Re: [Comments/Questions about this demo site] Integrating GBrowse and providing links to actual sequence data

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Re: [Comments/Questions about this demo site] Integrating GBrowse and providing links to actual sequence data

Stephen Ficklin-2
Hi Nipun,

I'm CC'ing the mailing list in my response.

Can you be more specific in how you would like to integrate GBrowse?  
Do you mean something similar to what we have on the Citrus Genome site:
http://www.citrusgenomedb.org/PAC:19274706?  (click the "Genomic
Location" link).  Here the feature is linked to GBrowse by clicking on
the link and an image of the gene from GBrowse is visible on the page.

Stephen

On 4/22/2012 11:23 PM, [hidden email] wrote:
> Nipun sent a message using the contact form at
> http://tripal.gmod-dev.oicr.on.ca/0.3.1b/contact.
>
> I am greatly interested in intergrating GBrowse in Tripal and possibly
> even a annotating tool such as Apollo. Also, how do I insert the links
> to the actual sequence data instead of uploading the entire set to the
> database?


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Re: [Comments/Questions about this demo site] Integrating GBrowse and providing links to actual sequence data

Stephen Ficklin-2
Hi Nipun,

I see.  On the citrus site GBrowse is not integrated into Drupal.   It
is a stand-alone CGI but the site header for GBrowse is identical to the
rest of the site.   You can set the site header using the GBrowse
configuration file.  We've experimented with using IFrames to embed
GBrowse and CMAP.  And that works well for integrating both of those
tools into the site, but makes it difficult to link into the tool.  If
you would like to try that route,  we have a Drupal module which will
allow you to embed any CGI into an Iframe.   I would be happy to share
that module with you if you would like to try that route.

Stephen

On 4/23/2012 10:41 AM, Nipun wrote:

> Yes, Tools->Citrus sinensis GBrowse
>
> On 4/23/12, Stephen Ficklin<[hidden email]>  wrote:
>> Hi Nipun,
>>
>> I'm CC'ing the mailing list in my response.
>>
>> Can you be more specific in how you would like to integrate GBrowse?
>> Do you mean something similar to what we have on the Citrus Genome site:
>> http://www.citrusgenomedb.org/PAC:19274706?  (click the "Genomic
>> Location" link).  Here the feature is linked to GBrowse by clicking on
>> the link and an image of the gene from GBrowse is visible on the page.
>>
>> Stephen
>>
>> On 4/22/2012 11:23 PM, [hidden email] wrote:
>>> Nipun sent a message using the contact form at
>>> http://tripal.gmod-dev.oicr.on.ca/0.3.1b/contact.
>>>
>>> I am greatly interested in intergrating GBrowse in Tripal and possibly
>>> even a annotating tool such as Apollo. Also, how do I insert the links
>>> to the actual sequence data instead of uploading the entire set to the
>>> database?
>>
>>
>>
>


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