Question: Linking Jbrowse to Galaxy/Taverna
1
gravatar for CikLa
4.7 years ago by
CikLa90
Malaysia
CikLa90 wrote:

Hi,

Anyone familiar with Jbrowse genome browser here? I wonder, can Jbrowse be linked to other party software such as Galaxy or Taverna? I found a tool named ABrowse (http://www.abrowse.org/), and seems like ABrowse can do that. Anyone?

jbrowse galaxy taverna • 2.2k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 4.7 years ago by CikLa90
1
gravatar for cmdcolin
4.7 years ago by
cmdcolin1.2k
United States
cmdcolin1.2k wrote:

I haven't seen ABrowse in action, but I looked at what are some features that ABrowse claims to have and here are some ideas about how JBrowse might offer similar functions

  • On-the-fly submit selected entries to Galaxy and WebLab for further analysis.

    You can add custom javascript callbacks to JBrowse to allow it to perform a variety of actions and so you could possibly use this to submit jobs to Galaxy.

    You might ask the JBrowse mailing list to see if they have examples of Galaxy integration.
     
  • Compatible with BioMart engine for bulk data retrieval.

    I know that BioMart has a SPARQL query interface, and since JBrowse supports SPARQL backend, you could possibly use JBrowse to retrieve and display data from BioMart.
     
  • SOAP-based web service interface, fully compatible with Taverna.

    JBrowse has no backend server side code, it's a 100% client based javascript app, so it doesn't really offer web-services like ABrowse might. There are some other software systems such as Intermine that have better integration with JBrowse and web services though.
     
  • Easy to install, configure and customize for different user requirements.

    I think JBrowse is also easy to install, configure, and customize (extensive customizations possible via javascript! no complex server side code :)

Feel free to ask the gmod-ajax mailing list for jbrowse topics, beginner or advanced!

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by cmdcolin1.2k

Hi cmdcolin,

Thanks for the reply. I also thinking the same, jbrowse has many support channel as compared to abrowse. But since I am new with this, that's why I'm asking here. Basic question here: how to link the information from the popup windows? For example in .

http://jbrowse.org/code/JBrowse-1.11.5/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A1..50001&tracks=DNA%2CTranscript%2Cvolvox-sorted-vcf%2Cvolvox_gff3&highlight=

Let say the name of a CDS is 'ctgA', so we want to link this variable into some entries in other database, can we do that? In normal html it's like a 'a href="https://www.google.com.my/search?q=ctgA"'. Any example for that?

Tq.

ADD REPLYlink written 4.7 years ago by CikLa90

The JBrowse configuration guide contains some details on customizing the popups (Here).

ADD REPLYlink modified 2.2 years ago • written 4.7 years ago by cmdcolin1.2k

Thanks cmdcolin, it's helpful though. I'll go through the customizing parts soon. Really appreciate! :)

ADD REPLYlink written 4.7 years ago by CikLa90

I misread you question the first time around. There's currently no way to link directly to the information from the popup panels, but there is some interest in turning various parts of jbrowse into separate modules so perhaps that would be possible after accounting for this.
 

ADD REPLYlink written 4.5 years ago by cmdcolin1.2k

Hi,

I wonder if JBrowse allows for advance customization? Let say, when I click a gene, there's a popup come out with selection checkboxes: blast, interpro, gene ontology. so if we check those 3 boxes, there are 3 new tabs open to run each analysis. if I not mistaken, this is called API, isn't it?

Ok, second example. Can we bookmark or favorite certain genes/features for further task?

Anyone offers this kind of service?

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by CikLa90

You might want to see if these programs (blast,interpro,go) have a "REST API". having a web-accessible API would make it easier for jbrowse to run that analysis. the ability to bookmark genes is not available yet, but that would be a good feature (it might not be too hard to create a plugin like this)

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by cmdcolin1.2k

Is there any tutorial on developing such plugin for Jbrowse? I'm planning to have an improved genome browser with customization of functions based on basic genome browser. That's the reason of asking this.

ADD REPLYlink written 4.5 years ago by CikLa90

There is a default plugin included in the jbrowse github called RegexSequenceSearch which is instructive for creating a regular plugin. There is also a script called new-plugin.pl that can create a template. It is also documented in the configuration guide. And then furthermore there are several projects using the plugin framework including the arabadopsis information portal (AIP) and webapollo.

ADD REPLYlink written 4.5 years ago by cmdcolin1.2k

Alright, so the point is yes, we can do the customization. Just wonder if I able to do it myself. Will look at it, thanks!

ADD REPLYlink written 4.5 years ago by CikLa90
2
gravatar for rasche.eric
3.6 years ago by
rasche.eric70
United States
rasche.eric70 wrote:

I know this is a year old post, but in the past 6 months I've integrated JBrowse as a Galaxy tool. You can see some of the details here: https://github.com/galaxyproject/tools-iuc/pull/507

If there are features you'd like to see that aren't in the current version, I'd be happy to hear about them and add them if I have time. It sounds like you'd like to submit sequences from JBrowse into Galaxy, that sounds like a plugin I could put together for JBrowse without too much trouble. I'll update this post if I ever get around to it :)

ADD COMMENTlink written 3.6 years ago by rasche.eric70
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