee >>>>>>>>>>>>> -- >>>>>>>>>>>>> View this message in context: >>>>>>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23767794.html >>>>>>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, >>>>>>>>>>>>> NYC. >>>>>>>>>>>>> CaT >>>>>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>>>>> professionals. >>>>>>>>>>>>> Meet >>>>>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>>>>> Processing, >>>>>>>>>>>>> & >>>>>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights >>>>>>>>>>>>> like >>>>>>>>>>>>> Barbarian >>>>>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Lincoln D. Stein >>>>>>>>>>>> Director, Informatics and Biocomputing Platform >>>>>>>>>>>> Ontario Institute for Cancer Research >>>>>>>>>>>> 101 College St., Suite 800 >>>>>>>>>>>> Toronto, ON, Canada M5G0A3 >>>>>>>>>>>> 416 673-8514 >>>>>>>>>>>> Assistant: Renata Musa <Renata.Musa@...> >>>>>>>>>>>> >>>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>>>> CaT >>>>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>>>> professionals. >>>>>>>>>>>> Meet >>>>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>>>> Processing, >>>>>>>>>>>> & >>>>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights >>>>>>>>>>>> like >>>>>>>>>>>> Barbarian >>>>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> View this message in context: >>>>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23768430.html >>>>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>>> CaT >>>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>>> professionals. >>>>>>>>>>> Meet >>>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>>> Processing, >>>>>>>>>>> & >>>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>>>> Barbarian >>>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>> Scott Cain, Ph. D. scott at >>>>>>>>>> scottcain >>>>>>>>>> dot net >>>>>>>>>> GMOD Coordinator (http://gmod.org/) >>>>>>>>>> 216-392-3087 >>>>>>>>>> Ontario Institute for Cancer Research >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>>> CaT >>>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>>> professionals. >>>>>>>>>> Meet >>>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>>> Processing, >>>>>>>>>> & >>>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>>> Barbarian >>>>>>>>>> Group, R/GA, & Big Spaceship. >>>>>>>>>> http://p.sf.net/sfu/creativitycat-com >>>>>>>>>> _______________________________________________ >>>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>>> Gmod-gbrowse@... >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> View this message in context: >>>>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23769972.html >>>>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. >>>>>>>>> CaT >>>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>>> professionals. >>>>>>>>> Meet >>>>>>>>> the minds behind Google Creative Lab, Visual Complexity, >>>>>>>>> Processing, >>>>>>>>> & >>>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>>> Barbarian >>>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>>> _______________________________________________ >>>>>>>>> Gmod-gbrowse mailing list >>>>>>>>> Gmod-gbrowse@... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> Scott Cain, Ph. D. scott at >>>>>>>> scottcain >>>>>>>> dot net >>>>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>>>>> Ontario Institute for Cancer Research >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>>> professionals. >>>>>>>> Meet >>>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>>> & >>>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>>> Barbarian >>>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>>> _______________________________________________ >>>>>>>> Gmod-gbrowse mailing list >>>>>>>> Gmod-gbrowse@... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770120.html >>>>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>>> is a gathering of tech-side developers & brand creativity >>>>>>> professionals. >>>>>>> Meet >>>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, >>>>>>> & >>>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>>> Barbarian >>>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse@... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ------------------------------------------------------------------------ >>>>>> Scott Cain, Ph. D. scott at >>>>>> scottcain >>>>>> dot net >>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>>> Ontario Institute for Cancer Research >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>>> is a gathering of tech-side developers & brand creativity >>>>>> professionals. >>>>>> Meet >>>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>>> Barbarian >>>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse@... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23770641.html >>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>>> is a gathering of tech-side developers & brand creativity >>>>> professionals. >>>>> Meet >>>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>>> Barbarian >>>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse@... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>>> ------------------------------------------------------------------------------ >>>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>>> is a gathering of tech-side developers & brand creativity professionals. >>>> Meet >>>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>>> iPhoneDevCamp as they present alongside digital heavyweights like >>>> Barbarian >>>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23784718.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >>> is a gathering of tech-side developers & brand creativity professionals. >>> Meet >>> the minds behind Google Creative Lab, Visual Complexity, Processing, & >>> iPhoneDevCamp as they present alongside digital heavyweights like >>> Barbarian >>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity professionals. >> Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/Add-your-own-track-on-chado-based-GBrowse-tp23767794p23786967.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
| < Prev | 1 - 2 | Next > |
| Free embeddable forum powered by Nabble | Forum Help |
