These are chat archives for biojs/biojs

25th
May 2018
Megh Thakkar
@Megh-Thakkar
May 25 2018 03:34
@rowlandm I made the pull request for the framework blog on Wednesday night itself, as discussed but the review is pending and hence I haven't merged it. You can have a preview of the blog post at https://megh-thakkar.github.io/biojs.github.io/2018-05-22-backend-website-project/.
Also, I spent the past three days comparing both the python frameworks and I have made a list of the functionality as I think biojs provides(for example, I am not completely aware of how the "Request a Component" feature functions). Based on this I have made a doc on which framework would work better keeping the scalability in mind. I would like to discuss that in depth during this Sunday's call.
rowlandm
@rowlandm
May 25 2018 03:39
Hey @Megh-Thakkar
Can you send that document please?
I didn't get an email.... hmmm
rowlandm
@rowlandm
May 25 2018 04:16
I saw the preview
Sorry - I wasn't watching that repo!
I made a comment. Just a minor change owuld be fine.
sree
@UXsree
May 25 2018 08:59
do we have a biojs library for performing Nucleotide BLAST?
Dennis Schwartz
@DennisSchwartz
May 25 2018 09:22
@UXsree I’m not sure, have you looked in the registry?
What are you trying to achieve? That sounds a bit like a backend task, maybe bionode (https://www.bionode.io/) has something for that.
sree
@UXsree
May 25 2018 09:30
image.png
@DennisSchwartz thanks for the response, I was trying to simulate something similar to this graph above, once we do a blast from this site https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch. But when I do the inspect in browser dev tools there are lots of JS associated with it.
Dennis Schwartz
@DennisSchwartz
May 25 2018 09:37
Ah I see. So you don’t want to run BLAST itself, you would like to visualise the results of a BLAST search?
Check out these modules in the registry: http://biojs.io/d/biojs-io-blast http://biojs.io/d/biojs-vis-blast
(The examples take a while to load)
sree
@UXsree
May 25 2018 09:46
yes exactly! don't want to run BLAST itself, just need to visualize the results
Dennis Schwartz
@DennisSchwartz
May 25 2018 09:55
Ok. The components above are your best bet for that using BioJS :) But feel free to search for yourself on biojs.io
Björn Grüning
@bgruening
May 25 2018 09:55
yes there is one, give me a sec
sree
@UXsree
May 25 2018 12:59
@bgruening @DennisSchwartz thanks for the timely help. But I was not able to run it as per the documentation. It fails @ npm install ./w
Dennis Schwartz
@DennisSchwartz
May 25 2018 13:18
are we talking biojs-vis-blast?
npm install biojs-vis-blast is working for me :)
Dennis Schwartz
@DennisSchwartz
May 25 2018 13:23
Oh I see what you mean.
There are some problems with the Installation instructions on the github page.
git clone https://github.com/rslprpr/biojs-vis-blast.git && cd biojs-vis-blast && npm i -g watchify && npm install && npm run watch && npm run sniper
Try running this and then open localhost:9090/snippets
But even then the snippets don’t really work for me. You can always try the biojs-io-blast components instead.
Dennis Schwartz
@DennisSchwartz
May 25 2018 13:30
Oh no! I meant this one actually: http://biojs.io/d/biojs-vis-blasterjs
Look to be much better documented and you can integrate it straight into your FE code: https://github.com/sing-group/biojs-vis-blasterjs
sree
@UXsree
May 25 2018 14:16
@DennisSchwartz thanks a lot!
Dennis Schwartz
@DennisSchwartz
May 25 2018 15:23
No worries! I hope it works.