Dictybase genome browser

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Dictybase genome browser

Chubb, Jonathan
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..


Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
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Re: Dictybase genome browser

Lincoln Stein
This seems to be a browser-specific issue. I just tested dictybase with both chrome and firefox and the restriction annnotator seems to be working fine (I looked at D. purpureum, since the plugin appears to be disabled for discoideum).

What web browser are you having trouble with?

Lincoln




On Wed, Apr 10, 2013 at 10:12 PM, Chubb, Jonathan <[hidden email]> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..


Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
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--
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 <[hidden email]>

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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Re: Dictybase genome browser

Scott Cain
Hi Lincoln,

Very strange indeed: on my Mac (Snow Leopard) using Firefox 20, Chrome 26, and Safari 5.1.8 (all current) and I hit "Go" on the restriction annotator, I get a 500 error in the console.  Of course, in the UI, all I see is the spinning wheel in the upper left since it's waiting for a track image that it will never get (so sad!).

I'm going to take a look on a local machine to see if I can reproduce.

Scott



On Fri, Apr 12, 2013 at 1:57 PM, Lincoln Stein <[hidden email]> wrote:
This seems to be a browser-specific issue. I just tested dictybase with both chrome and firefox and the restriction annnotator seems to be working fine (I looked at D. purpureum, since the plugin appears to be disabled for discoideum).

What web browser are you having trouble with?

Lincoln




On Wed, Apr 10, 2013 at 10:12 PM, Chubb, Jonathan <[hidden email]> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..


Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: Dictybase genome browser

Timothy Parnell
This might be a stupid comment, but did you click the "Restriction Sites" under the Select Tracks tab? I get the spinning wheel too after hitting the Go button, but then when I turn on the track it magically and instantly appears.

Tim

________________________________
From: Scott Cain [[hidden email]]
Sent: Friday, April 12, 2013 12:43 PM
To: Lincoln Stein
Cc: Chubb, Jonathan; [hidden email]
Subject: Re: [Gmod-gbrowse] Dictybase genome browser

Hi Lincoln,

Very strange indeed: on my Mac (Snow Leopard) using Firefox 20, Chrome 26, and Safari 5.1.8 (all current) and I hit "Go" on the restriction annotator, I get a 500 error in the console.  Of course, in the UI, all I see is the spinning wheel in the upper left since it's waiting for a track image that it will never get (so sad!).

I'm going to take a look on a local machine to see if I can reproduce.

Scott



On Fri, Apr 12, 2013 at 1:57 PM, Lincoln Stein <[hidden email]<mailto:[hidden email]>> wrote:
This seems to be a browser-specific issue. I just tested dictybase with both chrome and firefox and the restriction annnotator seems to be working fine (I looked at D. purpureum, since the plugin appears to be disabled for discoideum).

What web browser are you having trouble with?

Lincoln




On Wed, Apr 10, 2013 at 10:12 PM, Chubb, Jonathan <[hidden email]<mailto:[hidden email]>> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..

http://gmod.827538.n3.nabble.com/RestrictionAnnotator-plugin-is-not-working
-td4028306.html

Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
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<tel:416%20673-8514>
Assistant: Renata Musa <[hidden email]<mailto:[hidden email]>>

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
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

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: Dictybase genome browser

Scott Cain
In reply to this post by Scott Cain
Hi Lincoln,

I just reproduced this on a new AWS image with 2.54.  The only useful error message I get is:

Can't call method "name" on an undefined value at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render.pm line 202.

which is in the plugin_name method.  If you'd like for me to dig deeper let me know.  In Siddhartha's original report of this (from January), he indicated that he tested Wormbase's and Modencode's GBrowse instances (among others) and found it broken there too:

http://gmod.827538.n3.nabble.com/RestrictionAnnotator-plugin-is-not-working-tt4028306.html

Scott



On Fri, Apr 12, 2013 at 2:43 PM, Scott Cain <[hidden email]> wrote:
Hi Lincoln,

Very strange indeed: on my Mac (Snow Leopard) using Firefox 20, Chrome 26, and Safari 5.1.8 (all current) and I hit "Go" on the restriction annotator, I get a 500 error in the console.  Of course, in the UI, all I see is the spinning wheel in the upper left since it's waiting for a track image that it will never get (so sad!).

