[Gmod-ajax] Long ago promised features

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[Gmod-ajax] Long ago promised features

Keiran Raine
Hi all,

It’s nice to see the GSOC projects getting underway again but I’m wondering when features that were promised in JBrowse 2.0 will ever appear (or JBrowse 2.0) e.g.

  • Native authentication plugins
    • Currently need to generate cookies in another page prior to accessing JBrowse
      • No documentation of what needs to be set
      • Doesn’t handle per-dataset access rights (the drop down most use for species)
    • Provide server details for your site LDAP or single-sign-on services.
    • Specify users or groups that have access in config for datasets.

Also there is heavy support for CRAM (on the GitHub issue #546).  The benefits of CRAM are possibly more far-reaching than many realise, so here’s a list of pros and cons:

Cons:
Increased load on browser for on-click popups as a record only includes differences from reference seq (if maintaining same display as BAM)

Pros:
Faster initial load time - indices are compressed by default
Faster general load time - far less data to stream
Better for remote working - more likely to be limited by IO than CPU

I realise that the direction of development is now mostly driven by Apollo but from what I gather most of this work has been prototyped so it would be really great to see it being made available (even if the authentication could just be ported to the current work-stream).

Unfortunately these are fast becoming limiting factors in our continuing use of JBrowse as wrangling development time (in a group with limited JS skills) for something available in a different Genome Browser is challenging.

Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


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Re: Long ago promised features

Ian Holmes-2
Hi Keiran,

Good to hear from you. COSMIC is one of my favorite JBrowse sites!

We are actively working on authentication now. Yes, client-side authentication is prototyped in a different branch.

JBrowse development was driven by Apollo during 2014-15 mostly because the JBrowse project lacked a lead developer during that time. This was due to funding and recruitment hassles. It has also meant that we have had to triage some of the planned JBrowse 2 features. However we now have Eric Yao as lead dev and are picking up the pace again.

I am a big fan of CRAM (in the past wrote a proposal with Ewan B to develop CRAM-type stuff, didn't get funded though) and I would like to see it implemented as a native JBrowse format. Honestly, the fastest way for this to happen would be if Sanger/EBI could subcontract to us for this specific task. If you can tell the people holding the pointy sticks: we represent very good value! Absent that, I do expect that it will happen at some point. Your server-side on-the-fly conversion on the github issues page looks like an interesting solution and maybe that could be leveraged.


On Tue, Mar 8, 2016 at 10:47 AM, Keiran Raine <[hidden email]> wrote:
Hi all,

It’s nice to see the GSOC projects getting underway again but I’m wondering when features that were promised in JBrowse 2.0 will ever appear (or JBrowse 2.0) e.g.

  • Native authentication plugins
    • Currently need to generate cookies in another page prior to accessing JBrowse
      • No documentation of what needs to be set
      • Doesn’t handle per-dataset access rights (the drop down most use for species)
    • Provide server details for your site LDAP or single-sign-on services.
    • Specify users or groups that have access in config for datasets.

Also there is heavy support for CRAM (on the GitHub issue #546).  The benefits of CRAM are possibly more far-reaching than many realise, so here’s a list of pros and cons:

Cons:
Increased load on browser for on-click popups as a record only includes differences from reference seq (if maintaining same display as BAM)

Pros:
Faster initial load time - indices are compressed by default
Faster general load time - far less data to stream
Better for remote working - more likely to be limited by IO than CPU

I realise that the direction of development is now mostly driven by Apollo but from what I gather most of this work has been prototyped so it would be really great to see it being made available (even if the authentication could just be ported to the current work-stream).

Unfortunately these are fast becoming limiting factors in our continuing use of JBrowse as wrangling development time (in a group with limited JS skills) for something available in a different Genome Browser is challenging.

Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104


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Click to learn more.
http://makebettercode.com/inteldaal-eval
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