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phac-nml / irida

Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
https://irida.ca
Apache License 2.0
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Integrate phyloviz and microreact #219

Closed innovate-invent closed 2 years ago

innovate-invent commented 5 years ago

@tom114 @apetkau Hello, my name is Nolan Woods, I am working for Dr. Fiona Brinkman. She would like me to integrate Phyloviz and Microreact into IRIDAs visualization suite. Do you expect any issues with this?

Thanks

wwhsiao commented 5 years ago

Instead of Phyloviz, I would suggest GrapeTree for MLST viz. https://www.ncbi.nlm.nih.gov/pubmed/30049790

Welcome onboard, Nolan!

Cheers,

Will

William Hsiao, PhD Senior Scientist, BCCDC Public Health Laboratory Clinical Assistant Professor, Pathology & Laboratory Medicine, UBC Adjunct Professor, Molecular Biology and Biochemistry, SFU Rm 4066, 655 West 12th Avenue Vancouver, BC, V5Z 4R4 Canada Tel: 604-707-2561 Fax: 604-707-2603 On Dec 12, 2018, 2:38 PM -0800, Nolan Woods notifications@github.com, wrote:

@tom114 @apetkau Hello, my name is Nolan Woods, I am working for Dr. Fiona Brinkman. She would like me to integrate Phyloviz and Microreact into IRIDAs visualization suite. You you expect any issues with this? Thanks — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

innovate-invent commented 5 years ago

@fionabrinkman Will that suit your needs?

fionabrinkman commented 5 years ago

Its actually Claire who brought up wanting PhyloViz, so we should check in with her also, though as you know Nolan she also thinks new visualizations need to be implemented! It'd be good to also checkin with Thomas from the NLM and others mentioned to get their input. GrapeTree would indeed also be good. We really want a range of options, and certainly microreact is a nice tool, but note, Will, for the upcoming meeting of PIs next week we could review these options and come up with a prioritized list. Meanwhile, are you particularly keen on GrapeTree Will for a particular use case, just so I understand the need?

innovate-invent commented 5 years ago

ping @cbertell

tom114 commented 5 years ago

Hi @innovate-invent, thanks for the interest. A couple opinions here:

@joshsadam may have other opinions on this and insight on building in some other visualization tools.

apetkau commented 5 years ago

Thanks @innovate-invent, integrating these into IRIDA would be awesome :smile:

I agree with @tom114 that integration through the API is probably the easiest (e.g., pushing data from IRIDA into Phyloviz or Microreact to visualize data) but it depends on how we want people to use the visualization system.

For GrapeTree, it is very fast and can support very large amounts of data. It is incorporated into Enterobase (https://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html) and also BigsDB (https://bigsdb.readthedocs.io/en/latest/data_analysis.html#grapetree). I don't know if there is an API which can be used to push data into it but it looks like it is maybe more reasonable for direct integration (at least, it's been done before).

joshsadam commented 5 years ago

@apetkau and @tom114 have covered pretty much everything as far as I can see. I think we need to spend a little bit of time trying to decide what should actually be built into the IRIDA code base versus pushing out to external applications (even if we host these external applications for security reasons).

wwhsiao commented 5 years ago

Hi all,

I think my reason for GrapeTree is same as what Aaron said.  Joao is involved in the GrapeTree as well and I think it’s just more scalable then PhyloViz online.  Though I have to admit I have only limited experience with both.

Cheers,

Will

William Hsiao, PhD Senior Scientist, BCCDC Public Health Laboratory Clinical Assistant Professor, Pathology & Laboratory Medicine, UBC Adjunct Professor, Molecular Biology and Biochemistry, SFU Rm 4066, 655 West 12th Avenue Vancouver, BC, V5Z 4R4 Canada Tel: 604-707-2561 Fax: 604-707-2603 On Dec 13, 2018, 8:01 AM -0800, Aaron Petkau notifications@github.com, wrote:

Thanks @innovate-invent, integrating these into IRIDA would be awesome 😄 I agree with @tom114 that integration through the API is probably the easiest (e.g., pushing data from IRIDA into Phyloviz or Microreact to visualize data) but it depends on how we want people to use the visualization system. For GrapeTree, it is very fast and can support very large amounts of data. It is incorporated into Enterobase (https://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html) and also BigsDB (https://bigsdb.readthedocs.io/en/latest/data_analysis.html#grapetree). I don't know if there is an API which can be used to push data into it but it looks like it is maybe more reasonable for direct integration (at least, it's been done before). — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

happykhan commented 5 years ago

You can just pipe your newick & metadata into GrapeTree. The visual component is just js + html so that just needs to be hosted somewhere on your site & then you point it to the meta and tree. The files can be external; if you can get around CORS.

https://enterobase.readthedocs.io/en/latest/grapetree/grapetree-api.html

apetkau commented 5 years ago

Awesome, thanks @happykhan :smile:

innovate-invent commented 4 years ago

Thanks everyone for this advice, and sorry for the delay. I am just coming back to this project, along with another visualization that requires integration.

Was there ever a discussion about IRIDA hosted visualizations vs 3rd party visualizations? Is IRIDA specifically keeping visualizations out of scope for its code?

I also have the option of hosting the visualization in the Galaxy backend, but that would require bypassing IRIDA. This visualization is purely client-side so where it is actually hosted is not critical.

Is there any documentation related to adding some way for the user to access a visualization for an analysis?

Thanks

fionabrinkman commented 4 years ago

There is a new item that came up that might be a good start: Adding in ChewBBACA into IRIDA which is needed to meet a grant milestone. I’ve cc’d also Will who may comment more on this too, based on a recent email thread.

https://github.com/B-UMMI/chewBBACA/ https://github.com/B-UMMI/chewBBACA/

Best wishes, Fiona

__

Dr. Fiona S. L. Brinkman, PhD FRSC Distinguished Professor, Molecular Biology and Biochemistry Dept Associate Professor, School of Computing Science, and Faculty of Health Sciences Rm SSB 8166, 8888 University Drive Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 Phone: 778-782-5646 Fax: 778-782-5583 Office: SSB 7110 http://www.brinkman.mbb.sfu.ca

On Nov 25, 2019, at 3:54 PM, Nolan Woods notifications@github.com wrote:

Thanks everyone for this advice, and sorry for the delay. I am just coming back to this project, along with another visualization that requires integration.

Was there ever a discussion about IRIDA hosted visualizations vs 3rd party visualizations? Is IRIDA specifically keeping visualizations out of scope for its code?

I also have the option of hosting the visualization in the Galaxy backend, but that would require bypassing IRIDA. This visualization is purely client-side so where it is actually hosted is not critical.

Is there any documentation related to adding some way for the user to access a visualization for an analysis?

Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/phac-nml/irida/issues/219?email_source=notifications&email_token=AEMF576BRSB4U5F2LPKOFDTQVQ3OTA5CNFSM4GKCKTA2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFDYLXY#issuecomment-558335455, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEMF573IBP4BWQXKKMUO7GLQVQ3OTANCNFSM4GKCKTAQ.

fionabrinkman commented 4 years ago

Sorry, I meant to address this to Nolan!

On Nov 26, 2019, at 3:40 AM, Fiona Brinkman brinkman@sfu.ca wrote:

There is a new item that came up that might be a good start: Adding in ChewBBACA into IRIDA which is needed to meet a grant milestone. I’ve cc’d also Will who may comment more on this too, based on a recent email thread.

https://github.com/B-UMMI/chewBBACA/ https://github.com/B-UMMI/chewBBACA/

Best wishes, Fiona

__

Dr. Fiona S. L. Brinkman, PhD FRSC Distinguished Professor, Molecular Biology and Biochemistry Dept Associate Professor, School of Computing Science, and Faculty of Health Sciences Rm SSB 8166, 8888 University Drive Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 Phone: 778-782-5646 Fax: 778-782-5583 Office: SSB 7110 http://www.brinkman.mbb.sfu.ca http://www.brinkman.mbb.sfu.ca/

On Nov 25, 2019, at 3:54 PM, Nolan Woods <notifications@github.com mailto:notifications@github.com> wrote:

Thanks everyone for this advice, and sorry for the delay. I am just coming back to this project, along with another visualization that requires integration.

Was there ever a discussion about IRIDA hosted visualizations vs 3rd party visualizations? Is IRIDA specifically keeping visualizations out of scope for its code?

I also have the option of hosting the visualization in the Galaxy backend, but that would require bypassing IRIDA. This visualization is purely client-side so where it is actually hosted is not critical.

Is there any documentation related to adding some way for the user to access a visualization for an analysis?

Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/phac-nml/irida/issues/219?email_source=notifications&email_token=AEMF576BRSB4U5F2LPKOFDTQVQ3OTA5CNFSM4GKCKTA2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFDYLXY#issuecomment-558335455, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEMF573IBP4BWQXKKMUO7GLQVQ3OTANCNFSM4GKCKTAQ.