I'm going to take a look on a local machine to see if I can reproduce.

Scott



On Fri, Apr 12, 2013 at 1:57 PM, Lincoln Stein <[hidden email]> wrote:
This seems to be a browser-specific issue. I just tested dictybase with both chrome and firefox and the restriction annnotator seems to be working fine (I looked at D. purpureum, since the plugin appears to be disabled for discoideum).

What web browser are you having trouble with?

Lincoln




On Wed, Apr 10, 2013 at 10:12 PM, Chubb, Jonathan <[hidden email]> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..


Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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Re: Dictybase genome browser

Scott Cain
In reply to this post by Timothy Parnell
Ha! Apparently not a stupid question at all: that's true for me too.  I guess the problem is one of user interface: as a user, I expected the track to just appear after I hit "Go".  My suspicion that something was wrong was reinforced by the wheel that never stopped spinning and the 500 error in the browser console/apache error log. 

So, short term, DictyBase (and everybody else that uses the restriction annotator) needs to educate their users that it's not really broken and you need to turn the track on, and long term I think the UI should be changed to make it more user friendly.

Scott



On Fri, Apr 12, 2013 at 2:53 PM, Timothy Parnell <[hidden email]> wrote:
This might be a stupid comment, but did you click the "Restriction Sites" under the Select Tracks tab? I get the spinning wheel too after hitting the Go button, but then when I turn on the track it magically and instantly appears.

Tim

________________________________
From: Scott Cain [[hidden email]]
Sent: Friday, April 12, 2013 12:43 PM
To: Lincoln Stein
Cc: Chubb, Jonathan; [hidden email]
Subject: Re: [Gmod-gbrowse] Dictybase genome browser

Hi Lincoln,

Very strange indeed: on my Mac (Snow Leopard) using Firefox 20, Chrome 26, and Safari 5.1.8 (all current) and I hit "Go" on the restriction annotator, I get a 500 error in the console.  Of course, in the UI, all I see is the spinning wheel in the upper left since it's waiting for a track image that it will never get (so sad!).

I'm going to take a look on a local machine to see if I can reproduce.

Scott



On Fri, Apr 12, 2013 at 1:57 PM, Lincoln Stein <[hidden email]<mailto:[hidden email]>> wrote:
This seems to be a browser-specific issue. I just tested dictybase with both chrome and firefox and the restriction annnotator seems to be working fine (I looked at D. purpureum, since the plugin appears to be disabled for discoideum).

What web browser are you having trouble with?

Lincoln




On Wed, Apr 10, 2013 at 10:12 PM, Chubb, Jonathan <[hidden email]<mailto:[hidden email]>> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..

<a href="http://gmod.827538.n3.nabble.com/RestrictionAnnotator-plugin-is-not-working -td4028306.html" target="_blank">http://gmod.827538.n3.nabble.com/RestrictionAnnotator-plugin-is-not-working
-td4028306.html

Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
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
<a href="tel:416%20673-8514" value="+14166738514">416 673-8514<tel:416%20673-8514>
Assistant: Renata Musa <[hidden email]<mailto:[hidden email]>>

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">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

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Dictybase genome browser

Lincoln Stein
Ok, this is something I didn't try. I simply turned it on in the track list. "Go" should turn on the track, and not generate an error. I will fix that in the development version.

Lincoln


On Fri, Apr 12, 2013 at 8:16 PM, Scott Cain <[hidden email]> wrote:
Ha! Apparently not a stupid question at all: that's true for me too.  I guess the problem is one of user interface: as a user, I expected the track to just appear after I hit "Go".  My suspicion that something was wrong was reinforced by the wheel that never stopped spinning and the 500 error in the browser console/apache error log. 

So, short term, DictyBase (and everybody else that uses the restriction annotator) needs to educate their users that it's not really broken and you need to turn the track on, and long term I think the UI should be changed to make it more user friendly.

Scott



On Fri, Apr 12, 2013 at 2:53 PM, Timothy Parnell <[hidden email]> wrote:
This might be a stupid comment, but did you click the "Restriction Sites" under the Select Tracks tab? I get the spinning wheel too after hitting the Go button, but then when I turn on the track it magically and instantly appears.

Tim

________________________________
From: Scott Cain [[hidden email]]
Sent: Friday, April 12, 2013 12:43 PM
To: Lincoln Stein
Cc: Chubb, Jonathan; [hidden email]
Subject: Re: [Gmod-gbrowse] Dictybase genome browser

Hi Lincoln,

Very strange indeed: on my Mac (Snow Leopard) using Firefox 20, Chrome 26, and Safari 5.1.8 (all current) and I hit "Go" on the restriction annotator, I get a 500 error in the console.  Of course, in the UI, all I see is the spinning wheel in the upper left since it's waiting for a track image that it will never get (so sad!).

I'm going to take a look on a local machine to see if I can reproduce.

Scott



On Fri, Apr 12, 2013 at 1:57 PM, Lincoln Stein <[hidden email]<mailto:[hidden email]>> wrote:
This seems to be a browser-specific issue. I just tested dictybase with both chrome and firefox and the restriction annnotator seems to be working fine (I looked at D. purpureum, since the plugin appears to be disabled for discoideum).

What web browser are you having trouble with?

Lincoln




On Wed, Apr 10, 2013 at 10:12 PM, Chubb, Jonathan <[hidden email]<mailto:[hidden email]>> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..

http://gmod.827538.n3.nabble.com/RestrictionAnnotator-plugin-is-not-working
-td4028306.html


Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
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
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514<tel:416%20673-8514>
Assistant: Renata Musa <[hidden email]<mailto:[hidden email]>>

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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 <[hidden email]>

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Dictybase genome browser

Siddhartha Basu
Hi folks,
Thanks a lot for clearing up the issue,  i will inform our users
accordingly. Also incorporate the changes once the fix gets released.

thanks,
-siddhatha


On Fri, 12 Apr 2013, Lincoln Stein wrote:

>    Ok, this is something I didn't try. I simply turned it on in the track
>    list. "Go" should turn on the track, and not generate an error. I will fix
>    that in the development version.
>    Lincoln
>
>    On Fri, Apr 12, 2013 at 8:16 PM, Scott Cain <[hidden email]> wrote:
>
>      Ha! Apparently not a stupid question at all: that's true for me too.  I
>      guess the problem is one of user interface: as a user, I expected the
>      track to just appear after I hit "Go".  My suspicion that something was
>      wrong was reinforced by the wheel that never stopped spinning and the
>      500 error in the browser console/apache error log.
>
>      So, short term, DictyBase (and everybody else that uses the restriction
>      annotator) needs to educate their users that it's not really broken and
>      you need to turn the track on, and long term I think the UI should be
>      changed to make it more user friendly.
>
>      Scott
>
>      On Fri, Apr 12, 2013 at 2:53 PM, Timothy Parnell
>      <[hidden email]> wrote:
>
>        This might be a stupid comment, but did you click the "Restriction
>        Sites" under the Select Tracks tab? I get the spinning wheel too after
>        hitting the Go button, but then when I turn on the track it magically
>        and instantly appears.
>
>        Tim
>
>        ________________________________
>        From: Scott Cain [[hidden email]]
>        Sent: Friday, April 12, 2013 12:43 PM
>        To: Lincoln Stein
>        Cc: Chubb, Jonathan; [hidden email]
>        Subject: Re: [Gmod-gbrowse] Dictybase genome browser
>        Hi Lincoln,
>
>        Very strange indeed: on my Mac (Snow Leopard) using Firefox 20, Chrome
>        26, and Safari 5.1.8 (all current) and I hit "Go" on the restriction
>        annotator, I get a 500 error in the console.  Of course, in the UI,
>        all I see is the spinning wheel in the upper left since it's waiting
>        for a track image that it will never get (so sad!).
>
>        I'm going to take a look on a local machine to see if I can reproduce.
>
>        Scott
>
>        On Fri, Apr 12, 2013 at 1:57 PM, Lincoln Stein
>        <[hidden email]<mailto:[hidden email]>> wrote:
>        This seems to be a browser-specific issue. I just tested dictybase
>        with both chrome and firefox and the restriction annnotator seems to
>        be working fine (I looked at D. purpureum, since the plugin appears to
>        be disabled for discoideum).
>
>        What web browser are you having trouble with?
>
>        Lincoln
>
>        On Wed, Apr 10, 2013 at 10:12 PM, Chubb, Jonathan
>        <[hidden email]<mailto:[hidden email]>> wrote:
>        Hi there,
>        I've been using the Dictybase genome browser for 9 years now, and been
>        very frustrated at the sudden loss of the restriction annotator
>        plugin.  This is really useful, and used daily in the group!
>        As the legacy genome browser is due to be switched off at the
>        beginning of 2014, please could the restriction plugin be activated?
>         I think Dictybase may have already contacted you about this*..
>
>        http://gmod.827538.n3.nabble.com/RestrictionAnnotator-plugin-is-not-working
>        -td4028306.html
>
>        Thanks,
>
>        Jonathan Chubb PhD
>        Department of Cell and Developmental Biology and
>        MRC Laboratory for Molecular Cell Biology
>        University College London
>        Gower Street
>        London
>        WC1E 6BT
>
>        ------------------------------------------------------------------------------
>        Precog is a next-generation analytics platform capable of advanced
>        analytics on semi-structured data. The platform includes APIs for
>        building
>        apps and a phenomenal toolset for data science. Developers can use
>        our toolset for easy data analysis & visualization. Get a free
>        account!
>        http://www2.precog.com/precogplatform/slashdotnewsletter
>        _______________________________________________
>        Gmod-gbrowse mailing list
>        [hidden email]<mailto:[hidden email]>
>        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<tel:416%20673-8514>
>        Assistant: Renata Musa
>        <[hidden email]<mailto:[hidden email]>>
>        ------------------------------------------------------------------------------
>        Precog is a next-generation analytics platform capable of advanced
>        analytics on semi-structured data. The platform includes APIs for
>        building
>        apps and a phenomenal toolset for data science. Developers can use
>        our toolset for easy data analysis & visualization. Get a free
>        account!
>        http://www2.precog.com/precogplatform/slashdotnewsletter
>        _______________________________________________
>        Gmod-gbrowse mailing list
>        [hidden email]<mailto:[hidden email]>
>        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
>
>    --
>    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 <[hidden email]>

> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: Dictybase genome browser

Lincoln Stein
In reply to this post by Chubb, Jonathan
Hi Folks,

I've fixed the problem with the Restriction Annotator. Now hitting "Go" turns on the track as expected.

You can get the fixed version from github: https://github.com/GMOD/GBrowse

I'll make a full release after I fix the authentication plugin problems reported separately.

Lincoln


On Wed, Apr 10, 2013 at 4:12 PM, Chubb, Jonathan <[hidden email]> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..


Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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 <[hidden email]>

------------------------------------------------------------------------------
AlienVault Unified Security Management (USM) platform delivers complete
security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
http://p.sf.net/sfu/alienvault_d2d
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Re: Dictybase genome browser

Chubb, Jonathan
Cool.  Thanks!

Jonathan Chubb
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

From: Lincoln Stein <[hidden email]>
Date: Thu, 16 May 2013 14:35:11 -0500
To: Jonathan Chubb <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [Gmod-gbrowse] Dictybase genome browser

Hi Folks,

I've fixed the problem with the Restriction Annotator. Now hitting "Go" turns on the track as expected.

You can get the fixed version from github: https://github.com/GMOD/GBrowse

I'll make a full release after I fix the authentication plugin problems reported separately.

Lincoln


On Wed, Apr 10, 2013 at 4:12 PM, Chubb, Jonathan <[hidden email]> wrote:
Hi there,
I've been using the Dictybase genome browser for 9 years now, and been very frustrated at the sudden loss of the restriction annotator plugin.  This is really useful, and used daily in the group!
As the legacy genome browser is due to be switched off at the beginning of 2014, please could the restriction plugin be activated?  I think Dictybase may have already contacted you about this…..


Thanks,

Jonathan Chubb PhD
Department of Cell and Developmental Biology and
MRC Laboratory for Molecular Cell Biology
University College London
Gower Street
London
WC1E 6BT

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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 <[hidden email]>

------------------------------------------------------------------------------
AlienVault Unified Security Management (USM) platform delivers complete
security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
http://p.sf.net/sfu/alienvault_d2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse